SENSE mRNA-Seq for Illumina Publications
The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and induces tumorigenic properties
Christine Hoesl, Enrica Zanuttigh, Thomas Fröhlich, Julia Philippou-Massier, Stefan Krebs, Helmut Blum, Maik Dahlhoff
Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, doi:10.1016/j.bbamcr.2020.118717
Cutaneous squamous cell carcinoma (cSCC) is the most prominent tumor of non-melanoma skin cancers and the most aggressive tumor among keratinocyte carcinoma of the skin, showing a high potential for local invasion and metastasis. The cSCC incidences increased dramatically in recent years and the disease occurs more commonly than any other malignancy. The secretome of cancer cells is currently the focus of many studies in order to identify new marker proteins for different types of cancer and to investigate its influence on the tumor microenvironment. In our study we evaluated whether the secretome of cSCC cells has an impact on keratinocytes, the surrounding tissue cells of cSCC. Therefore, we analyzed and compared the secretome of human A431 cancer cells and of HaCaT keratinocytes by mass spectrometry. In a second experiment, keratinocytes were exposed to the secretome of A431 cells and vice versa and the transcriptome was analyzed by next-generation sequencing. HaCaT cells incubated with A431 conditioned medium revealed a significantly activated mammalian target of rapamycin pathway with a concomitant increase in proliferation and migration. In conclusion, our data demonstrate the impact of the secretome of cancer cells on the transcription machinery of the cells surrounding the tumor, leading to a tumorigenic cell fate.
Features SENSE mRNA-Seq Library Prep Kit
Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction
Johanna Fitz, Tobias Neumann, Monika Steininger, Eva-Maria Wiedemann, Adriana Cantoran Garcia, Alexander Athanasiadis, Ursula E. Schoeberl & Rushad Pavri
Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer–gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer–promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters.
Features SENSE mRNA-Seq Library Prep Kit
Tenogenic Contribution to Skeletal Muscle Regeneration: The Secretome of Scleraxis Overexpressing Mesenchymal Stem Cells Enhances Myogenic Differentiation In Vitro
Maximilian Strenzke, Paolo Alberton, Attila Aszodi, Denitsa Docheva, Elisabeth Haas, Christian Kammerlander, Wolfgang Böcker and Maximilian Michael Saller
International journal of molecular sciences, doi:10.3390/ijms21061965
Integrity of the musculoskeletal system is essential for the transfer of muscular contraction force to the associated bones. Tendons and skeletal muscles intertwine, but on a cellular level, the myotendinous junctions (MTJs) display a sharp transition zone with a highly specific molecular adaption. The function of MTJs could go beyond a mere structural role and might include homeostasis of this musculoskeletal tissue compound, thus also being involved in skeletal muscle regeneration. Repair processes recapitulate several developmental mechanisms, and as myotendinous interaction does occur already during development, MTJs could likewise contribute to muscle regeneration. Recent studies identified tendon-related, scleraxis-expressing cells that reside in close proximity to the MTJs and the muscle belly. As the muscle-specific function of these scleraxis positive cells is unknown, we compared the influence of two immortalized mesenchymal stem cell (MSC) lines—differing only by the overexpression of scleraxis—on myoblasts morphology, metabolism, migration, fusion, and alignment. Our results revealed a significant increase in myoblast fusion and metabolic activity when exposed to the secretome derived from scleraxis-overexpressing MSCs. However, we found no significant changes in myoblast migration and myofiber alignment. Further analysis of differentially expressed genes between native MSCs and scleraxis-overexpressing MSCs by RNA sequencing unraveled potential candidate genes, i.e., extracellular matrix (ECM) proteins, transmembrane receptors, or proteases that might enhance myoblast fusion. Our results suggest that musculotendinous interaction is essential for the development and healing of skeletal muscles.
Features SENSE mRNA-Seq Library Prep Kit
Substrate Specificity of the TRAMP Nuclear Surveillance Complexes
Clémentine Delan-Forino, Christos Spanos, Juri Rappsilber, David Tollervey
During nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduced Mtr4 recruitment and increased RNA abundance for mRNAs specifically showing high Trf5 binding.
Features SENSE mRNA-Seq Library Prep Kit
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol
Evelyn Fessler, Eva-Maria Eckl, Sabine Schmitt, Igor Alves Mancilla, Matthias F. Meyer-Bender, Monika Hanf, Julia Philippou-Massier, Stefan Krebs, Hans Zischka & Lucas T. Jae
Mitochondrial fidelity is tightly linked to overall cellular homeostasis and is compromised in ageing and various pathologies. Mitochondrial malfunction needs to be relayed to the cytosol, where an integrated stress response is triggered by the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) in mammalian cells. eIF2α phosphorylation is mediated by the four eIF2α kinases GCN2, HRI, PERK and PKR, which are activated by diverse types of cellular stress. However, the machinery that communicates mitochondrial perturbation to the cytosol to trigger the integrated stress response remains unknown. Here we combine genome engineering and haploid genetics to unbiasedly identify genes that affect the induction of C/EBP homologous protein (CHOP), a key factor in the integrated stress response. We show that the mitochondrial protease OMA1 and the poorly characterized protein DELE1, together with HRI, constitute the missing pathway that is triggered by mitochondrial stress. Mechanistically, stress-induced activation of OMA1 causes DELE1 to be cleaved into a short form that accumulates in the cytosol, where it binds to and activates HRI via its C-terminal portion. Obstruction of this pathway can be beneficial or adverse depending on the type of mitochondrial perturbation. In addition to the core pathway components, our comparative genetic screening strategy identifies a suite of additional regulators. Together, these findings could be used to inform future strategies to modulate the cellular response to mitochondrial dysfunction in the context of human disease.
Features SENSE mRNA-Seq Library Prep Kit
Population Specific Adaptations in Venom Production to Abiotic Stressors in a Widely Distributed Cnidarian
Maria Y. Sachkova, Jason Macrander, Joachim M. Surm, Reuven Aharoni, Shelcie S. Menard-Harvey, Amy Klock, Whitney B. Leach, Adam M. Reitzel, Yehu Moran
Nematostella vectensis is a sea anemone (Actiniaria, Cnidaria) inhabiting estuaries over a broad geographic range where environmental conditions such as temperatures and salinity vary widely. In cnidarians, antagonistic interactions with predators and prey are mediated by their venom, which may be metabolically expensive. In this study, we challenged Nematostella polyps with heat, salinity, UV light stressors and a combination of all three to determine how abiotic stressors impact toxin expression for individuals collected across this species’ range. Transcriptomics and proteomics revealed that the highly abundant toxin Nv1 was the most downregulated gene under heat stress conditions in multiple populations. Physiological measurements demonstrated that venom is metabolically costly to produce suggesting that downregulating venom expression under stressful conditions may be advantageous. Strikingly, under a range of abiotic stressors, individuals from different geographic locations along this latitudinal cline modulate venom production levels differently in a pattern reflecting local adaptation.
Features SENSE mRNA-Seq Library Prep Kit
Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses
Pawel Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech Karlowski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska, Andrzej Pacak
Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level.
Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.
Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
Features SIRVs (Spike-in RNA Variant Control Mixes) and SENSE mRNA-Seq Library Prep Kit
COMPOSITUM 1 (COM1) contributes to the architectural simplification of barley inflorescence via cell wall-mediated and meristem identity signals
N. Poursarebani, C. Trautewig, M. Melzer, T. Nussbaumer, U. Lundqvist, T. Rutten, T. Schmutzer, R. Brandt, A. Himmelbach, L. Altschmied, R. Koppolu, H. M. Youssef, M. Dalmais, A. Bendahmane, N. Stein, Z. Xin, T. Schnurbusch
Grasses have varying inflorescence shapes; however, little is known about the genetic mechanis ms specifying such shapes among tribes. We identified the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressed in inflorescence meristematic boundaries of differe nt grasses. COM1 specifies branch-inhibition in Triticeae (barley) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts revealed barley COM1 regulates cell growth, affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity module has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.
Features SENSE mRNA-Seq Library Prep Kit
Differences in the Inflammatory Response of White Adipose Tissue and Adipose-Derived Stem Cells
Sara Taha, Elias Volkmer, Elisabeth Haas, Paolo Alberton, Tobias Straub, Diana David-Rus, Attila Aszodi, Riccardo Giunta and Maximilian Michael Saller
International journal of molecular sciences, doi:10.3390/ijms21031086
The application of liposuctioned white adipose tissue (L-WAT) and adipose-derived stem cells (ADSCs) as a novel immunomodulatory treatment option is the currently subject of various clinical trials. Because it is crucial to understand the underlying therapeutic mechanisms, the latest studies focused on the immunomodulatory functions of L-WAT or ADSCs. However, studies that examine the specific transcriptional adaptation of these treatment options to an extrinsic inflammatory stimulus in an unbiased manner are scarce. The aim of this study was to compare the gene expression profile of L-WAT and ADSCs, when subjected to tumor necrosis factor alpha (TNFα), and to identify key factors that might be therapeutically relevant when using L-WAT or ADSCs as an immuno-modulator. Fat tissue was harvested by liposuction from five human donors. ADSCs were isolated from the same donors and shortly subjected to expansion culture. L-WAT and ADSCs were treated with human recombinant TNFα, to trigger a strong inflammatory response. Subsequently, an mRNA deep next-generation sequencing was performed to evaluate the different inflammatory responses of L-WAT and ADSCs. We found significant gene expression changes in both experimental groups after TNFα incubation. However, ADSCs showed a more homogenous gene expression profile by predominantly expressing genes involved in immunomodulatory processes such as CCL19, CCL5, TNFSF15 and IL1b when compared to L-WAT, which reacted rather heterogeneously. As RNA sequencing between L-WAT and ADSCS treated with TNFα revealed that L-WAT responded very heterogeneously to TNFα treatment, we therefore conclude that ADSCs are more reliable and predictable when used therapeutically. Our study furthermore yields insight into potential biological processes regarding immune system response, inflammatory response, and cell activation. Our results can help to better understand the different immunomodulatory effects of L-WAT and ADSCs.
Features SENSE mRNA-Seq Library Prep Kit
Rapid and scalable profiling of nascent RNA with fastGRO
Elisa Barbieri, Connor Hill, Mathieu Quesnel-Vallieres, Yoseph Barash, Alessandro Gardini
Genome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Over the past decade, next-generation sequencing has fostered development of a handful of techniques (i.e. GRO-seq, PRO-seq, TT-seq and NET-seq) that map unprocessed transcripts originating from both the coding and the noncoding portion of the genome. Unlike steady-state RNA sequencing, nascent RNA profiling mirrors the real-time activity of RNA Polymerases and provides an accurate readout of transcriptome-wide variations that occur during short time frames (i.e. response to external stimuli or rapid metabolic changes). Some species of nuclear RNAs, albeit functional, have a short half-life and can only be accurately gauged by nascent RNA techniques (i.e. lincRNAs and eRNAs). Furthermore, these techniques capture uncapped post-cleavage RNA at termination sites or promoter-associated antisense RNAs, providing a unique insight into RNAPII dynamics and processivity.
Here we present a run-on assay with 4s-UTP labelling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5×10^6 cells.
Features SLAMseq Metabolic RNA Labeling Kit for RNA-Seq and SENSE mRNA-Seq Library Prep Kit
Rapid and scalable profiling of nascent RNA with fastGRO
Elisa Barbieri, Connor Hill, Mathieu Quesnel-Vallieres, Yoseph Barash, Alessandro Gardini
Genome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Over the past decade, next-generation sequencing has fostered development of a handful of techniques (i.e. GRO-seq, PRO-seq, TT-seq and NET-seq) that map unprocessed transcripts originating from both the coding and the noncoding portion of the genome. Unlike steady-state RNA sequencing, nascent RNA profiling mirrors the real-time activity of RNA Polymerases and provides an accurate readout of transcriptome-wide variations that occur during short time frames (i.e. response to external stimuli or rapid metabolic changes). Some species of nuclear RNAs, albeit functional, have a short half-life and can only be accurately gauged by nascent RNA techniques (i.e. lincRNAs and eRNAs). Furthermore, these techniques capture uncapped post-cleavage RNA at termination sites or promoter-associated antisense RNAs, providing a unique insight into RNAPII dynamics and processivity.
Here we present a run-on assay with 4s-UTP labelling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5×10^6 cells.
Features SLAMseq Metabolic RNA Labeling Kit for RNA-Seq and SENSE mRNA-Seq Library Prep Kit
Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality
Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma May, C. Joel McManus, Norma V. Solis, Scott G. Filler,Aaron P. Mitchell
Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality.
Features SENSE mRNA-Seq Library Prep Kit
Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with Acute Myeloid Leukaemia
Stefan Bamopoulos, Aarif Batcha, Vindi Jurinovic, Maja Rothenberg-Thurley, Hanna Janke, Bianka Ksienzyk, Julia Philippou-Massier, Alexander Graf, Stefan Krebs, Helmut Blum, Stephanie Schneider, Nikola Konstandin, Maria Cristina Sauerland, Dennis Goerlich, Wolfgang E Berdel, Bernhard J Woermann, Stefan K Bohlander, Stefan Canzar, Ulrich Mansmann, Wolfgang Hiddemann, Jan Braess, Karsten Spiekermann, Klaus H Metzeler, Tobias Herold
Previous studies have demonstrated that splicing factor mutations are recurrent events in hematopoietic malignancies. Their clinical characteristics and aberrant splicing patterns have been explored in myelodysplasia, however, their functional consequences in acute myeloid leukaemia are largely unknown. The aim of this study was the comprehensive clinical and functional analysis of mutations in the three most commonly afflicted splicing factor genes: SRSF2, U2AF1 and SF3B1. To this end, we examined the prognostic role of splicing factor mutations in two large independent cohorts, encompassing a total of 2678 acute myeloid leukaemia patients treated with intensive chemotherapy. The clinical analysis was complemented by RNA-sequencing of 246 patients to identify targets of splicing dysregulation. Results were validated in an additional RNA-sequencing dataset of 177 patients. Patients with splicing factor mutations show inferior relapse-free and overall survival, however, these mutations do not represent independent prognostic markers. Differential isoform expression analysis revealed a characteristic expression profile for each splicing factor mutation with a strong dysregulation of several isoforms. Furthermore, by establishing a custom differential splice junction usage pipeline we accurately detected aberrant splicing in splicing factor mutated samples. Mutated samples were characterized by predominantly decreased splice junction utilization of a large number of genes. A large proportion of differentially used spliced junctions were novel. Targets of splicing dysregulation included several genes with a known role in acute myeloid leukaemia. In SRSF2(P95H) mutants we further explored the possibility of a cascading effect through the dysregulation of the splicing pathway. Taken together, our findings suggest that splicing factor mutations does not represent independent prognostic markers. However, they do have genome-wide consequences on gene splicing leading to dysregulated isoform expression of several genes.
Features SENSE mRNA-Seq Library Prep Kit
Docetaxel‐resistant prostate cancer cells become sensitive to gemcitabine due to the upregulation of ABCB1
Ho Kyung Seo MD, PhD, Sang‐Jin Lee PhD, Whi‐An Kwon MD, PhD, Kyung‐Chae Jeong PhD
Background
Docetaxel is the preferred chemotherapeutic agent for hormone‐refractory prostate cancer (PC) patients. However, patients eventually develop docetaxel resistance, and no effective treatment options are available for them.
Objective
We aimed to establish docetaxel resistance in castration‐resistant prostate cancer (CRPC) cell lines (DU145/TXR, PC‐3/TXR, and CWR22/TXR) and characterized transcriptional changes upon acquiring resistance to the docetaxel.
Methods
Human PC cells (DU145, PC‐3, CWR22) and all docetaxel‐resistant cells were maintained in Roswell Park Memorial Institute Medium (RPMI) 1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. ABCB1 was detected by using both parental and docetaxel‐resistant CRPCs prepared for flow cytometry. For the evaluation of tumor‐suppressive effects under each chemotherapeutic agent, subcutaneous xenografts of DU145 or DU145/TXR were implanted at the mouse flank.
Results
The P‐glycoprotein‐encoding gene ABCB1 was distinctively upregulated in the resistant cells, and its overexpression played an essential role in docetaxel resistance in CRPC. When tested for the cytotoxicity of gemcitabine, another option for chemotherapy, the docetaxel‐resistant cells were shown to become sensitive to the drug, implying additional phenotypic transformation in the docetaxel‐resistant cells. Studies using xenograft animal models demonstrated that the growth of tumors composed of both docetaxel‐sensitive and docetaxel‐resistant cells was deterred most profoundly when docetaxel and gemcitabine were administered together.
Conclusion
This study suggests that when a drug develops therapeutic resistance, sensitivity tests could be another option, ultimately providing insight into a novel alternative clinical strategy.
Features SENSE mRNA-Seq Library Prep Kit
Active poly‐GA vaccination prevents microglia activation and motor deficits in a C9orf72 mouse model
Qihui Zhou, Nikola Mareljic, Meike Michaelsen, Samira Parhizkar, Steffanie Heindl, Brigitte Nuscher, Daniel Farny, Mareike Czuppa, Carina Schludi, Alexander Graf, Stefan Krebs, Helmut Blum, Regina Feederle, Stefan Roth, Christian Haass, Thomas Arzberger, Arthur Liesz, Dieter Edbauer
The C9orf72 repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD). Non‐canonical translation of the expanded repeat results in abundant poly‐GA inclusion pathology throughout the CNS. (GA)149‐CFP expression in mice triggers motor deficits and neuroinflammation. Since poly‐GA is transmitted between cells, we investigated the therapeutic potential of anti‐GA antibodies by vaccinating (GA)149‐CFP mice. To overcome poor immunogenicity, we compared the antibody response of multivalent ovalbumin‐(GA)10 conjugates and pre‐aggregated carrier‐free (GA)15. Only ovalbumin‐(GA)10 immunization induced a strong anti‐GA response. The resulting antisera detected poly‐GA aggregates in cell culture and patient tissue. Ovalbumin‐(GA)10 immunization largely rescued the motor function in (GA)149‐CFP transgenic mice and reduced poly‐GA inclusions. Transcriptome analysis showed less neuroinflammation in ovalbumin‐(GA)10‐immunized poly‐GA mice, which was corroborated by semiquantitative and morphological analysis of microglia/macrophages. Moreover, cytoplasmic TDP‐43 mislocalization and levels of the neurofilament light chain in the CSF were reduced, suggesting neuroaxonal damage is reduced. Our data suggest that immunotherapy may be a viable primary prevention strategy for ALS/FTD in C9orf72 mutation carriers.
Features SENSE mRNA-Seq Library Prep Kit
Identification of transcription factors that bind to the 5′-UTR of the barley PHO2 gene
Paweł Sega, Katarzyna Kruszka, Łukasz Szewc, Zofia Szweykowska-Kulińska & Andrzej Pacak
In barley and other higher plants, phosphate homeostasis is maintained by a regulatory network involving the PHO2 (PHOSPHATE2) encoding ubiquitin-conjugating (UBC) E2 enzyme, the PHR1 (PHOSPHATE STARVATION RESPONSE 1) transcription factor (TF), IPS1 (INDUCED BYPHOSPHATESTARVATION1) RNA, and miR399. During phosphate ion (Pi) deprivation, PHR1 positively regulates MIR399 expression, after transcription and processing mature miR399 guides the Ago protein to the 5′-UTR of PHO2 transcripts. Non-coding IPS1 RNA is highly expressed during Pi starvation, and the sequestration of miR399 molecules protects PHO2 mRNA from complete degradation. Here, we reveal new cis– and trans-regulatory elements that are crucial for efficient PHO2 gene expression in barley. We found that the 5′-UTR of PHO2 contains two PHR1 binding sites (P1BSs) and one Pi-responsive PHO element. Using a yeast one-hybrid (Y1H) assay, we identified two candidate proteins that might mediate this transcriptional regulation: a barley PHR1 ortholog and a TF containing an uncharacterized MYB domain. Additional results classified this new potential TF as belonging to the APL (ALTERED PHLOEM DEVELOPMENT) protein family, and we observed its nuclear localization in barley protoplasts. Pi starvation induced the accumulation of barley APL transcripts in both the shoots and roots. Interestingly, the deletion of the P1BS motif from the first intron of the barley 5′-UTR led to a significant increase in the transcription of a downstream β-glucuronidase (GUS) reporter gene in tobacco leaves. Our work extends the current knowledge about putative cis– and trans-regulatory elements that may affect the expression of the barley PHO2 gene.
Features SENSE mRNA-Seq Library Prep Kit
Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation
Phongthana Pasookhush, Charles Hindmarch, Paisarn Sithigorngul, Siwaporn Longyant, William G. Bendena & Parin Chaivisuthangkura
Background
Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on how M. rosenbergii post-larvae launches an immune response to an infection with MrNV is not currently available. We therefore compared the whole transcriptomic sequence of M. rosenbergii post-larvae before and after MrNV infection.
Results
Transcriptome for M. rosenbergii post-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N50 of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection of MrNV.
Conclusions
This study reported a highly complete transcriptome from the post-larvae stage of giant river prawn, M. rosenbergii. Differential abundant transcripts during MrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in the M. rosenbergii post-larvae after MrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.
Features SENSE mRNA-Seq Library Prep Kit
Penta-O-galloyl-β-D-glucose from Paeonia lactiflora Pall. root extract enhances the expression of skin barrier genes via EGR3
Kyu-Han Kim, Jin Sup, Shim Hyoung-June Kim, Eui Dong Son
Ethnopharmacoligical relevance
Paeonia lactiflora Pall. has long been used to treat inflammatory skin diseases, such as psoriasis.
Aim of the study: The skin acts as a barrier and provides protection against various stresses by expressing skin barrier genes during keratinocyte differentiation. However, the effect of Paeonia lactiflora Pall. root extract on the expression of skin barrier genes has not been investigated. Here, we aimed to show that treatment of keratinocytes with Paeonia lactiflora Pall. root can upregulate genes related to keratinocyte differentiation.
Materials and methods
To determine the effect Paeonia lactiflora Pall. root extract, RNA-Seq, gene ontology, and gene set enrichment analysis were performed. Reverse transcriptase quantitative polymerase chain reaction analysis was performed to confirm the increased expression of skin barrier genes.
Results
Treatment with Paeonia lactiflora Pall. root enhanced the expression of skin barrier genes, including the filaggrin, loricrin, and involucrin. Moreover, we found that penta-O-galloyl-β-D-glucose (PGG), one of the ingredients in Paeonia lactiflora Pall. root, enhanced the expression of skin barrier genes, by upregulating the expression of the transcription factor EGR3.
Conclusions
PGG and Paeonia lactiflora Pall. root extract have therapeutic potential for the treatment of diseases related to skin barrier disruption and can be used in cosmetics to enhance skin barrier function.
Features SENSE mRNA-Seq Library Prep Kit
A kinase-independent role for CDK8 in BCR-ABL1+ leukemia
Ingeborg Menzl, Tinghu Zhang, Angelika Berger-Becvar, Reinhard Grausenburger, Gerwin Heller, Michaela Prchal-Murphy, Leo Edlinger, Vanessa M. Knab, Iris Z. Uras, Eva Grundschober, Karin Bauer, Mareike Roth, Anna Skucha, Yao Liu, John M. Hatcher, Yanke Liang, Nicholas P. Kwiatkowski, Daniela Fux, Andrea Hoelbl-Kovacic, Stefan Kubicek, Junia V. Melo, Peter Valent, Thomas Weichhart, Florian Grebien, Johannes Zuber, Nathanael S. Gray & Veronika Sexl
Cyclin-dependent kinases (CDKs) are frequently deregulated in cancer and represent promising drug targets. We provide evidence that CDK8 has a key role in B-ALL. Loss of CDK8 in leukemia mouse models significantly enhances disease latency and prevents disease maintenance. Loss of CDK8 is associated with pronounced transcriptional changes, whereas inhibiting CDK8 kinase activity has minimal effects. Gene set enrichment analysis suggests that the mTOR signaling pathway is deregulated in CDK8-deficient cells and, accordingly, these cells are highly sensitive to mTOR inhibitors. Analysis of large cohorts of human ALL and AML patients reveals a significant correlation between the level of CDK8 and of mTOR pathway members. We have synthesized a small molecule YKL-06-101 that combines mTOR inhibition and degradation of CDK8, and induces cell death in human leukemic cells. We propose that simultaneous CDK8 degradation and mTOR inhibition might represent a potential therapeutic strategy for the treatment of ALL patients.
Features SENSE mRNA-Seq Library Prep Kit
LIN28A loss of function is associated with Parkinson’s disease pathogenesis
Mi‐Yoon Chang, Boram Oh, Jang‐Eun Choi, Yanuar Alan Sulistio, Hye‐Ji Woo, Ayoung Jo, Jinil Kim, Eun‐Hee Kim, Seung Won Kim, Jungwook Hwang, Jungyun Park, Jae‐Jin Song, Oh‐Chan Kwon, Hyongbum Henry Kim, Young‐Hoon Kim, Joo Yeon Ko, Jun Young Heo, Min Joung Lee, Moses Lee, Murim Choi, Sun Ju Chung, Hyun‐Seob Lee, Sang‐Hun Lee
Parkinson’s disease (PD) is neurodegenerative movement disorder characterized by degeneration of midbrain‐type dopamine (mDA) neurons in the substantia nigra (SN). The RNA‐binding protein Lin28 plays a role in neuronal stem cell development and neuronal differentiation. In this study, we reveal that Lin28 conditional knockout (cKO) mice show degeneration of mDA neurons in the SN, as well as PD‐related behavioral deficits. We identify a loss‐of‐function variant of LIN28A (R192G substitution) in two early‐onset PD patients. Using an isogenic human embryonic stem cell (hESC)/human induced pluripotent stem cell (hiPSC)‐based disease model, we find that the Lin28 R192G variant leads to developmental defects and PD‐related phenotypes in mDA neuronal cells that can be rescued by expression of wild‐type Lin28A. Cell transplantation experiments in PD model rats show that correction of the LIN28A variant in the donor patient (pt)‐hiPSCs leads to improved behavioral phenotypes. Our data link LIN28A to PD pathogenesis and suggest future personalized medicine targeting this variant in patients.
Features SENSE mRNA-Seq Library Prep Kit
Reduction in Toxicity of Nano-Ag-Polyvinyl-pyrrolidone Using Hydra Proteins and Peptides during Zebrafish Embryogenesis
Soon Seok Kim, Jin Ah Lee, Min-Kyeong Yeo
Hydra magnipapillata cells reduce the toxicity of silver nanomaterials to zebrafish (Danio rerio) embryos. In this study, we investigated whether Hydra protein (HP) and Hydra basal disc peptide (Hym176) materials reduce nano-Ag-polyvinylpyrrolidone (N-Ag-PVP) toxicity during embryogenesis of the nanosensitive organism zebrafish. Protein (HP) was extracted from Hydra, and peptide (Hym176) was extracted from the hydra basal disc, which is attractive to nanomaterials and related to the immune system. The experimental conditions were exposure to N-Ag-PVP, HP, N-Ag-PVP+HP, Hym176, or N-Ag-PVP+Hym176 during embryo development. N-Ag-PVP+HP group showed lower toxicity than N-Ag-PVP group. In addition, in the N-Ag-PVP+HP group formed aggregated nanomaterials (≥200 nm size) through electrostatic bonding. In the gene expression profile, HP group differed in gene expression profile compared the other experimental groups and it was no genetic toxicity. HP showed a tendency to reduce side effects and abnormal gene expression produced by N-Ag-PVP with no evidence of inherent toxicity. Considering the potential nanotoxicity effects of released nanomaterials on the ecosystem, the reduction of nanotoxicity observed with HP natural materials should be regarded with great interest in terms of the overall health of the ecosystem.
Features Poly(A) RNA Selection Kit and SENSE mRNA-Seq Library Prep Kit
Alternative splicing regulates stochastic NLRP3 activity
Florian Hoss, James L. Mueller, Francisca Rojas Ringeling, Juan F. Rodriguez-Alcazar, Rebecca Brinkschulte, Gerald Seifert, Rainer Stahl, Lori Broderick, Chris D. Putnam, Richard D. Kolodner, Stefan Canzar, Matthias Geyer, Hal M. Hoffman & Eicke Latz
Leucine-rich repeat (LRR) domains are evolutionarily conserved in proteins that function in development and immunity. Here we report strict exonic modularity of LRR domains of several human gene families, which is a precondition for alternative splicing (AS). We provide evidence for AS of LRR domain within several Nod-like receptors, most prominently the inflammasome sensor NLRP3. Human NLRP3, but not mouse NLRP3, is expressed as two major isoforms, the full-length variant and a variant lacking exon 5. Moreover, NLRP3 AS is stochastically regulated, with NLRP3 ∆ exon 5 lacking the interaction surface for NEK7 and hence loss of activity. Our data thus reveals unexpected regulatory roles of AS through differential utilization of LRRs modules in vertebrate innate immunity.
Features SENSE mRNA-Seq Library Prep Kit
A genome‐wide screen identifies IRF2 as a key regulator of caspase‐4 in human cells
Sacha Benaoudia, Amandine Martin, Marta Puig Gamez, Gabrielle Gay, Brice Lagrange, Maxence Cornut, Kyrylo Krasnykov, Jean‐Baptiste Claude, Cyril F Bourgeois, Sandrine Hughes, Benjamin Gillet, Omran Allatif, Antoine Corbin, Romeo Ricci, Thomas Henry
Caspase‐4, the cytosolic LPS sensor, and gasdermin D, its downstream effector, constitute the non‐canonical inflammasome, which drives inflammatory responses during Gram‐negative bacterial infections. It remains unclear whether other proteins regulate cytosolic LPS sensing, particularly in human cells. Here, we conduct a genome‐wide CRISPR/Cas9 screen in a human monocyte cell line to identify genes controlling cytosolic LPS‐mediated pyroptosis. We find that the transcription factor, IRF2, is required for pyroptosis following cytosolic LPS delivery and functions by directly regulating caspase‐4 levels in human monocytes and iPSC‐derived monocytes. CASP4, GSDMD, and IRF2 are the only genes identified with high significance in this screen highlighting the simplicity of the non‐canonical inflammasome. Upon IFN‐γ priming, IRF1 induction compensates IRF2 deficiency, leading to robust caspase‐4 expression. Deficiency in IRF2 results in dampened inflammasome responses upon infection with Gram‐negative bacteria. This study emphasizes the central role of IRF family members as specific regulators of the non‐canonical inflammasome.
Features SENSE mRNA-Seq Library Prep Kit
Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants
Stefan Ciaghi, Arne Schwelm & Sigrid Neuhauser
Background
Clubroot disease caused by Plasmodiophora brassicae (Phytomyxea, Rhizaria) is one of the economically most important diseases of Brassica crops. The formation of hypertrophied roots accompanied by altered metabolism and hormone homeostasis is typical for infected plants. Not all roots of infected plants show the same phenotypic changes. While some roots remain uninfected, others develop galls of diverse size. The aim of this study was to analyse and compare the intra-plant heterogeneity of P. brassicae root galls and symptomless roots of the same host plants (Brassica oleracea var. gongylodes) collected from a commercial field in Austria using transcriptome analyses.
Results
Transcriptomes were markedly different between symptomless roots and gall tissue. Symptomless roots showed transcriptomic traits previously described for resistant plants. Genes involved in host cell wall synthesis and reinforcement were up-regulated in symptomless roots indicating elevated tolerance against P. brassicae. By contrast, genes involved in cell wall degradation and modification processes like expansion were up-regulated in root galls. Hormone metabolism differed between symptomless roots and galls. Brassinosteroid-synthesis was down-regulated in root galls, whereas jasmonic acid synthesis was down-regulated in symptomless roots. Cytokinin metabolism and signalling were up-regulated in symptomless roots with the exception of one CKX6 homolog, which was strongly down-regulated. Salicylic acid (SA) mediated defence response was up-regulated in symptomless roots, compared with root gall tissue. This is probably caused by a secreted benzoic acid/salicylic acid methyl transferase from the pathogen (PbBSMT), which was one of the highest expressed pathogen genes in gall tissue. The PbBSMT derived Methyl-SA potentially leads to increased pathogen tolerance in uninfected roots.
Conclusions
Infected and uninfected roots of clubroot infected plants showed transcriptomic differences similar to those previously described between clubroot resistant and susceptible hosts. The here described intra-plant heterogeneity suggests, that for a better understanding of clubroot disease targeted, spatial analyses of clubroot infected plants will be vital in understanding this economically important disease.
Features SENSE mRNA-Seq Library Prep Kit
IPSC-derived neuronal cultures expressing the Alzheimer’s disease associated rare TREM2 R47H variant enables the construction of an Aβ-induced gene regulatory network
Soraia Martins, Andreas Müller-Schiffmann, Martina Bohndorf, Wasco Wruck, Kristel Sleegers, Christine Van Broeckhoven, Carsten Korth, James Adjaye
Recently, genes associated with immune response and inflammation have been identified as genetic risk factors for late-onset Alzheimer’s disease (LOAD). One of them is the rare p.Arg47His (R47H) variant within triggering receptor expressed on myeloid cells 2 (TREM2), which has been shown to increase the risk for developing AD 2-3-fold. Here, we report the generation and characterization of a model of LOAD using lymphoblast-derived iPSCs from patients harbouring the R47H mutation in TREM2 (AD TREM2 iPSCs), as well as from control individuals without dementia (CON iPSCs). iPSCs efficiently differentiate into mature neuronal cultures and comparative global transcriptome analysis identified a distinct gene expression profile in AD TREM2 neuronal cultures. Furthermore, manipulation of the iPSC-derived functional neuronal cultures with an Aβ-S8C dimer highlighted metabolic pathways, phagosome and immune response as the most perturbed pathways in AD TREM2 neuronal cultures. Through the construction of an Aβ-induced gene regulatory network, we were able to identify an Aβ signature linked to protein processing in the endoplasmic reticulum (ER) which emphasised ER-stress, as a potential causal role in LOAD. Overall, this study has shown that our AD-iPSC based model can be used for in-depth studies to better understand the molecular mechanisms underlying the etiology of LOAD and provides new opportunities for screening of potential therapeutic targets.
Features SENSE mRNA-Seq Library Prep Kit
Features SENSE mRNA-Seq Library Prep Kit
Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts
Hana Benchetrit, Mohammad Jaber, Valery Zayat, Shulamit Sebban, Avital Pushett, Kirill Makedonski, Zvi Zakheim, Ahmed Radwan, Noam Maoz, Rachel Lasry, Noa Renous, Michal Inbar, Oren Ram, Tommy Kaplan, Yosef Buganim
Features SENSE mRNA-Seq Library Prep Kit
A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma
Saiful E. Syafruddin, Paulo Rodrigues, Erika Vojtasova, Saroor A. Patel, M. Nazhif Zaini, Johanna Burge, Anne Y. Warren, Grant D. Stewart, Tim Eisen, Dóra Bihary, Shamith A. Samarajiwa & Sakari Vanharanta
Transcriptional networks are critical for the establishment of tissue-specific cellular states in health and disease, including cancer. Yet, the transcriptional circuits that control carcinogenesis remain poorly understood. Here we report that Kruppel like factor 6 (KLF6), a transcription factor of the zinc finger family, regulates lipid homeostasis in clear cell renal cell carcinoma (ccRCC). We show that KLF6 supports the expression of lipid metabolism genes and promotes the expression of PDGFB, which activates mTOR signalling and the downstream lipid metabolism regulators SREBF1 and SREBF2. KLF6 expression is driven by a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway. These results suggest an underlying mechanism for high mTOR activity in ccRCC cells. More generally, the link between super enhancer-driven transcriptional networks and essential metabolic pathways may provide clues to the mechanisms that maintain the stability of cell identity-defining transcriptional programmes in cancer.
Features SENSE mRNA-Seq Library Prep Kit
Circuit diversification in a biofilm regulatory network
Manning Y. Huang, Carol A. Woolford, Gemma May, C. Joel McManus, Aaron P. Mitchell
Genotype-phenotype relationships can vary extensively among members of a species. One cause of this variation is circuit diversification, the alteration of gene regulatory relationships among members of a species. Circuit diversification is thought to be a starting point for the circuit divergence or rewiring that occurs during speciation. How widespread is circuit diversification? Here we address this question with the fungal pathogen Candida albicans, which forms biofilms rich in distinctive hyphal cells as a prelude to infection. Our understanding of the biofilm/hyphal regulatory network comes primarily from studies of one clinical isolate, strain SC5314, and its marked derivatives. We used CRISPR-based methods to create mutations of four key biofilm transcription factor genes–BCR1, UME6, BRG1, and EFG1 –in SC5314 and four additional clinical isolates. Phenotypic analysis revealed that mutations in BCR1 or UME6 have variable impact across strains, while mutations in BRG1 or EFG1 had uniformly severe impact. Gene expression, sampled with Nanostring probes and examined comprehensively for EFG1 via RNA-Seq, indicates that regulatory relationships are highly variable among isolates. Our results suggest that genotype-phenotype relationships vary in this strain panel in part because of differences in control of BRG1 by BCR1, a hypothesis that is supported through engineered constitutive expression of BRG1. Overall, the data show that circuit diversification is the rule, not the exception, in this biofilm/hyphal regulatory network.
Features SENSE mRNA-Seq Library Prep Kit
Asxl1 ablation in mouse embryonic stem cells impairs neural differentiation without affecting self-renewal
SoJung An, Ui-Hyun Park, Seungtae Moon, Myengmo Kang, Hyesook Youn, Jin-Taek Hwang, Eun-Joo Kim, Soo-Jong Um
Biochemical and Biophysical Research Communications, doi:10.1016/j.bbrc.2018.12.047
Features SENSE mRNA-Seq Library Prep Kit
Background
Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed.
Methods
Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine.
Results
Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes.
Conclusions
Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.
Features SENSE mRNA-Seq Library Prep Kit
Phytophthora infestans sporangia produced in culture and on tomato leaflet lesions show marked differences in indirect germination rates, aggressiveness, and global transcription profiles
William Fry, Sean P Patev, Kevin Meyers, Kan Bao, Zhangjun Fei
Molecular Plant-Microbe Interactions, doi: 10.1094/MPMI-09-18-0255-TA
Features SENSE mRNA-Seq Library Prep Kit and SPLIT RNA Extraction Kit
Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Lorea Blazquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, Andre Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Features SENSE mRNA‐Seq Library Prep Kit
The first transcriptomic resource for the Antarctic scallop Adamussium colbecki
Giulia Moro, Francesco Buonocore, Marco Barucca, Francesca Spazzali, Adriana Canapa, Alberto Pallavicini, Giuseppe Scapigliati, Marco Gerdol
Features SENSE mRNA‐Seq Library Prep Kit
Shep interacts with posttranscriptional regulators to control dendrite morphogenesis in sensory neurons
Eugenia C. Olesnicky, Simona Antonacci, Niko Popitsch, Meghan C. Lybecker, M. Brandon Titus, Racquel Valadez, Paul G. Derkach, Amber Marean, Katherine Miller, Samuel K. Mathai, Darrell J. Killian
Features SENSE mRNA‐Seq Library Prep Kit
Circulating HLA-DR+CD4+ effector memory T cells resistant to CCR5 and PD-L1 mediated suppression compromise regulatory T cell function in tuberculosis
Asma Ahmed, Vasista Adiga, Soumya Nayak, J. Anto Jesuraj Uday Kumar, Chirag Dhar, Pravat Nalini Sahoo, Bharath K. Sundararaj, George D. Souza, Annapurna Vyakarnam
Features SENSE mRNA‐Seq Library Prep Kit
Mbf1 ensures Polycomb silencing by protecting E(z) mRNA from degradation by Pacman
Kenichi Nishioka, Xian-Feng Wang, Hitomi Miyazaki, Hidenobu Soejima, Susumu Hirose
Features SENSE mRNA‐Seq Library Prep Kit
Kaposi’s Sarcoma-Associated Herpesvirus Infection Modulates the Proliferation of Glioma Stem-Like Cells.
Jeon H, Kang YH, Yoo SM, Park MJ, Park JB, Lee SH, Lee MS
Journal of Microbiology and Biotechnology, doi:10.4014/jmb.1709.09001
Features SENSE mRNA‐Seq Library Prep Kit
The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments
Daniel B Mills, Warren R Francis, Sergio Vargas, Morten Larsen, Coen PH Elemans, Donald E Canfield, Gert Wörheide
Features SENSE mRNA‐Seq Library Prep Kit
Integrated ‘omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes
Jarno E.J. Wolters, Simone G.J. van Breda, Jonas Grossmann, Claudia Fortes, Florian Caiment, Jos C.S. Kleinjans
Features SENSE mRNA‐Seq Library Prep Kit
The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals
Shady Younis, Milena Schönke, Julie Massart, Rikke Hjortebjerg, Elisabeth Sundström, Ulla Gustafson, Marie Björnholm, Anna Krook, Jan Frystyk, Juleen R. Zierath and Leif Andersson
Features SENSE mRNA‐Seq Library Prep Kit
Prepubertal Ovariectomy Exaggerates Adult Affective Behaviors and Alters the Hippocampal Transcriptome in a Genetic Rat Model of Depression
Neha S. Raghavan, Hao Chen, Matthew Schipma, Wendy Luo, Sarah Chung, Lei Wang and Eva E. Redei
Features SENSE mRNA‐Seq Library Prep Kit
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
Christine Gault, Karl Kremling, Edward S. Buckler
Features SENSE mRNA‐Seq Library Prep Kit
Jjj1 Is a Negative Regulator of Pdr1-Mediated Fluconazole Resistance in Candida glabrata
Sarah G. Whaley, Kelly E. Caudle, Lucia Simonicova, Qing Zhang, W. Scott Moye-Rowley, P. David Rogers
The high prevalence of fluconazole resistance among clinical isolates of Candida glabrata has greatly hampered the utility of fluconazole for the treatment of invasive candidiasis. Fluconazole resistance in this yeast is almost exclusively due to activating mutations in the transcription factor Pdr1, which result in upregulation of the ABC transporter genes CDR1, PDH1, and SNQ2 and therefore increased fluconazole efflux. However, the regulation of Pdr1 is poorly understood. In order to identify genes that interact with the Pdr1 transcriptional pathway and influence the susceptibility of C. glabrata to fluconazole, we screened a collection of deletion mutants for those exhibiting increased resistance to fluconazole. Deletion of the gene coding for a protein homologous to the Saccharomyces cerevisiae J protein Jjj1 resulted in decreased fluconazole susceptibility. We used the SAT1 flipper method to generate independent deletion mutants for JJJ1 in an SDD clinical isolate. Expression of both CDR1 and PDR1was increased in the absence of JJJ1. In the absence of CDR1 or PDR1, deletion of JJJ1 has only a modest effect on fluconazole susceptibility. Transcriptional profiling using transcriptome sequencing (RNA-seq) revealed upregulation of genes of the Pdr1 regulon in the absence of JJJ1. Jjj1 appears to be a negative regulator of fluconazole resistance in C. glabrata and acts primarily through upregulation of the ABC transporter gene CDR1 via activation of the Pdr1 transcriptional pathway.
Features SENSE mRNA‐Seq Library Prep Kit
Artificial Light at Night (ALAN), an alarm to ovarian physiology: A study of possible chronodisruption on zebrafish (Danio rerio)
Zeeshan Ahmad Khan, Rajendra Kumar Labala, Thangal Yumnamcha, Sijagurumayum Dharmajyoti Devi, Gopinath Mondal, Haobijam Sanjita Devi, Chongtham Rajiv, Rupjyoti Bharali, Asamanja Chattoraj
Science of The Total Environment, doi:10.1016/j.scitotenv.2018.02.101
The ALAN is drawing the attention of researchers and environmentalists for its ever-increasing evidence on its capacity of “desynchronization” of organismal physiology. Photoperiod and circadian cycles are critical parameters to influence the biology of reproduction in several animals, including fish. The present study is the first proof of the development of an ovarian tumour with the effect of light in zebrafish (Danio rerio), an excellent model for circadian-related studies. Results of three experimental conditions, continuous light for one week, LLW, one month, LLM, and for one year, LLY revealed a clear desynchronization of clock associated genes (Clock1a, Bmal1a, Per2, and Cry2a). Interestingly, loss of rhythmicity and low concentration of melatonin found in these conditions in whole brain, retina, ovary, and serum through ELISA. RNA-Seq data of ovarian samples revealed the upregulation of Mid2, Tfg, Irak1, Pim2, Tradd, Tmem101, Nfkbib genes and ultimately increase the expression of NF-κB, a cellular transformer for tumourigenesis, confirmed by the western blot. The appearance of TNFα, inflammatory cytokines and activator of NF-κB also increased. Histology approved the formation of thecoma and granulosa cell tumour in the one year exposed ovarian sample. The whole transcriptome data analysis revealed 1791 significantly upregulated genes in an ovarian tumour. Among these genes, DAVID functional annotation tool identified 438 genes, directly linked to other physiological disorders. This study evidenced of an ovarian tumour induced by ALAN in zebrafish.
Features SENSE mRNA‐Seq Library Prep Kit
Sox7 promotes high-grade glioma by increasing VEGFR2-mediated vascular abnormality
Il-Kug Kim, Kangsan Kim, Eunhyeong Lee, Dong Sun Oh, Chan Soon Park, Seongyeol Park, Jee Myung Yang, Ju-Hee Kim, Hyung-Seok Kim, David T. Shima, Jeong Hoon Kim, Seok Ho Hong, Young Hyun Cho, Young Hoon Kim, Jong Bae Park, Gou Young Koh, Young Seok Ju, Heung Kyu Lee, Seungjoo Lee, Injune Kim
High-grade glioma (HGG) is highly angiogenic, but antiangiogenic therapy has transient clinical benefit in only a fraction of patients. Vascular regulators of these heterogeneous responses remain undetermined. We found up-regulation of Sox7 and down-regulation of Sox17 in tumor endothelial cells (tECs) in mouse HGG. Sox7 deletion suppressed VEGFR2 expression, vascular abnormality, hypoxia-driven invasion, regulatory T cell infiltration, and tumor growth. Conversely, Sox17 deletion exacerbated these phenotypes by up-regulating Sox7 in tECs. Anti-VEGFR2 antibody treatment delayed tumor growth by normalizing Sox17-deficient abnormal vessels with high Sox7 levels but promoted it by regressing Sox7-deficient vessels, recapitulating variable therapeutic responses to antiangiogenic therapy in HGG patients. Our findings establish that Sox7 promotes tumor growth via vessel abnormalization, and its level determines the therapeutic outcome of VEGFR2 inhibition in HGG. In 189 HGG patients, Sox7 expression was heterogeneous in tumor vessels, and high Sox7 levels correlated with poor survival, early recurrence, and impaired vascular function, emphasizing the clinical relevance of Sox7 in HGG.
Features SENSE mRNA‐Seq Library Prep Kit
Human tripartite motif protein 52 is required for cell context-dependent proliferation
Stefan Benke, Benedikt Agerer, Lisa Haas, Martin Stöger, Alexander Lercher, Lisa Gabler, Izabella Kiss, Sara Scinicariello, Walter Berger, Andreas Bergthaler, Anna C. Obenauf and Gijs A. Versteeg
Tripartite motif (TRIM) proteins have been shown to play important roles in cancer development and progression by modulating cell proliferation or resistance from cell death during non-homeostatic stress conditions found in tumor micro-environments. In this study, we set out to investigate the importance for cellular fitness of the virtually uncharacterized family member TRIM52.
The human TRIM52 gene has arisen recently in evolution, making it unlikely that TRIM52 is required for basic cellular functions in normal cells. However, a recent genome-wide ablation screening study has suggested that TRIM52 may be essential for optimal proliferation or survival in certain genetic cancer backgrounds. Identifying genes which fit this concept of genetic context-dependent fitness in cancer cells is of interest as they are promising targets for tumor-specific therapy.
We report here that TRIM52 ablation significantly diminished the proliferation of specific glioblastoma cell lines in cell culture and mouse xenografts by compromising their cell cycle progression in a p53-dependent manner. Together, our findings point to a non-redundant TRIM52 function that is required for optimal proliferation.
Features SENSE mRNA‐Seq Library Prep Kit
Regulation of chitinase-3-like-1 in T cell elicits Th1 and cytotoxic responses to inhibit lung metastasis
Do-Hyun Kim, Hong-Jai Park, Sangho Lim, Ja-Hyun Koo, Hong-Gyun Lee, Jin Ouk Choi, Ji Hoon Oh, Sang-Jun Ha, Min-Jong Kang, Chang-Min Lee, Chun Geun Lee, Jack A. Elias & Je-Min Choi
Features SENSE mRNA‐Seq Library Prep Kit
Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells
Yoav Lubelsky & Igor Ulitsky
Features SENSE mRNA‐Seq Library Prep Kit
A 29-Gene And Cytogenetic Score For The Prediction Of Resistance To Induction Treatment In Acute Myeloid Leukemia
Tobias Herold, Vindi Jurinovic, Aarif M. N. Batcha, Stefanos A. Bamopoulos, Maja Rothenberg-Thurley, Bianka Ksienzyk, Luise Hartmann, Philipp A. Greif, Julia Phillippou-Massier, Stefan Krebs, Helmut Blum, Susanne Amler, Stephanie Schneider, Nikola Konstandin, Maria Cristina Sauerland, Dennis Görlich, Wolfgang E. Berdel, Bernhard J. Wörmann, Johanna Tischer, Marion Subklewe, Stefan K. Bohlander, Jan Braess, Wolfgang Hiddemann, Klaus H. Metzeler, Ulrich Mansmann, Karsten Spiekermann
Features SENSE mRNA‐Seq Library Prep Kit
Transcriptome analysis for UVB-induced phototoxicity in mouse retina
Mi-Jin An, Chul-Hong Kim, Gyu-You Nam, Dae-Hyun Kim, Sangmyung Rhee, Sung-Jin Cho, Jung-Woong Kim
Features SENSE mRNA‐Seq Library Prep Kit
Gangjihwan, a polyherbal composition, inhibits fat accumulation through the modulation of lipogenic transcription factors SREBP1C, PPARγ and C/EBPα
Jaewoong Jang, Yoonju Jung, Seyeon Chae, Soo Hyun Cho, Michung Yoon, Heejung Yang, Soon Shik Shin, Yoosik Yoon
Ethnopharmacological relevance
Gangjihwan (DF) which is composed of Ephedra intermedia, Lithospermum erythrorhizon, and Rheum palmatum has been used for the treatment of obesity in traditional medical clinics in Korea.
Aim of the study
This study was conducted to standardize DF and elucidate its mechanism of action for inhibiting fat accumulation in adipocytes and adipose tissues.
Materials and Methods
The herbal ingredients of DF were extracted in water, 30% ethanol or 70% ethanol and freeze-dried followed by HPLC analyses. 3T3-L1 adipocytes and high-fat diet-induced obese mice were treated with each of the three DF preparations. Messenger RNA and protein expression levels were measured by real-time qPCR and Western blotting. RNA-Seq analyses were conducted to examine the effects of DF treatment on whole transcriptome of adipocyte.
Results
(-)-Ephedrine and (+)-pseudoephedrine from E. intermedia, aloe-emodin and chrysophanol from R. palmatum and shikonin from L. erythrorhizon were identified as phytochemical components of DF. DF caused dose-dependent inhibition of fat accumulation in 3T3-L1 adipocytes. It also significantly reduced adipose tissue mass and adipocyte size in high-fat diet-induced obese mice. DF was found to down-regulate the expressions of the lipogenic transcription factors such as sterol regulatory element binding protein 1 C (SREBP1C), peroxisome proliferator activated receptor gamma (PPARγ), and CCAAT/enhancer binding protein alpha (C/EBPα). Among the three preparations of DF, the 70% ethanol extract was the most effective. RNA-Seq analyses showed that DF treatment decreased the expression levels of up-regulators and increased those of down-regulators of lipogenic transcription factors.
Conclusions
DF preparations, among which 70% ethanol extract was the most effective, reduced fat accumulation in 3T3-L1 adipocytes and high-fat diet-induced obese mice through the down-regulation of lipogenic transcription factors SREBP1C, PPARγ and C/EBPα.
Features SENSE mRNA‐Seq Library Prep Kit
The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization
Marco Gerdol, Yuki Fujii, Imtiaj Hasan, Toru Koike, Shunsuke Shimojo, Francesca Spazzali, Kaname Yamamoto, Yasuhiro Ozeki, Alberto Pallavicini and Hideaki Fujita
Features SENSE mRNA‐Seq Library Prep Kit
Transforming Growth Factor Beta Promotes Liver Tumorigenesis in Mice via Upregulation of Snail
Hyuk Moon, Hye-Lim Ju, Sook In Chung, Kyung Joo Cho, Jung Woo Eun, Suk Woo Nam, Kwang-Hyub Han, Diego F. Calvisi, Simon Weonsang Ro
Features SENSE mRNA‐Seq Library Prep Kit
Comprehensive Expression Profiling and Functional Network Analysis of Porphyra-334, One Mycosporine-Like Amino Acid (MAA), in Human Keratinocyte Exposed with UV-radiation
Sung-Suk Suh, Sung Gu Lee, Ui Joung Youn, Se Jong Han, Il-Chan Kim and Sanghee Kim
Features SENSE mRNA‐Seq Library Prep Kit
Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1
Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel & Dirk Eick
Features SENSE mRNA‐Seq Library Prep Kit
ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay
Masayuki Sakurai, Yusuke Shiromoto, Hiromitsu Ota, Chunzi Song, Andrew V Kossenkov, Jayamanna Wickramasinghe, Louise C Showe, Emmanuel Skordalakes, Hsin-Yao Tang, David W Speicher & Kazuko Nishikura
Nature Structural & Molecular Biology (2017), doi:10.1038/nsmb.3403
Features SENSE mRNA‐Seq Library Prep Kit
Short-term application of dexamethasone on stem cells derived from human gingiva reduces the expression of RUNX2 and β-catenin
Bo-Bae Kim, Minji Kim, Yun-Hee Park, Youngkyung Ko, Jun-Beom Park
Journal of International Medical Research, doi:10.1177/0300060517701035
Next-generation sequencing was performed to evaluate the effects of short-term application of dexamethasone on human gingiva-derived mesenchymal stem cells.
Methods
Human gingiva-derived stem cells were treated with a final concentration of 10−7 M dexamethasone and the same concentration of vehicle control. This was followed by mRNA sequencing and data analysis, gene ontology and pathway analysis, quantitative real-time polymerase chain reaction of mRNA, and western blot analysis of RUNX2 and β-catenin.
Results
In total, 26,364 mRNAs were differentially expressed. Comparison of the results of dexamethasone versus control at 2 hours revealed that 7 mRNAs were upregulated and 25 mRNAs were downregulated. The application of dexamethasone reduced the expression of RUNX2 and β-catenin in human gingiva-derived mesenchymal stem cells.
Conclusion
The effects of dexamethasone on stem cells were evaluated with mRNA sequencing, and validation of the expression was performed with qualitative real-time polymerase chain reaction and western blot analysis. The results of this study can provide new insights into the role of mRNA sequencing in maxillofacial areas.
Features SENSE mRNA‐Seq Library Prep Kit
Ninjurin1 Is Up-regulated in Circulating Prostate Tumor Cells and Plays a Critical Role in Prostate Cancer Cell Motility
Juri Park, Jae-Young Joung, Ji-Eun Hwang, Dongwan Hong, Weon Seo Park, Sang-Jin Lee, and Kang Hyun Lee
Anticancer Research 37: 1687-1696 (2017), doi:10.21873/anticanres.11500
Materials and Methods: Ninjurin1 expression was evaluated in CTCs harvested from seven locally advanced patients with no metastatic hallmarks using real-time polymerase chain reaction (PCR). The role of Ninjurin1 in cell motility was investigated using small interfering RNA (siRNA), neutralizing antibodies against Ninjurin1 and Ninjurin1-overexpressing adenoviruses.
Results: Ninjurin1 was ranked as the most significantly up-regulated adhesion protein identified by RNA-Seq analysis. Both Ninjurin1 down-regulation by siRNA and neutralizing antibodies blocking Ninjurin1 homophilic interactions effectively inhibited cell motility. In contrast, cell motility was enhanced in prostate cancer cells infected with adenovirus enabling Ninjurin1 overexpression.
Conclusion: Ninjurin1-neutralizing antibodies or Ninjurin1-targeting siRNA merit further development for patients with metastatic potential.
Features SENSE mRNA‐Seq Library Prep Kit
Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder
Dora C. Tărlungeanu, Elena Deliu, Christoph P. Dotter, Majdi Kara, Philipp Christoph Janiesch, Mariafrancesca Scalise, Michele Galluccio, Mateja Tesulov, Emanuela Morelli, Fatma Mujgan Sonmez, Kaya Bilguvar, Ryuichi Ohgaki, Yoshikatsu Kanai, Anide Johansen, Seham Esharif, Tawfeg Ben-Omran, Meral Topcu, Avner Schlessinger, Cesare Indiveri, Kent E. Duncan, Ahmet Okay Caglayan, Murat Gunel, Joseph G. Gleeson, Gaia Novarino
Features SENSE mRNA‐Seq Library Prep Kit
InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data
Konstantin Okonechnikov, Aki Imai-Matsushima, Lukas Paul, Alexander Seitz, Thomas F. Meyer, Fernando Garcia-Alcalde
Features SENSE mRNA‐Seq Library Prep Kit
Features SPLIT RNA Extraction Kit
Chemical Hybridization of Glucagon and Thyroid Hormone Optimizes Therapeutic Impact for Metabolic Disease.
Brian Finan, Christoffer Clemmensen, Zhimeng Zhu, Kerstin Stemmer, Karine Gauthier, Luisa Müller, Meri De Angelis, Kristin Moreth, Frauke Neff, Diego Perez-Tilve, Katrin Fischer, Dominik Lutter, Miguel A. Sánchez-Garrido, Peng Liu, Jan Tuckermann, Mohsen Malehmir, Marc E. Healy, Achim Weber, Mathias Heikenwalder, Martin Jastroch, Maximilian Kleinert, Sigrid Jall, Sara Brandt, Frédéric Flamant, Karl-Werner Schramm, Heike Biebermann, Yvonne Döring, Christian Weber, Kirk M. Habegger, Michaela Keuper, Vasily Gelfanov, Fa Liu, Josef Köhrle, Jan Rozman, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabě de Angelis, Susanna M. Hofmann, Bin Yang, Matthias H. Tschöp, Richard DiMarchi, Timo D. Müller
Features SENSE mRNA‐Seq Library Prep Kit
The complete nucleotide sequence and genomic characterization of grapevine asteroid mosaic associated virus
José Vargas-Asencio, Klaudia Wojciechowska, Maia Baskerville, Annika L. Gomez, Keith L. Perry, Jeremy R. Thompson
Virus Research, Volume 227, doi:10.1016/j.virusres.2016.10.001
Features SENSE mRNA‐Seq Library Prep Kit
Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila
Vasiliy O. Sysoev, Bernd Fischer, Christian K. Frese, Ishaan Gupta, Jeroen Krijgsveld, Matthias W. Hentze, Alfredo Castello & Anne Ephrussi
Nature Communications 7, Article number: 12128, doi:10.1038/ncomms12128
Features SENSE mRNA‐Seq Library Prep Kit
Ad5/35E1aPSESE4: A novel approach to marking circulating prostate tumor cells with a replication competent adenovirus controlled by PSA/PSMA transcription regulatory elements
Ji-Eun Hwang, Jae Young Joung, Seung-Phil Shin, Moon-Kyung Choi, Jeong Eun Kim, Yon Hui Kim, Weon Seo Park, Sang-Jin Lee, Kang-Hyun Lee
Features SENSE mRNA-Seq Library Prep Kit
The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.
Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC.
Features SENSE mRNA-Seq Library Prep Kit
Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency
Shen-Hsi Yang, Tüzer Kalkan, Claire Morissroe, Hendrik Marks, Hendrik Stunnenberg, Austin Smith, Andrew D. Sharrocks
Cell Rep. 2014 June 26; 7(6): 1968–1981. doi: 10.1016/j.celrep.2014.05.037
Features SENSE mRNA-Seq Library Prep Kit
Mutations in CECR1 associated with a neutrophil signature in peripheral blood
Alexandre Belot, Evangeline Wassmer, Marinka Twilt, Jean-Christophe Lega, Leo AH Zeef, Anthony Oojageer, Paul R Kasher, Anne-Laure Mathieu, Christophe Malcus, Julie Demaret, Nicole Fabien, Sophie Collardeau-Frachon, Laura Mechtouff, Laurent Derex, Thierry Walzer, Gillian I Rice, Isabelle Durieu, Yanick J Crow
Pediatr Rheumatol Online J. 2014; 12: 44. doi: 10.1186/1546-0096-12-44
A reduction of ADA2 activity due to autosomal recessive loss of function mutations in CECR1 results in a newly described vasculopathic phenotype reminiscent of polyarteritis nodosa, with manifestations ranging from fatal systemic vasculitis with multiple strokes in children to limited cutaneous disease in middle-aged individuals. Evidence indicates that ADA2 is essential for the endothelial integrity of small vessels. However, CECR1 is not expressed, nor is the ADA2 protein detectable, in cultured human endothelial cells, thus implicating additional cell types or circulating factors in disease pathogenesis.
Methods
Considering the phenotypic overlap of ADA2 deficiency with the type I interferonopathy Aicardi-Goutières syndrome due to mutations in SAMHD1, we looked for the presence of an interferon signature in the peripheral blood of two newly ascertained ADA2-deficient patients.
Results
We identified biallelic CECR1 mutations in two patients consistent with ADA2 deficiency. Both patients demonstrated an upregulation of interferon stimulated gene transcripts in peripheral blood. More strikingly however, genome-wide analysis revealed a marked overexpression of neutrophil-derived genes, suggesting that the vasculitis seen in ADA2 deficiency may be an indirect effect resulting from chronic and marked activity of neutrophils.
Conclusions
We hypothesise that ADA2 may act as a regulator of neutrophil activation, and that a reduction of ADA2 activity results in significant endothelial damage via a neutrophil-driven process.
Features SENSE mRNA-Seq Library Prep Kit