Transcriptome analysis reveals gene expression changes of pigs infected with non-lethal African swine fever virus

African swine fever (ASF) is an important viral disease of swine caused by the African swine fever virus (ASFV), which threatens swine production profoundly. To better understand the gene expression changes when pig infected with ASFV, RNA sequencing was performed to characterize differentially expressed genes (DEGs) of six tissues from Kenya domestic pigs and Landrace × Yorkshire (L/Y) pigs infected with ASFV Kenya1033 in vivo. As results, a total of 209, 522, 34, 505, 634 and 138 DEGs (q-value < 0.05 and |Log2foldchange| values >2) were detected in the kidney, liver, mesenteric lymph node, peripheral blood mononuclear cell, submandibular lymph node and spleen, respectively. The expression profiles of DEGs shared in the multiple tissues illustrated variation in regulation function in the different tissues. Functional annotation analysis and interaction of proteins encoded by DEGs revealed that genes including IFIT1, IFITM1, MX1, OASL, ISG15, SAMHD1, IFINA1, S100A12 and S100A8 enriched in the immune and antivirus pathways were significantly changed when the hosts were infected with ASFV. The genes mentioned could play crucial roles in the process of the reaction to non-lethal ASF infection, which may will help to improve the ASF tolerance in the pig population through molecular breeding strategies.

Selective Neuronal Knockout of STAT3 Function Inhibits Epilepsy Progression, Improves Cognition, and Restores Dysregulated Gene Networks in a Temporal Lobe Epilepsy Model

OBJECTIVE

Temporal lobe epilepsy (TLE) is a progressive disorder mediated by pathological changes in molecular cascades and hippocampal neural circuit remodeling that results in spontaneous seizures and cognitive dysfunction. Targeting these cascades may provide disease-modifying treatments for TLE patients. Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) inhibitors have emerged as potential disease-modifying therapies; a more detailed understanding of JAK/STAT participation in epileptogenic responses is required, however, to increase the therapeutic efficacy and reduce adverse effects associated with global inhibition.

METHODS

We developed a mouse line in which tamoxifen treatment conditionally abolishes STAT3 signaling from forebrain excitatory neurons (nSTAT3KO). Seizure frequency (continuous in vivo electroencephalography) and memory (contextual fear conditioning and motor learning) were analyzed in wild-type and nSTAT3KO mice after intrahippocampal kainate (IHKA) injection as a model of TLE. Hippocampal RNA was obtained 24 h after IHKA and subjected to deep sequencing.

RESULTS

Selective STAT3 knock-out in excitatory neurons reduced seizure progression and hippocampal memory deficits without reducing the extent of cell death or mossy fiber sprouting induced by IHKA injection. Gene expression was rescued in major networks associated with response to brain injury, neuronal plasticity, and learning and memory. We also provide the first evidence that neuronal STAT3 may directly influence brain inflammation.

INTERPRETATION

Inhibiting neuronal STAT3 signaling improved outcomes in an animal model of TLE, prevented progression of seizures and cognitive co-morbidities while rescuing pathogenic changes in gene expression of major networks associated with epileptogenesis. Specifically targeting neuronal STAT3 may be an effective disease-modifying strategy for TLE. ANN NEUROL 2023;94:106-122.

Distinct Transcriptomic Responses to Aβ plaques, Neurofibrillary Tangles, and APOE in Alzheimer's Disease

INTRODUCTION

Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE -linked differences remain unclear.

METHODS

We performed laser capture microdissection of Aβ plaques, the 50μm halo around them, tangles with the 50μm halo around them, and areas distant (>50μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing.

RESULTS

Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque>peri-plaque>tangle>distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques.

DISCUSSION

Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.

RNA-Sequencing of Heterorhabditis nematodes to identify factors involved in symbiosis with Photorhabdus bacteria

Background

Nematodes are a major group of soil inhabiting organisms. Heterorhabditis nematodes are insect-pathogenic nematodes and live in a close symbiotic association with Photorhabdus bacteria. Heterorhabditis-Photorhabdus pair offers a powerful and genetically tractable model to study animal-microbe symbiosis. It is possible to generate symbiont bacteria free (axenic) stages in Heterorhabditis. Here, we compared the transcriptome of symbiotic early-adult stage Heterorhabditis nematodes with axenic early-adult nematodes to determine the nematode genes and pathways involved in symbiosis with Photorhabdus bacteria.

Results

A de-novo reference transcriptome assembly of 95.7 Mb was created for H. bacteriophora by using all the reads. The assembly contained 46,599 transcripts with N50 value of 2,681 bp and the average transcript length was 2,054 bp. The differentially expressed transcripts were identified by mapping reads from symbiotic and axenic nematodes to the reference assembly. A total of 754 differentially expressed transcripts were identified in symbiotic nematodes as compared to the axenic nematodes. The ribosomal pathway was identified as the most affected among the differentially expressed transcripts. Additionally, 12,151 transcripts were unique to symbiotic nematodes. Endocytosis, cAMP signalling and focal adhesion were the top three enriched pathways in symbiotic nematodes, while a large number of transcripts coding for various responses against bacteria, such as bacterial recognition, canonical immune signalling pathways, and antimicrobial effectors could also be identified.

Conclusions

The symbiotic Heterorhabditis nematodes respond to the presence of symbiotic bacteria by expressing various transcripts involved in a multi-layered immune response which might represent non-systemic and evolved localized responses to maintain mutualistic bacteria at non-threatening levels. Subject to further functional validation of the identified transcripts, our findings suggest that Heterorhabditis nematode immune system plays a critical role in maintenance of symbiosis with Photorhabdus bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08952-4.

Chronic Exposure to Waterpipe Smoke Elicits Immunomodulatory and Carcinogenic Effects in the Lung

Effects of waterpipe smoking on lung pathobiology and carcinogenesis remain sparse despite the worldwide emergence of this tobacco vector. To address this gap, we investigated the effects of chronic waterpipe smoke (WPS) exposure on lung pathobiology, host immunity, and tumorigenesis using an experimental animal model that is prone to tobacco carcinogens and an exploratory observational analysis of human waterpipe smokers and nonsmokers. Mice exhibited elevated incidence of lung tumors following heavy WPS exposure (5 days/week for 20 weeks) compared to littermates with light WPS (once/week for 20 weeks) or control air. Lungs of mice exposed to heavy WPS showed augmented CD8+ and CD4+ T cell counts along with elevated protumor immune phenotypes including increased IL17A in T/B cells, PD-L1 on tumor and immune cells, and the proinflammatory cytokine IL1β in myeloid cells. RNA-sequencing (RNA-seq) analysis showed reduced antitumor immune gene signatures in animals exposed to heavy WPS relative to control air. We also performed RNA-seq analysis of airway epithelia from bronchial brushings of cancer-free waterpipe smokers and nonsmokers undergoing diagnostic bronchoscopy. Transcriptomes of normal airway cells in waterpipe smokers, relative to waterpipe nonsmokers, harbored gene programs that were associated with poor clinical outcomes in patients with lung adenocarcinoma, alluding to a WPS-associated molecular injury, like that established in response to cigarette smoking. Our findings support the notion that WPS exhibits carcinogenic effects and constitutes a possible risk factor for lung cancer as well as warrant future studies that can guide evidence-based policies for mitigating waterpipe smoking.

PREVENTION RELEVANCE

Potential carcinogenic effects of waterpipe smoking are very poorly understood despite its emergence as a socially acceptable form of smoking. Our work highlights carcinogenic effects of waterpipe smoking in the lung and, thus, accentuate the need for inclusion of individuals with exclusive waterpipe smoking in prevention and smoking cessation studies.

Saliva and Lung Microbiome Associations with Electronic Cigarette Use and Smoking

The microbiome has increasingly been linked to cancer. Little is known about the lung and oral cavity microbiomes in smokers, and even less for electronic cigarette (EC) users, compared with never-smokers. In a cross-sectional study (n = 28) of smokers, EC users, and never-smokers, bronchoalveolar lavage and saliva samples underwent metatranscriptome profiling to examine associations with lung and oral microbiomes. Pairwise comparisons assessed differentially abundant bacteria species. Total bacterial load was similar between groups, with no differences in bacterial diversity across lung microbiomes. In lungs, 44 bacteria species differed significantly (FDR < 0.1) between smokers/never-smokers, with most decreased in smokers. Twelve species differed between smokers/EC users, all decreased in smokers of which Neisseria sp. KEM232 and Curvibacter sp. AEP1-3 were observed. Among the top five decreased species in both comparisons, Neisseria elongata, Neisseria sicca, and Haemophilus parainfluenzae were observed. In the oral microbiome, 152 species were differentially abundant for smokers/never-smokers, and 17 between smokers/electronic cigarette users, but only 21 species were differentially abundant in both the lung and oral cavity. EC use is not associated with changes in the lung microbiome compared with never-smokers, indicating EC toxicity does not affect microbiota. Statistically different bacteria in smokers compared with EC users and never-smokers were almost all decreased, potentially due to toxic effects of cigarette smoke. The low numbers of overlapping oral and lung microbes suggest that the oral microbiome is not a surrogate for analyzing smoking-related effects in the lung.

PREVENTION RELEVANCE

The microbiome affects cancer and other disease risk. The effects of e-cig usage on the lung microbiome are essentially unknown. Given the importance of lung microbiome dysbiosis populated by oral species which have been observed to drive lung cancer progression, it is important to study effects of e-cig use on microbiome.

Noninvasive Tape-Stripping with High-Resolution RNA Profiling Effectively Captures a Preinflammatory State in Nonlesional Psoriatic Skin

Tape stripping is a minimally invasive, nonscarring method that can be utilized to assess gene expression in the skin but is infrequently used given technical constraints. By comparing different tape stripping technologies and full-thickness skin biopsy results of lesional and nonlesional psoriatic skin from the same patients, we demonstrate that tape stripping with optimized high-resolution transcriptomic profiling can be used to effectively assess and characterize inflammatory responses in the skin. Upon comparison with single-cell RNA-sequencing data from psoriatic full-thickness skin biopsies, we illustrate that tape-stripping efficiently captures the transcriptome of the upper layers of the epidermis with sufficient resolution to assess the molecular components of the feed-forward immune amplification pathway in psoriasis. Notably, nonlesional psoriatic skin sampled by tape stripping demonstrates activated, proinflammatory changes when compared to healthy control skin, suggesting a prepsoriatic state, which is not captured on full-thickness skin biopsy transcriptome profiling. This work illustrates an approach to assess inflammatory response in the epidermis by combining noninvasive sampling with high throughput RNA-sequencing, providing a foundation for biomarker discoveries and mechanism of action studies for inflammatory skin conditions.

Comprehensive lncRNA and mRNA profiles in peripheral blood mononuclear cells derived from ankylosing spondylitis patients by RNA-sequencing analysis

The present study aimed to investigate the comprehensive expression profiles of long non-coding RNA (lncRNA) in ankylosing spondylitis (AS).The peripheral blood samples were collected from 6 AS patients and 6 age- and gender-matched healthy controls (HCs), and separated for peripheral blood mononuclear cells, followed by RNA-sequencing. Further bioinformatics analyses were performed to explore the significantly enriched biological processes, signaling pathways of differentially expressed lncRNAs (DElncRNAs) (based on cis-target and trans-target genes) and differentially expressed mRNAs (DEmRNAs).Principal component analysis plots indicated that both lncRNA and mRNA expression profiles could distinguish AS patients from HCs; heatmap diagram exhibited a relatively good consistency and tendency of lncRNA and mRNA expression profiles in AS patients and HCs, respectively; volcano plots exhibited 114 upregulated and 45 downregulated DElncRNAs, 284 upregulated and 435 downregulated DEmRNAs in AS patients compared with HCs; Gene ontology enrichment analyses indicated that DElncRNAs (based on cis-target and trans-target genes) and DEmRNAs were enriched in molecular functions (including DNA binding, protein binding, etc) and biological process (including immune response, inflammatory response, etc); Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that these DElncRNAs (based on cis-target and trans-target genes) and DEmRNAs were enriched in immune and inflammation-related signaling, such as B cell receptor signaling pathway, TNF signaling pathway, NF-kappa B signaling pathway, etc.Our study displays the comprehensive expression profiles and functions of lncRNAs involved in AS, which provides reference for further researches discovering candidate lncRNAs with value in assisting early AS diagnosis.

Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples

Aim:

Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. The present study is aimed at assessing the overall accuracy of RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world diagnostics.

Methods:

Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex^© Solid tumor kit through the manufacturer’s pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)].

Results:

The combination of FusionPlex^© Solid tumor with ArcherDX^® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens.

Conclusions:

Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.

Magnolin exhibits anti-inflammatory effects on chondrocytes via the NF-κB pathway for attenuating anterior cruciate ligament transection-induced osteoarthritis

Purpose: This study aimed to investigate whether magnolin (MGL) possesses the capability of suppressing inflammatory responses that can in turn alleviate osteoarthritis (OA).Methods: We investigated the effects of MGL on the viability of rat chondrocytes at concentrations of 5 to 100 µM, and selected 10 µM for further study. We elucidated the molecular mechanisms and signaling pathways mediating these effects via RNA sequencing, qRT-PCR, immunofluorescent staining, and Western blotting techniques. Following this, we established an anterior cruciate ligament (ACL) transection-induced OA rat model, and injected MGL into the knee articular cavities to verify the in vivo anti-inflammatory effects of MGL.Results: We found that MGL could recover the TNF-α-induced upregulation of IL-1β, COX2, ADAMTS-5, and MMP-1/3/13 at the gene/protein level, as well as the downregulation of cartilaginous ECM synthesis. Gene expression profiles of different groups identified 49 common differentially expressed genes (DEGs), which were mainly enriched in the structural constituents of the ribosome, the extracellular space, and inflammatory response. The NF-κB pathway was highly enriched, and the expression levels of DEGs associated with it (Nfkbia, Ptgs2, Rela, Tnfrsf1a, Tradd, Traf2) under TNF-α stimulation were reversed by MGL. Further studies proved that MGL simultaneously suppressed the cell nucleus translocation of p65 and the phosphorylation of IκBα. Moreover, in vivo, MGL suppressed cartilage matrix degradation, inhibited MMP-13 expression, and promoted cartilage matrix construction by upregulating SOX9 synthesis.Conclusion: MGL demonstrated significant anti-inflammatory bioactivity on chondrocytes by suppressing the activation of NF-κB pathway, which in turn exhibited a significant alleviation of OA.

RNA-sequencing of peripheral blood circular RNAs in Parkinson disease

BACKGROUND

Circular RNAs (circRNAs) play an important role in many neurological diseases and can serve as biomarkers for these diseases. However, the information about circRNAs in Parkinson disease (PD) remained limited. In this study, we aimed to determine the circRNAs expression profile in PD patients and discuss the significance of circRNAs in the diagnosis of PD.

METHODS AND RESULTS

Using RNA-sequencing in peripheral blood RNAs, we showed that a significant number of mRNAs or circRNAs were differentially expressed between PD patients and normal controls (NCs), which included 273 up-regulated and 493 down-regulated mRNAs, and 129 up-regulated and 282 down-regulated circRNAs, respectively. Functional analysis was performed using the Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway analysis, and the results showed that the second most enriched KEGG pathway was PD. These data suggest that the levels of mRNAs and circRNAs in peripheral blood could be potentially used as biomarkers for PD. In addition, we correlated mRNAs and circRNAs by constructing a competing endogenous RNA (ceRNA) network in PD. The resulted-in ceRNA network included 10 differentially expressed mRNAs from PD pathway, 13 predicted miRNAs, and 10 differentially expressed circRNAs.

CONCLUSION

Collectively, we first characterized the expression profiles of circRNAs and mRNAs in peripheral blood from PD patients and proposed their possible characters in the pathogenesis of PD. These results provided valuable insights into the clues underlying the pathogenesis of PD.

Transcriptional adaptation of Mycobacterium ulcerans in an original mouse model: New insights into the regulation of mycolactone

Mycobacterium ulcerans is the causal agent of Buruli ulcer, a chronic infectious disease and the third most common mycobacterial disease worldwide. Without early treatment, M. ulcerans provokes massive skin ulcers, caused by the mycolactone toxin, its main virulence factor. However, spontaneous healing may occur in Buruli ulcer patients several months or years after the disease onset. We have shown, in an original mouse model, that bacterial load remains high and viable in spontaneously healed tissues, with a switch of M. ulcerans to low levels of mycolactone production, adapting its strategy to survive in such a hostile environment. This original model offers the possibility to investigate the regulation of mycolactone production, by using an RNA-seq strategy to study bacterial adaptation during mouse infection. Pathway analysis and characterization of the tissue environment showed that the bacillus adapted to its new environment by modifying its metabolic activity and switching nutrient sources. Thus, M. ulcerans ensures its survival in healing tissues by reducing its secondary metabolism, leading to an inhibition of mycolactone synthesis. These findings shed new light on mycolactone regulation and pave the way for new therapeutic strategies.

Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window

OBJECTIVE

 Abnormalities in the eutopic endometrium of women with endometriosis may be related to disease-associated infertility. Although previous RNA-sequencing analysis did not show differential expression in endometrial transcripts of endometriosis patients, other molecular alterations could impact protein synthesis and endometrial receptivity. Our aim was to screen for functional mutations in the transcripts of eutopic endometria of infertile women with endometriosis and controls during the implantation window.

METHODS

 Data from RNA-Sequencing of endometrial biopsies collected during the implantation window from 17 patients (6 infertile women with endometriosis, 6 infertile controls, 5 fertile controls) were analyzed for variant discovery and identification of functional mutations. A targeted study of the alterations found was performed to understand the data into disease's context.

RESULTS

 None of the variants identified was common to other samples within the same group, and no mutation was repeated among patients with endometriosis, infertile and fertile controls. In the endometriosis group, nine predicted deleterious mutations were identified, but only one was previously associated to a clinical condition with no endometrial impact. When crossing the mutated genes with the descriptors endometriosis and/or endometrium, the gene CMKLR1 was associated either with inflammatory response in endometriosis or with endometrial processes for pregnancy establishment.

CONCLUSION

 Despite no pattern of mutation having been found, we ponder the small sample size and the analysis on RNA-sequencing data. Considering the purpose of the study of screening and the importance of the CMKLR1 gene on endometrial modulation, it could be a candidate gene for powered further studies evaluating mutations in eutopic endometria from endometriosis patients.

Differentially-expressed mRNAs, microRNAs and long noncoding RNAs in intervertebral disc degeneration identified by RNA-sequencing

The underlying molecular mechanisms of intervertebral disc degeneration (IDD) remain unclear. This study aimed to identify the crucial molecules and explore the function of noncoding RNAs and related pathways in IDD. We randomly selected three samples each from an IDD and a spinal cord injury group (control) for RNA-sequencing. We identified 463 differentially-expressed long noncoding RNAs (lncRNAs), 47 differentially-expressed microRNAs (miRNAs), and 1,334 differentially-expressed mRNAs in IDD. Three hundred fifty-eight lncRNAs as cis-regulators could potentially target 865 genes. Protein–protein interaction (PPI) network analysis confirmed that IL-6, VEGFA, IGF1, MMP9, CXCL8, FGF2, IL1B, CCND1, ITGAM, PTPRC, FOS and PTGS2 were hub genes. We built a competing endogenous RNA (ceRNA) network and identified lncRNA XIST–hsa-miR-4775–PLA2G7 and lncRNA XIST–hsa-miR-424-5p–AMOT/TGFBR3 ceRNA axes. Quantitative real-time PCR (qRT-PCR) was implemented in 15 IDD samples and 15 controls to validate differentially-expressed genes in ceRNA axes. From the ceRNA network, gene ontology (GO) enrichment analysis indicated that noncoding RNAs were associated with several biological processes, including extracellular matrix organization, extracellular structure organization, leukocyte migration, and mesenchyme development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that noncoding RNAs were associated with several pathways including the AGE-RAGE signaling pathway, PI3K-Akt signaling pathway, axon guidance, and osteoclast differentiation. These results indicate that some specific noncoding RNAs and ceRNA axes may be vital during the development of IDD, and may have potential as alternative diagnostic biomarkers as well as novel therapeutic strategies for IDD.

PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways

Melanoma is one of the most serious forms of skin cancer, and its increasing incidence coupled with nonlasting therapeutic options for metastatic disease highlights the need for additional novel approaches for its management. In this study, we determined the potential interactions between polo-like kinase 1 (PLK1, a serine/threonine kinase involved in mitotic regulation) and NOTCH1 (a type I transmembrane protein deciding cell fate during development) in melanoma. Employing an in-house human melanoma tissue microarray (TMA) containing multiple cases of melanomas and benign nevi, coupled with high-throughput, multispectral quantitative fluorescence imaging analysis, we found a positive correlation between PLK1 and NOTCH1 in melanoma. Furthermore, The Cancer Genome Atlas database analysis of patients with melanoma showed an association of higher mRNA levels of PLK1 and NOTCH1 with poor overall, as well as disease-free, survival. Next, utilizing small-molecule inhibitors of PLK1 and NOTCH (BI 6727 and MK-0752, respectively), we found a synergistic antiproliferative response of combined treatment in multiple human melanoma cells. To determine the molecular targets of the overall and synergistic responses of combined PLK1 and NOTCH inhibition, we conducted RNA-sequencing analysis employing a unique regression model with interaction terms. We identified the modulations of several key genes relevant to melanoma progression/metastasis, including MAPK, PI3K, and RAS, as well as some new genes such as Apobec3G, BTK, and FCER1G, which have not been well studied in melanoma. In conclusion, our study demonstrated a synergistic antiproliferative response of concomitant targeting of PLK1 and NOTCH in melanoma, unraveling a potential novel therapeutic approach for detailed preclinical/clinical evaluation.

Detection of NRG1 Gene Fusions in Solid Tumors

PURPOSE

NRG1 gene fusions are rare but potentially actionable oncogenic drivers that are present in some solid tumors. Details regarding the incidence of these gene rearrangements are lacking. Here, we assessed the incidence of NRG1 fusions across multiple tumor types and described fusion partners.

EXPERIMENTAL DESIGN

Tumor specimens submitted for molecular profiling at a Clinical Laboratory Improvement Amendments (CLIA)-certified genomics laboratory and that underwent fusion testing by anchored multiplex PCR for targeted RNA sequencing were retrospectively identified. The overall and tumor-specific incidence was noted, as was the specific fusion partner.

RESULTS

Out of 21,858 tumor specimens profiled from September 2015 to December 2018, 41 cases (0.2%) harbored an NRG1 fusion. Multiple fusion partners were identified. Fusion events were seen across tumor types. The greatest incidence was in non-small cell lung cancer (NSCLC, 25), though this represented only 0.3% of NSCLC cases tested. Other tumor types harboring an NRG1 fusion included gallbladder cancer, renal cell carcinoma, bladder cancer, ovarian cancer, pancreatic cancer, breast cancer, neuroendocrine tumor, sarcoma, and colorectal cancer.

CONCLUSIONS

NRG1 fusions can be detected at a low incidence across multiple tumor types with significant heterogeneity in fusion partner.See related commentary by Dimou and Camidge, p. 4865.

Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells

NOP2/Sun domain family member 2 (NSUN2) is upregulated in numerous types of tumors and may be implicated in multiple biological processes, including cell proliferation, migration and human tumorigenesis. However, little is known about how NSUN2 serves a role in these processes. In the present study, expression profiles of long noncoding RNAs (lncRNAs) and mRNAs were developed in NSUN2‑deficient HepG2 cells by RNA‑sequencing analysis. A total of 757 lncRNAs were differentially expressed, 392 of which were upregulated, and 365 were downregulated compared with wild‑type HepG2 cells. Moreover, 212 lncRNAs were co‑expressed with 368 target mRNAs. It was also observed that 253 pairs of lncRNAs and mRNAs exhibited negative correlations and that 290 pairs had positive correlations. Bioinformatics analysis indicated that these lncRNAs regulated by NSUN2 were associated with 'signal transduction', 'extracellular exosome' and 'calcium ion binding', and were enriched in 'pathways in cancer', 'PI3K‑Akt signaling pathway' and 'ECM‑receptor interaction pathway'. These results illustrate the landscape and co‑expression network of lncRNAs regulated by NSUN2 and provide invaluable information for studying the molecular function of NSUN2.

Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO2 Nanoparticle Fuel Borne Catalyst

It is important to understand molecular effects on plants exposed to compounds released from use of products containing engineered nanomaterials. Here, we present mRNA sequencing data on transcriptome impacts to Douglas-fir following 2 weeks of sublethal exposure to 30:1 diluted airborne emissions released from combustion of diesel fuel containing engineered CeO₂ nanoparticle catalysts (DECe). Our hypothesis was that chamber exposure to DECe would induce distinct transcriptome changes in seedling needles compared with responses to conventional diesel exhaust (DE) or filtered DECe Gas Phase. Significantly increased uptake/binding of Ce in needles of DECe treated seedlings was 2.7X above background levels and was associated with altered gene expression patterns. All 225 Blast2GO gene ontologies (GOs) enriched by up-regulated DECe transcripts were nested within GOs for DE, however, 29 of 31 enriched GOs for down-regulated DECe transcripts were unique. MapMan analysis also identified three pathways enriched with DECe down-regulated transcripts. There was prominent representation of genes with attenuated expression in transferase, transporter, RNA regulation and protein degradation GOs and pathways. CeO₂ nanoparticle additive decreased and shifted molecular impact of diesel emissions. Wide-spread use of such products and chronic environmental exposure to DECe may adversely affect plant physiology and development.

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription reflect changes in protein synthesis, but many exceptions have been observed. Recently, a technique called ribosome profiling (or Ribo-Seq) has emerged as a powerful method that allows identification, with high accuracy, which regions of mRNA are translated into proteins and quantification of translation at the genome-wide level. Here, we present a generalized protocol for genome-wide quantification of translation using Ribo-Seq in budding yeast. In addition, combining Ribo-Seq data with mRNA abundance measurements allows us to simultaneously quantify translation efficiency of thousands of mRNA transcripts in the same sample and compare changes in these parameters in response to experimental manipulations or in different physiological states. We describe a detailed protocol for generation of ribosome footprints using nuclease digestion, isolation of intact ribosome-footprint complexes via sucrose gradient fractionation, and preparation of DNA libraries for deep sequencing along with appropriate quality controls necessary to ensure accurate analysis of in vivo translation.

Altered expression of MALAT1 lncRNA in nonalcoholic steatohepatitis fibrosis regulates CXCL5 in hepatic stellate cells

In the present study, we sought to identify long noncoding RNA (lncRNA) expression profiles in nonalcoholic steatohepatitis (NASH) patients with histologic evidence of lobular inflammation and advanced fibrosis. We profiled lncRNA expression using RNA-sequencing of wedge liver biopsies from 24 nonalcoholic fatty liver disease (NAFLD) patients with normal liver histology, 53 NAFLD patients with lobular inflammation, and 65 NAFLD patients with advanced fibrosis. Transcript profiling identified 4432 and 4057 differentially expressed lncRNAs in comparisons of normal tissue with lobular inflammation and fibrosis samples, respectively. Functional enrichment analysis revealed lncRNA participation in transforming growth factor beta 1 and tumor necrosis factor signaling, insulin resistance, and extracellular matrix maintenance. Several lncRNAs were highly expressed in fibrosis relative to normal tissue, including nuclear paraspeckle assembly transcript 1, hepatocellular carcinoma upregulated lncRNA, and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). Two potential target mRNAs, syndecan 4 (SDC4), and C-X-C motif chemokine ligand 5 (CXCL5) were identified for hepatocellular carcinoma upregulated lncRNA and MALAT1, respectively, but only CXCL5 showed differential expression among the different histologic classes. Knockdown of MALAT1 expression reduced CXCL5 transcript and protein levels by 50% and 30%, respectively, in HepG2 cells. The expression of MALAT1 and CXCL5 was upregulated in activated hepatic stellate (LX-2) cells compared to cells in the quiescent state, and MALAT1 expression was regulated by hyperglycemia and insulin in HepG2 cells, but only by insulin in LX-2 cells. Dysregulated lncRNA expression is associated with inflammation and fibrosis in NASH. Functionally relevant differences in MALAT1 expression may contribute to the development of fibrosis in NASH through mechanisms involving inflammatory chemokines.

Association between hypoxic volume and underlying hypoxia-induced gene expression in oropharyngeal squamous cell carcinoma

BACKGROUND

Hypoxia imaging is a promising tool for targeted therapy but the links between imaging features and underlying molecular characteristics of the tumour have not been investigated. The aim of this study was to compare hypoxia biomarkers and gene expression in oropharyngeal squamous cell carcinoma (OPSCC) diagnostic biopsies with hypoxia imaged with 64Cu-ATSM PET/CT.

METHODS

64Cu-ATSM imaging, molecular and clinical data were obtained for 15 patients. Primary tumour SUVmax, tumour to muscle ratio (TMR) and hypoxic volume were tested for association with reported hypoxia gene signatures in diagnostic biopsies. A putative gene signature for hypoxia in OPSCCs (hypoxic volume-associated gene signature (HVS)) was derived.

RESULTS

Hypoxic volume was significantly associated with a reported hypoxia gene signature (rho=0.57, P=0.045), but SUVmax and TMR were not. Immunohistochemical staining with the hypoxia marker carbonic anhydrase 9 (CA9) was associated with a gene expression hypoxia response (rho=0.63, P=0.01). Sixteen genes were positively and five genes negatively associated with hypoxic volume (adjusted P<0.1; eight genes had adjusted P<0.05; HVS). This signature was associated with inferior 3-year progression-free survival (HR=1.5 (1.0-2.2), P=0.047) in an independent patient cohort.

CONCLUSIONS

64Cu-ATSM-defined hypoxic volume was associated with underlying hypoxia gene expression response. A 21-gene signature derived from hypoxic volume from patients with OPSCCs in our study may be linked to progression-free survival.

Characterizing the neurotranscriptomic states in alternative stress coping styles

BACKGROUND

Animals experience stress in many contexts and often successfully cope. Individuals exhibiting the proactive versus reactive stress coping styles display qualitatively different behavioral and neuroendocrine responses to stressors. The predisposition to exhibiting a particular coping style is due to genetic and environmental factors. In this study we explore the neurotranscriptomic and gene network biases that are associated with differences between zebrafish (Danio rerio) lines selected for proactive and reactive coping styles and reared in a common garden environment.

RESULTS

Using RNA-sequencing we quantified the basal transcriptomes from the brains of wild-derived zebrafish lines selectively bred to exhibit the proactive or reactive stress coping style. We identified 1953 genes that differed in baseline gene expression levels. Weighted gene coexpression network analyses identified one gene module associated with line differences. Together with our previous pharmacological experiment, we identified a core set of 62 genes associated with line differences. Gene ontology analyses reveal that many of these core genes are implicated in neurometabolism (e.g. organic acid biosynthetic and fatty acid metabolic processes).

CONCLUSIONS

Our results show that proactive and reactive stress coping individuals display distinct basal neurotranscriptomic states. Differences in baseline expression of select genes or regulation of specific gene modules are linked to the magnitude of the behavioral response and the display of a coping style, respectively. Our results expand the molecular mechanisms of stress coping from one focused on the neurotransmitter systems to a more complex system that involves an organism's capability to handle neurometabolic loads and allows for comparisons with other animal taxa to uncover potential conserved mechanisms.

Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana

BACKGROUND

Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. The aim of this study was to characterize the defence response of E. grandis against C. austroafricana.

RESULTS

Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction.

CONCLUSION

The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials.

Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance

BACKGROUND

Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean.

RESULTS

Contrasting data from PI 416937 and the cultivar 'Benning', we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit, noting both the well-known reduction in photosynthesis genes as well as the less understood up-regulation of the protein transport pathway. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI 416937's unique drought avoidance strategy.

CONCLUSIONS

There is a general and functionally significant transcriptional response to water deficit that involves not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Genes that show a genotypic difference are more likely to show an environmental response than genes that are constant between genotypes. In this study, at least five genes that clearly exhibited a genotype x environment response fell within known QTL and are very good candidates for further research into slow-wilting.

Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing

A study of genome-wide gene expression in major depressive disorder (MDD) was undertaken in a large population-based sample to determine whether altered expression levels of genes and pathways could provide insights into biological mechanisms that are relevant to this disorder. Gene expression studies have the potential to detect changes that may be because of differences in common or rare genomic sequence variation, environmental factors or their interaction. We recruited a European ancestry sample of 463 individuals with recurrent MDD and 459 controls, obtained self-report and semi-structured interview data about psychiatric and medical history and other environmental variables, sequenced RNA from whole blood and genotyped a genome-wide panel of common single-nucleotide polymorphisms. We used analytical methods to identify MDD-related genes and pathways using all of these sources of information. In analyses of association between MDD and expression levels of 13 857 single autosomal genes, accounting for multiple technical, physiological and environmental covariates, a significant excess of low P-values was observed, but there was no significant single-gene association after genome-wide correction. Pathway-based analyses of expression data detected significant association of MDD with increased expression of genes in the interferon α/β signaling pathway. This finding could not be explained by potentially confounding diseases and medications (including antidepressants) or by computationally estimated proportions of white blood cell types. Although cause-effect relationships cannot be determined from these data, the results support the hypothesis that altered immune signaling has a role in the pathogenesis, manifestation, and/or the persistence and progression of MDD.

Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods

BACKGROUND

Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 ([O3] have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the world's most important legume crop and is sensitive to O3. Current ground-level [O3] are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated [O3] using RNA-Sequencing.

RESULTS

Elevated [O3] elicited a strong transcriptional response in flower and pod tissues, with increased expression of genes involved in signaling in both tissues. Flower tissues also responded to elevated [O3] by increasing expression of genes encoding matrix metalloproteinases (MMPs). MMPs are zinc- and calcium-dependent endopeptidases that have roles in programmed cell death, senescence and stress response in plants. Pod tissues responded to elevated [O3] by increasing expression of xyloglucan endotransglucosylase/hydrolase genes, which may be involved with increased pod dehiscence in elevated [O3].

CONCLUSIONS

This study established that gene expression in reproductive tissues of soybean are impacted by elevated [O3], and flowers and pods have distinct transcriptomic responses to elevated [O3].

Populus tremula (European aspen) shows no evidence of sexual dimorphism

BACKGROUND

Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. Such sexual dimorphism would result in sex biased gene expression patterns in non-floral organs for autosomal genes associated with the control and development of such phenotypic traits.

RESULTS

We examined morphological, biochemical and herbivory traits to test for sexually dimorphic resource allocation strategies within collections of sexually mature and immature Populus tremula (European aspen) trees. In addition we profiled gene expression in mature leaves of sexually mature wild trees using whole-genome oligonucleotide microarrays and RNA-Sequencing.

CONCLUSIONS

We found no evidence of sexual dimorphism or differential resource investment strategies between males and females in either sexually immature or mature trees. Similarly, single-gene differential expression and machine learning approaches revealed no evidence of large-scale sex biased gene expression. However, two significantly differentially expressed genes were identified from the RNA-Seq data, one of which is a robust diagnostic marker of sex in P. tremula.

DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression

BACKGROUND

Next-generation sequencing (NGS) has advanced the application of high-throughput sequencing technologies in genetic and genomic variation analysis. Due to the large dynamic range of expression levels, RNA-seq is more prone to detect transcripts with low expression. It is clear that genes with no mapped reads are not expressed; however, there is ongoing debate about the level of abundance that constitutes biologically meaningful expression. To date, there is no consensus on the definition of low expression. Since random variation is high in regions with low expression and distributions of transcript expression are affected by numerous experimental factors, methods to differentiate low and high expressed data in a sample are critical to interpreting classes of abundance levels in RNA-seq data.

RESULTS

A data-adaptive approach was developed to estimate the lower bound of high expression for RNA-seq data. The Kolmgorov-Smirnov statistic and multivariate adaptive regression splines were used to determine the optimal cutoff value for separating transcripts with high and low expression. Results from the proposed method were compared to results obtained by estimating the theoretical cutoff of a fitted two-component mixture distribution. The robustness of the proposed method was demonstrated by analyzing different RNA-seq datasets that varied by sequencing depth, species, scale of measurement, and empirical density shape.

CONCLUSIONS

The analysis of real and simulated data presented here illustrates the need to employ data-adaptive methodology in lieu of arbitrary cutoffs to distinguish low expressed RNA-seq data from high expression. Our results also present the drawbacks of characterizing the data by a two-component mixture distribution when classes of gene expression are not well separated. The ability to ascertain stably expressed RNA-seq data is essential in the filtering process of data analysis, and methodologies that consider the underlying data structure demonstrate superior performance in preserving most of the interpretable and meaningful data. The proposed algorithm for classifying low and high regions of transcript abundance promises wide-range application in the continuing development of RNA-seq analysis.

A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat

BACKGROUND

The past decade has seen an abundance of transcriptional profiling studies of preclinical models of persistent pain, predominantly employing microarray technology. In this study we directly compare exon microarrays to RNA-seq and investigate the ability of both platforms to detect differentially expressed genes following nerve injury using the L5 spinal nerve transection model of neuropathic pain. We also investigate the effects of increasing RNA-seq sequencing depth. Finally we take advantage of the "agnostic" approach of RNA-seq to discover areas of expression outside of annotated exons that show marked changes in expression following nerve injury.

RESULTS

RNA-seq and microarrays largely agree in terms of the genes called as differentially expressed. However, RNA-seq is able to interrogate a much larger proportion of the genome. It can also detect a greater number of differentially expressed genes than microarrays, across a wider range of fold changes and is able to assign a larger range of expression values to the genes it measures. The number of differentially expressed genes detected increases with sequencing depth. RNA-seq also allows the discovery of a number of genes displaying unusual and interesting patterns of non-exonic expression following nerve injury, an effect that cannot be detected using microarrays.

CONCLUSION

We recommend the use of RNA-seq for future high-throughput transcriptomic experiments in pain studies. RNA-seq allowed the identification of a larger number of putative candidate pain genes than microarrays and can also detect a wider range of expression values in a neuropathic pain model. In addition, RNA-seq can interrogate the whole genome regardless of prior annotations, being able to detect transcription from areas of the genome not currently annotated as exons. Some of these areas are differentially expressed following nerve injury, and may represent novel genes or isoforms. We also recommend the use of a high sequencing depth in order to detect differential expression for genes with low levels of expression.

Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

BACKGROUND

A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such as Trichoderma reesei and Aspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw.

RESULTS

In T. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24h exposure to straw (approximately 13% of the total mRNA) but were less than recorded in A. niger (approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction in A. niger were also uncovered in T. reesei and categories of enzymes induced were in general similar to those in A. niger. Similarly to A. niger, antisense transcripts are present in T. reesei and their expression is regulated by the growth condition.

CONCLUSIONS

T. reesei uses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, to A. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development

BACKGROUND

Soybean (Glycine max L.) is one of the most important oil crops in the world. It is desirable to increase oil yields from soybean, and so this has been a major goal of oilseed engineering. However, it is still uncertain how many genes and which genes are involved in lipid biosynthesis.

RESULTS

Here, we evaluated changes in gene expression over the course of seed development using Illumina (formerly Solexa) RNA-sequencing. Tissues at 15 days after flowering (DAF) served as the control, and a total of 11592, 16594, and 16255 differentially expressed unigenes were identified at 35, 55, and 65 DAF, respectively. Gene Ontology analyses detected 113 co-expressed unigenes associated with lipid biosynthesis. Of these, 15 showed significant changes in expression levels (log2fold values ≥ 1) during seed development. Pathway analysis revealed 24 co-expressed transcripts involved in lipid biosynthesis and fatty acid biosynthesis pathways. We selected 12 differentially expressed genes and analyzed their expressions using qRT-PCR. The results were consistent with those obtained from Solexa sequencing.

CONCLUSION

These results provide a comprehensive molecular biology background for research on soybean seed development, particularly with respect to the process of oil accumulation. All of the genes identified in our research have significance for breeding soybeans with increased oil contents.