Ever wonder what goes on behind the scenes in R&D at QIAGEN Digital Insights? Our team of expert scientists is busy collaborating with researchers worldwide. They conduct Sample to Insight studies using QIAGEN’s sample preparation kits and bioinformatics software to elaborate proof of concept studies and contribute to active research efforts. This helps us bring extra value to our customers by helping them apply our solutions to answer their research questions. Here we share two recent research studies comparing molecular signaling in sepsis and COVID-19 to discover new biomarkers.
Progranulin signaling in sepsis, community‑acquired bacterial pneumonia and COVID‑19: A comparative, observational study
Researchers from multiple institutions in Germany collaborated with QIAGEN Digital Insights scientists Dr. Jean-Noël Billaud, Dr. Joseph Pearson and Dr. Nirav Amin in this recent observational study by Brandes et al. The team studied the functional role of the pleiotropic growth factor progranulin in cohorts of sepsis patient cases and compared progranulin plasma levels among sepsis, systemic inflammatory response syndrome (SIRS), severe localized infections, community-acquired bacterial pneumonia and COVID-19.
They used QIAGEN Ingenuity Pathway Analysis (IPA) to analyze differential expression data from blood taken from septic-shock patient cases and healthy controls and constructed molecular response networks for progranulin. The team used QIAGEN OmicSoft Suite to process and analyze the mRNA sequencing data from the case vs. control groups and sent the results directly to QIAGEN IPA for further biological analysis. Using IPA, the team identified miRNA and mRNA regulation and networks resulting from their high-throughput miRNA/mRNA expression data.
The team found statistically significant molecular differences in the plasma among these disorders. They discovered important relationships between disease severity and progranulin concentrations, identifying the important role of progranulin signaling in the early antimicrobial response in sepsis. This study provides evidence for potentially using progranulin as a biomarker for sepsis and pneumonia, which could be developed to differentiate between these disorders.
This study demonstrates a fantastic example of Sample to Insight workflow implementation using QIAGEN solutions. Prior to molecular analysis of NGS data from mRNA sequencing, QIAGEN’s PAXgene blood miRNA Kit was used for extraction of cellular RNA from whole blood. QIAGEN’s QuantiTect Reverse Transcription Kit was then used for reverse transcription of the isolated mRNA and QIAGEN’s miRCURY LNA SYBR Green PCR Kit was used to set up a real-time PCR reaction prior to amplification using QIAGEN’s Rotor-Gene Q thermal cycler.
Well done to the QIAGEN Digital Insights team and their collaborators on their impactful publication!
Differences in molecular signaling networks underly the clinical distinction between COVID-19 ARDS and the sepsis-induced ARDS phenotypes
Dr. Florian Brandes of the University Hospital, Ludwig-Maximilians-University in Munich, received a prestigious research prize from a major German conference on Intensive Care Medicine for his abstract on molecular signaling networks in different acute respiratory distress syndrome (ARDS) phenotypes. Dr. Jean-Noël Billaud, Senior Principal Scientist for QIAGEN Digital Insights, collaborated on the study. The team researched differentially and significantly regulated miRNA and target mRNA from COVID-19-induced ARDS patient cases, bacterial-induced sepsis-ARDS patient cases and 20 healthy controls. They used QIAGEN IPA to construct signaling networks, comparing the three groups. Their analyses conclude that COVID-ARDS is a unique clinical entity with specific molecular signaling cascades that are unique from sepsis-induced ARDS. Their study suggests that novel biomarkers and different therapeutic approaches should be used from those used in sepsis-ARDS.
Congratulations to our collaborator, Dr. Brandes, on receiving this prestigious award.
Learn more about how QIAGEN Digital Insights helped discover progranulin as a potential biomarker for sepsis, and read the published study here.
Learn more here about SARS-CoV-2 analysis solutions from QIAGEN Digital Insights.
Discover more about QIAGEN’s Sample to Insight research solutions for COVID-19.
Read about how researchers across the world are using QIAGEN Digital Insights solutions to accelerate their work in a variety of applications
Making sense of complex 'omics data, and developing the infrastructure to compile, store, search, analyze and visualize relevant information has significant challenges and may pose a burden to researchers without bioinformatics skills. Yet powerful insights derived from 'omics data help innovate, integrate and translate scientific results into impactful discoveries. Many noteworthy papers cite QIAGEN Digital Insights solutions and demonstrate how our tools help drive research insights and discoveries. These papers use QIAGEN Ingenuity Pathway Analysis (IPA), QIAGEN CLC and/or QIAGEN OmicSoft to help drive success. The QIAGEN Digital Insights portfolio encompasses a comprehensive, easy-to-use toolbox that ensures continuity in the NGS workflow. Here, we have curated a selection of just a few recent papers to offer a sense of the diversity of the research for which QIAGEN Digital Insights solutions makes a difference.
Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H
First author: Yuki Shibayama
Did you know on average pancreatic cancer patients acquire over 67 non-synonymous mutations? The team at Kagawa University used QIAGEN IPA to study the role of (pro)renin receptor [(P)RR] in causing genomic instability. Read their full paper here.
Glioblastoma stem cells induce quiescence in surrounding neural stem cells via Notch signaling
First author: Katerina Lawlor
Did you know cancer cells are not only good at proliferating but can also suppress other cells from growing? See how the team at Imperial College London investigates this phenomenon using QIAGEN IPA to understand how cancer cells induce quiescence in glioblastomas. Read their full paper here.
Multiparametric profiling of engineered nanomaterials: Unmasking the surface coating effect
First author: Audrey Gallud
Discover this fascinating research by scientists at the Karolinska Institutet who study the cytotoxic effects of engineered nanomaterials (ENMs). See how the team uses QIAGEN IPA to understand the mechanism behind the cytotoxic effects of ENMs and how to mitigate the risks. Read the full article here.
Innate immune training of granulopoiesis promotes anti-tumor activity
First author: Lydia Kalafati
Check out this exciting research by L. Kalafati and colleagues at TU Dresden, who try to promote the anti-tumor activity of trained neutrophils. See how the team uses QIAGEN IPA to understand the molecular mechanism behind reprogramming caused by trained immunity agonists. Read the paper here.
Liver-expressed cd302 and cr1l limit hepatitis C virus cross-species transmission to mice
First author: Richard J. P. Brown
Did you know the hepatitis C virus (HCV) affects 71 million people worldwide but only infects humans? Read how researchers at Paul Ehrlich Institute (PEI) use QIAGEN IPA and QIAGEN CLC Genomics Workbench to understand how mice are able to prevent HCV infection. Read their full paper here.
Vascular disease and thrombosis in SARS-CoV-2-infected rhesus macaques
First author: Malika Aid
Is there a connection between thrombosis and SARS-CoV-2 infection? Read how the team at Beth Israel Deaconess Medical Center uses QIAGEN IPA to understand the critical interactions between various pathways that lead to SARS-CoV-2-induced blood clotting in rhesus macaques. Read their full paper here.
Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4+ T cells in COVID-19
First author: Benjamin Meckiff
Check out this critical coronavirus research by B. Meckiff and colleagues at the La Jolla Institute for Immunology, who study the role of CD4+ T cells in COVID-19. See how the team uses QIAGEN IPA to understand how different subsets of CD4+ T cells play a role in pathogenic immune responses to SARS-CoV-2 infection. Read the full article here.
Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models
First author: Michael R. Garvin
Can mutations in coronavirus spike proteins help it escape current vaccines? See how a group at Oak Ridge National Laboratory predicts mutational hotspots in the viral genome using QIAGEN CLC Genomics and AI models. Read the full article here.
Genomic evidence for reinfection with SARS-CoV-2: A case study
Co-author: Joel Sevinsky
Is SARS-COV-2 reinfection possible? Joel Sevinsky and his colleagues in the Nevada public health arena report the first SARS-Cov-2 reinfection case in the US. See how the team uses QIAGEN CLC Genomics Workbench for bioinformatics analysis of their SARS-CoV-2 samples to discover whether it was the same virus or a genetically different specimen. Read the full article here.
Two distinct immunopathological profiles in autopsy lungs of COVID-19
First author: Ronny Nienhold
Is unlocking differences in immune response the key to treating ARDS in COVID-19? Dig into this important coronavirus research from R. Nienhold and colleagues at Cantonal Hospital Baselland who study different immunopathological profiles in COVID-19 patients. See how the team uses QIAGEN CLC Genomics Workbench to understand the different immune patterns observed in post mortem COVID-19 lung tissue. See their full article here.
A mouse-adapted SARS-CoV-2 induces acute lung injury and mortality in standard laboratory mice
First author: Sarah R. Leist
Did you know coronaviruses are responsible for three epidemics in the 21st century? Great work by S. Leist and colleagues at the University of North Carolina at Chapel Hill, who created a mouse-adapted SARS-CoV-2 to understand the virus better. See how the team uses QIAGEN CLC Genomics Workbench to characterize this animal model and discover mechanisms for SARS-CoV-2 pathogenesis to test potential therapeutics. Read their full paper here.
Single-cell transcriptomics implicate novel monocyte and T cell immune dysregulation in sarcoidosis
First author: Lori Garman
Single-cell analysis improves our understanding of multimodal diseases. Don't miss this exciting cancer research by L. Garman and colleagues, who study the role of immune cells in sarcoidosis. The team uses QIAGEN IPA and QIAGEN OmicSoft DiseaseLand to identify dysregulated pathways using single-cell analysis. Read the full paper here.
Non-human primate blood–brain barrier and in vitro brain endothelium: From transcriptome to the establishment of a new model
First author: Catarina Chaves
Congratulations to the researchers at Sanofi for publishing their findings on a comparative model for the human blood-brain barrier (hBBB). See how the team uses QIAGEN IPA and QIAGEN OmicSoft Studio to investigate the transcriptome of brain capillaries from a non-human primate, and compare it to the hBBB. Read the full paper here.
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs
First author: Saee Paliwal
Do we need better models for validating preclinical drug target candidates? How can we test these models? Read how researchers at BenevolentAI use QIAGEN OmicSoft DiseaseLand to evaluate the robustness of their computational model, Rosalind. Read the full paper here.
Get in touch with us! To request information on our QIAGEN Digital Insight solutions, contact bioinformaticssales@qiagen.com.
Recently, there have been many noteworthy papers citing QIAGEN CLC Genomics Workbench, a comprehensive, easy-to-use toolbox that ensures continuity in your NGS workflow. Here, we round up just a few of them to offer a sense of the diversity of the research for which QIAGEN CLC Genomics Workbench makes a difference. Below are some examples of how researchers from all over the world use this solution as a tool for metagenomic analysis to characterize dengue viruses and pathogens, create de novo assemblies or investigate ocular diseases.
Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020
First author: Yong Zhang
Should we be looking for new mutations in SARS-CoV-2 that make it more virulent? Researchers from the Chinese Center for Disease Control and Prevention perform genomic characterization of SARS-CoV-2 identified in a reemerging outbreak in China. Discover how they use QIAGEN CLC Genomics Workbench to help trace the source of the virus in this second outbreak in Beijing’s Xinfadi market. Read their full article here.
Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China
First author: Jing Yang
Crucial coronavirus research from the Chinese Academy of Sciences looking into the re-emergence of the SARS-CoV-2 virus in China. Discover how they use the nanopore and MiSeq system together with QIAGEN CLC Genomics Workbench to trace the source of the virus in this second outbreak in Beijing. Get the full article here.
Systematic reconstruction of the complete two-component sensorial network in Staphylococcus aureus
First author: B. Rapun-Araiz
High-impact research by B. Rapun-Araiz and colleagues at Universidad Publica de Navarra in Spain who investigate the targets of two-component signal transduction systems (TCSs) in bacteria. See how they use QIAGEN CLC Genomics Workbench to map the complete TCS regulon in Staphylococcus aureus. Read the full paper here.
Remdesivir inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice
First author: Andrea J. Pruijssers
Excellent research by A. Pruijssers and colleagues at Vanderbilt University who study how Remdesivir inhibits SARS-CoV-2 in human lung cells. See how they use QIAGEN CLC Main Workbench to help investigate the efficacy of Remdesivir against SARS-CoV-2 in vitro and in vivo. Read the full article here.
Lysosomal recycling of amino acids affects ER quality control
First author: Ryo Higuchi-Sanabria
Exciting research from the Howard Hughes Medical Institute, where researchers investigate the role of lysosomes in amino acid recycling. Learn how they use QIAGEN CLC Genomics Workbench to understand how reduced lysine and arginine can cause increased sensitivity to proteotoxic stress in the endoplasmic reticulum (ER). Read the full paper here.
Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins
First author: Tommy Tsan-Yuk Lam
Coronavirus researchers from Hong Kong University use QIAGEN extraction kits and QIAGEN CLC Genomics Workbench to identify SARS-CoV-2 in Malayan pangolins. Their research helps reveal how pangolins may have facilitated the coronavirus transfer to humans, causing the COVID-19 disease. Read their Nature publication here.
Influenza A viruses are transmitted via the air from the nasal respiratory epithelium of ferrets
First author: Mathilde Richard
In honor of Global Hand Hygiene Day, remember to wash your hands! Check out this paper by researchers at Erasmus University Medical Center, who use QIAGEN CLC Genomics Workbench to investigate how influenza and other respiratory viruses are transmitted from nasal tracts using ferrets as a model. Read their full paper in Nature Communications.
Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018
First author: Yangun Wang
Learn about the critical research by Dr. Y. Wang and team from Guangzhou Medical University who studied a subgenotype of human coronavirus, NL63. They used QIAGEN CLC Genomics Workbench to investigate how this virus undergoes continuous mutation and has the potential to cause severe lower respiratory tract infection in humans. Read their research here.
Discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing
First author: Bei Li
Dr. B. Li and colleagues from Wuhan Institute of Virology have been observing bats for potential coronavirus outbreaks after the SARS and MERS incidents. With the current pandemic, better surveillance practices are necessary to predict and mitigate the emergence of these viruses in humans. See how the team uses QIAGEN CLC Genomics Workbench and QIAGEN extraction kits in a capture-based NGS approach to overcome cost challenges. Discover their research here.
The splicing factor hnRNP M is a critical regulator of innate immune gene expression in macrophages
First author: Kelsi O. West
Great research from Texas A&M HSC where K. West and colleagues look at how pre-mRNA splicing decisions influence or are affected by macrophage activation. See how they use QIAGEN CLC Genomics and QIAGEN IPA to understand this link to the innate immune response in this Cell reports paper.
Microbiota dysbiosis and its pathophysiological significance in bowel obstruction
First author: Shrilakshmi Hedge
April is IBS awareness month. Check out this intriguing research by S. Hegde and colleagues from UTMB who look at how bowel obstruction may cause changes to the gut microbiota composition. See how the team utilizes a complete Sample to Insight approach using QIAGEN's extraction kits for bacterial DNA and RNA and QIAGEN CLC Microbial Genomics Module to identify bacterial species affected
Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signaling
First author: Thomas Aga Legøy
Exciting research from the University of Bergen, where a team uses every part of the QIAGEN RNA-seq solution from Sample to Insight. See how QIAGEN CLC Genomics Workbench, QIAGEN IPA and other QIAGEN products help the team understand the development process of human-induced pluripotent stem cells into pancreatic islet cells. You can access the full Scientific Reports paper here.
Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
First author: Ryoko Araki
Crucial research for cell replacement therapy by Dr. R. Araki and colleagues from the National Institute of Radiological Sciences (NIRS) in Japan where they study how point mutations in reprogrammed pluripotent stem cells prevent their therapeutic application. Learn how the team uses QIAGEN CLC Genomics Workbench to understand how a cell cycle checkpoint deficiency causes a cancer-like state in these cells. Read the full Nature Sciences article here.
Applied shotgun metagenomics approach for the genetic characterization of dengue viruses
First author: Erley Lizarazo
Dengue virus (DENV) is the fastest pandemic-prone arthropod-borne virus, and is detected through virus serology, isolation of the virus or molecular identification. In this Science Direct paper, an international team of researchers optimized DENV detection using shotgun metagenomics. CLC Genomics Workbench was used to identify, genotype and characterize DENV in tested samples, including SNV calling. Importantly, researchers were able to identify multiple DENV serotypes in the same sample using CLC Genomics Workbench and have defined shotgun metagenomics as a suitable technique for detection and typing of DENV.
FDA-ARGOS is a database with public quality-controlled reference genomes
First author: Heike Sichtig
For correct microbial detection and identification by NGS, quality-controlled and tested databases are fundamental. In a Nature Communications paper, researchers from multiple US government labs and organizations, including NCBI, present the FDA-ARGOS quality-controlled reference genomes as a public database and demonstrate its utility in two example cases. In the first case, CLC Genomics Workbench was used to analyze sequencing reads. For metagenomic analysis, paired-end reads were trimmed and scored on the Phred scale, and trimmed reads were mapped to the Enterococcus avium assembly and Homo sapiens assembly using CLC genomics workbench. The researchers showed an accurate microbial identification of E. avium from metagenomic samples with the FDA-ARGOS reference genomes compared to non-curated GenBank genomes. For Ebola virus molecular inversion probes (MIPS), there was 100% concordance between the gold standard real-time PCR comparator and the in silico target sequence comparison, supporting the feasibility of this strategy for use in NGS-based assay evaluation studies.
A comparison of three different bioinformatics analyses of the 16S–23S rRNA encoding region for bacterial identification
First author: Nilay Peker
To optimize the development of antimicrobial therapy, rapid and reliable identification of pathogens from samples are required. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used, species identification and discrimination are not always possible due to high sequence homology of the 16S rRNA gene among species. Recently, next-generation sequencing (NGS) of the 16S-23S rRNA encoding region has been proposed as a means for reliable identification of pathogens from samples. However, data analysis is time-consuming, and a database for the complete 16S-23S rRNA encoding regions is not available.
In this study, researchers from the University of Groningen in the Netherlands compared speed and accuracy of different data analysis approaches for 16S-23S rRNA NGS data: de novo assembly followed by BLAST, operational taxonomic unit (OTU) clustering or mapping, using an in-house developed 16S-23S rRNA encoding region database for identification of bacterial species. CLC Genomics Workbench was used for de novo assembly, mapping, and OTU clustering using the CLC Microbial Genomics Module. Furthermore, the researchers’ in-house developed 16S-23S rRNA database was uploaded to CLC Genomics Workbench. The researchers concluded that de novo assembly and BLAST appear to be the optimal approaches for data analysis, with the fastest turnaround time and highest sensitivity for sequencing the 16S-23S rRNA gene.
Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis
First author: Luigi Donato
Retinitis pigmentosa (RP) is an inherited ocular disease characterized by progressive retinal disruption. One of the leading causes of RP is oxidative stress which arrests the metabolic support of photoreceptors. In this study, a group of researchers from Italy investigated the role of oxidative stress in RP onset and progression by whole transcriptome analysis of human retinal pigment epithelium cells, untreated or treated with 100 µg/ml oxLDL to induce oxidative stress. CLC Genomics Workbench was used for data analysis, including trimming of low-quality reads and quantification of gene expression. As a result, the researchers discovered 29 candidate genes associated with RP.
Request your no-obligation trial of QIAGEN CLC Genomics Workbench today!
Read about how researchers across the world are using QIAGEN Digital Insights solutions to accelerate their work in a variety of applications
Powerful insights help innovate, integrate and translate scientific results into impactful discoveries. Many noteworthy papers cite QIAGEN Digital Insights solutions and demonstrate how our tools help drive research insights and discoveries. These papers use QIAGEN Ingenuity Pathway Analysis (IPA), QIAGEN CLC and/or QIAGEN OmicSoft to help drive success. The QIAGEN Digital Insights portfolio encompasses a comprehensive, easy-to-use toolbox that ensures continuity in NGS workflow. Here, we have curated a selection of just a few recent papers to offer a sense of the diversity of the research for which QIAGEN Digital Insights solutions makes a difference.
Viral cGAMP nuclease reveals the essential role of DNA sensing in protection against acute lethal virus infection
First author: Bruno Hernáez
Check out this fascinating research from Dr. B. Hernáez and colleagues at the Autonomous University of Madrid who investigate the ability of native cells to detect viral infection. Read how the team uses QIAGEN IPA to understand the role of DNA-sensing pathways in cellular detection and protection against acute lethal viral infection. Read their full paper here.
3D curvature-instructed endothelial flow response and tissue vascularization
First author: Christian Mandrycky
Can the way blood flows in three dimensions affect cellular transcriptomics? Read this exciting research by Dr. C. Mandrycky and colleagues at the University of Washington who try to understand the effects of vascularization in a three-dimensional space. Learn how the team uses QIAGEN IPA to understand the single-cell transcriptomic changes that occur in endothelial cells when a spiral blood flow is applied. Read the full article here.
Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis
First author: Alyssa M. Flores
Discover this fascinating nanotechnology research out of Stanford University by Dr. A Flores and colleagues, who investigate phagocytosis as a therapy for clearing atherosclerotic plaques. See how the team uses QIAGEN IPA to show the effectiveness of drug dispensing nanoparticles in reducing pro-inflammatory pathways and potentially preventing atherosclerosis. Read their full paper here.
Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19
First author: Aymeric Silvin
Don’t miss this critical research by Dr. A. Silvin and colleagues from Inserm, who investigate biomarkers to predict the development of severe COVID-19 in patients. Delve into their study, and learn how QIAGEN IPA supports their understanding of how the accumulation of calprotectin and abnormal monocytes may help differentiate between severe and mild COVID-19. Read the full article here.
Type I and III interferons disrupt lung epithelial repair during recovery from viral infection
First author: Jack Major
Immunologists at the Francis Crick Institute investigate the harmful effects of excessive cytokine signaling during respiratory viral infection. Learn how they use QIAGEN IPA to investigate how IFN signaling interferes with lung repair during influenza/viral recovery. Read their full paper in Science here.
Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and - independent cellular responses in Alzheimer’s disease
First author: Yingyue Zhou
Are we a step closer to understanding Alzheimer’s risk? Learn about fascinating research by Y. Zhou and colleagues at Washington University in St. Louis who study the role of microglia receptor TREM2 in Alzheimer's pathogenesis. See how they use QIAGEN IPA to investigate how TREM2 increases AD risk and activation of disease-associated microglia. Read the full article here.
Elevated glucose levels favor SARS-CoV-2 infection and monocyte response through a HIF-1α/glycolysis-dependent axis
First Author: Ana Campos Codo
Discover why diabetic patients may be more at risk of developing severe COVID-19. Researchers at the Universidade Estadual de Campinas investigate the role of elevated blood glucose levels in inducing cytokine storms in severe COVID-19 patients. See how the team uses QIAGEN IPA to investigate how the HIF-1α axis in monocytes causes T-cell dysfunction and reduces epithelial cell survival. Read their full paper here.
Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020
First author: Yong Zhang
Should we be looking for new mutations in SARS-CoV-2 that make it more virulent? Researchers from the Chinese Center for Disease Control and Prevention perform genomic characterization of SARS-CoV-2 identified in a reemerging outbreak in China. Discover how they use QIAGEN CLC Genomics Workbench to help trace the source of the virus in this second outbreak in Beijing’s Xinfadi market. Read their full article here.
Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China
First author: Jing Yang
Crucial coronavirus research from the Chinese Academy of Sciences looking into the re-emergence of the SARS-CoV-2 virus in China. Discover how they use the nanopore and MiSeq system together with QIAGEN CLC Genomics Workbench to trace the source of the virus in this second outbreak in Beijing. Get the full article here.
Systematic reconstruction of the complete two-component sensorial network in Staphylococcus aureus
First author: B. Rapun-Araiz
High-impact research by B. Rapun-Araiz and colleagues at Universidad Publica de Navarra in Spain who investigate the targets of two-component signal transduction systems (TCSs) in bacteria. See how they use QIAGEN CLC Genomics Workbench to map the complete TCS regulon in Staphylococcus aureus. Read the full paper here.
Remdesivir inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice
First author: Andrea J. Pruijssers
Excellent research by A. Pruijssers and colleagues at Vanderbilt University who study how Remdesivir inhibits SARS-CoV-2 in human lung cells. See how they use QIAGEN CLC Main Workbench to help investigate the efficacy of Remdesivir against SARS-CoV-2 in vitro and in vivo. Read the full article here.
Lysosomal recycling of amino acids affects ER quality control
First author: Ryo Higuchi-Sanabria
Exciting research from the Howard Hughes Medical Institute, where researchers investigate the role of lysosomes in amino acid recycling. Learn how they use QIAGEN CLC Genomics Workbench to understand how reduced lysine and arginine can cause increased sensitivity to proteotoxic stress in the endoplasmic reticulum (ER). Read the full paper here.
Liver-specific knockdown of class IIa HDACs has limited efficacy on glucose metabolism but entails severe organ side effects in mice
First author: Nicole Ziegler
Could HDAC inhibitors serve as epigenetic therapy? Intriguing research by Dr. N. Ziegler and colleagues at Sanofi investigate the therapeutic potential of class IIa HDAC inhibition. See how the team uses QIAGEN OmicSoft Studio to understand the consequences of this inhibition, which has a limited effect on glucose metabolism but causes severe side effects in the kidney and spleen. Read the full paper here.
The evolving systemic biomarker milieu in obese ZSF1 rat model of human cardiometabolic syndrome: Characterization of the model and cardioprotective effect of GDF15
First Author: Marina Stolina
Can we develop biomarkers to predict cardiometabolic syndrome using the obese ZSF1 rat model? Read this paper to learn how researchers at Amgen use QIAGEN IPA and OmicSoft Studio to characterize the obese ZSF1 rat model to develop biomarkers that predict cardiometabolic syndrome, a global health issue, to better understand the cardioprotective effects of GDF15. Read the full article here.
Elucidation of mechanisms of topotecan-induced cell death in human breast MCF-7 cancer cells by gene expression analysis
First author: Birandra K. Sinha
Fascinating research by Dr. B Sinha and colleagues at the National Institute of Environmental Health Sciences (NIEHA), who investigate the mechanisms of topotecan-induced cell death in human breast cancer cells. Learn how the team uses QIAGEN OmicSoft Studio to understand the role of reactive oxygen species in inducing tumor cell killing. Read the full paper here.
ABHD11, a new diacylglycerol lipase involved in weight gain regulation
First author: Johanna Escoubet
Exciting discovery by J. Escoubet and colleagues at Sanofi who study a new diacylglycerol lipase involved in weight gain regulation. Learn how they use QIAGEN ArrayStudio to understand how inhibiting ABHD11 helps reduce intestinal fat absorption. Read the full paper here.
To request information on the QIAGEN Digital Insight solutions, contact bioinformaticssales@qiagen.com.
Researchers across the world are using QIAGEN Digital Insights solutions to accelerate their work in a variety of applications
Powerful insights help innovate, integrate and translate scientific results into impactful discoveries. Many noteworthy papers cite QIAGEN Digital Insights solutions and demonstrate how our tools help drive research insights and discoveries. These papers use QIAGEN Ingenuity Pathway Analysis (IPA), QIAGEN CLC and/or QIAGEN OmicSoft to help drive success. The QIAGEN Digital Insights portfolio encompasses a comprehensive, easy-to-use toolbox that ensures continuity in NGS workflow. Here, we have curated a selection of just a few recent papers to offer a sense of the diversity of the research for which QIAGEN Digital Insights solutions makes a difference.
Proteomic and metabolomic characterization of COVID-19 patient sera
First author: Bo Shen
Virologists at Wenzhou Medical University use machine learning to help identify potentially severe COVID19 cases. Learn how they use QIAGEN IPA to understand proteomic and metabolomic changes to identify blood markers that could predict COVID-19 severity. Read their full paper here.
Co-expression of SARS-CoV-2 entry genes in the superficial adult human conjunctival, limbal and corneal epithelium suggests an additional route of entry via the ocular surface
First author: Joseph Collin
Potential SARS-CoV-2 transmission through the eyes? Discover this fascinating research by Dr. J. Collin and colleagues at Newcastle University, who are studying a possible ocular route of transmission for SARS-CoV-2. Learn how the team uses QIAGEN IPA's Upstream Regulator Analysis to understand how the virus may exploit ACE2 and TMPRSS2 co-expression in the eyes to gain systemic entry. Read the full article here.
Activin-mediated alterations of the fibroblast transcriptome and matrisome control the biomechanical properties of skin wounds
First Author: Mateusz Wietecha
Novel research by Dr. M. Wietecha and colleagues at ETH Zurich who study scar tissue formation during wound healing. Learn how the team uses QIAGEN CLC Genomics Workbench and QIAGEN IPA to understand how activin A affects the wound healing process and could be a key factor in wound fibrosis. Read their full paper here in Nature Communications.
RasGRP1 is a causal factor in the development of l-DOPA–induced dyskinesia in Parkinson’s disease
First author: Mehdi Eshraghi
Parkinson’s researchers at the Scripps Research Institute investigate the role of RasGRP1 in causing L-DOPA–induced dyskinesia. Learn how the team uses QIAGEN IPA to understand the molecular mechanism of how this guanine nucleotide exchange factor contributes to this disease. Read their full paper here.
Conditional deletion of Nedd4-2 in lung epithelial cells causes progressive pulmonary fibrosis in adult mice
First author: Julia Duerr
Researchers at the University of Heidelberg use QIAGEN IPA to investigate the role of Nedd4-2 in progressive idiopathic pulmonary fibrosis. See how QIAGEN IPA helps the team identify processes and pathways affected by treatment with the anti-fibrotic drug pirfenidone in a Nedd4-2 conditional deletion mouse model. Read their full paper in Nature Communications.
Concise whole blood transcriptional signatures for incipient tuberculosis: A systematic review and patient-level pooled meta-analysis
First author: Rishi K. Gupta
Critical tuberculosis research by R. Gupta and colleagues from University College London who investigate transcriptional signatures to identify potential tuberculosis infection in patients. See how the team uses QIAGEN IPA to research blood transcriptional biomarkers that could be used to identify high-risk tuberculosis patients. Read the full paper from Lancet Respiratory Medicine.
Mitochondria-endoplasmic reticulum contacts in reactive astrocytes promote vascular remodeling
First author: Jana Goebel
In honor of brain injury awareness month, we are highlighting fascinating research from the University of Cologne, Germany, where J. Gӧbel and colleagues look at the physical interaction between the endoplasmic reticulum and mitochondria and its role in promoting vascular remodeling in astrocytes. See how the team uses QIAGEN IPA to investigate this mitochondrial dynamic in brain injury wound healing. Read the full paper in Cell Metabolism.
Transcriptional regulation of CCL2 by PARP1 is a driver for invasiveness in breast cancer
First author: Pranabananda Dutta
Dutta and colleagues at Charles Drew University are studying the role of PARP1 in metastatic breast cancer. The team uses QIAGEN CLC Genomics Workbench and QIAGEN IPA to understand how PARP1 interacts with CCL2, a driver for invasiveness in breast cancer. Access their full article here.
Evolution of a new function by fusion between phage DNA and a bacterial gene
First author: Omar Warsi
Discover fascinating research by Dr. Warsi and colleagues at Uppsala University, where they conferred a new function in bacteria by creating a chimeric fusion between phage DNA and a bacterial gene. The team used QIAGEN CLC Genomics Workbench to understand how the fusion of mobile genetic elements generates novel functions in bacteria. Read their full paper here.
SGLT2 inhibition modulates NLRP3 inflammasome activity via ketones and insulin in diabetes with cardiovascular disease
First author: So Ra Kim
Discover exciting research by S. R. Kim and colleagues at Yonsei University who study the role of SGLT2 in modulating NLRP3 inflammasome activity in diabetic patients. They use the powerful QIAGEN CLC Genomics Workbench to investigate how SGLT2 inhibition helps reduce cardiovascular events. Read the full paper in Nature Communications here.
A novel coronavirus from patients with pneumonia in China, 2019
First author: Na Zhu
Exciting coronavirus research by N. Zhu and colleagues at The Chinese Center for Disease Control, who report how they identified the novel coronavirus responsible for COVID-19. Discover how the team uses QIAGEN CLC Genomics Workbench in the data analysis of next-generation sequencing of samples from pneumonia patients in Wuhan, China. Read their New England Journal of Medicine publication here.
Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome
First author: Takuro Horii
Discover this fantastic research by T. Horii and colleagues at Gunma University in Japan, where they are working on creating an epigenetic mouse disease model using targeted methylation of the genome. Learn how the team uses QIAGEN extraction kits and QIAGEN CLC Genomics Workbench to create a Silver-Russell syndrome animal model using targeted demethylation. Read the full paper here.
Metabolic alterations in spheroid-cultured hepatic stellate cells
First author: Koichi Fujisawa
Researchers at Yamaguchi University are studying transcriptomic and metabolomic changes in hepatic stellate cells in spheroid culture to better understand liver fibrosis. Discover how they use QIAGEN OmicSoft Suite and QIAGEN IPA to identify key changes that deepen our understanding of liver fibrosis. Read the full paper here.
Systems biology analysis of the antagonizing effects of HIV-1 TAT expression in the brain over transcriptional changes caused by methamphetamine sensitization
First author: Liana Basova
What's the connection between drug use and certain viruses? Discover this fascinating research by Dr. L. Basova and colleagues at the San Diego Biomedical Research Institute, who investigate the effects of reward circuitry inhibiting the TAT protein in HIV patients using methamphetamines. See how the team uses QIAGEN OmicSoft ArrayStudio together with QIAGEN IPA to understand how TAT has an antagonizing effect on meth-induced transcriptional changes in a neuroHIV mouse model. Read the full paper in Viruses.
Antitumor potency of an anti-CD19 chimeric antigen receptor T-cell therapy, lisocabtagene maraleucel in combination with ibrutinib or acalabrutinib
First author: Jim S. Qin
Cancer researchers at Juno Therapeutics investigate the effectiveness of a new anti-CD19 T-cell therapy. See how the team uses QIAGEN ArrayStudio to research a combination therapy of lisocabtagene maraleucel and ibrutinib or acalabrutinib in hopes to improve outcomes in CD19+ B-cell malignancies. Read the full paper here.
Mitochondrial dysfunction and DNA damage accompany enhanced levels of formaldehyde in cultured primary human fibroblasts
First author: Cristina A. Nadalutti
Researchers at the National Institute of Environmental Health Sciences (NIEHS) use QIAGEN OmicSoft Array Suite to study how increases in cellular formaldehyde cause mitochondrial dysfunction and DNA damage in cultured primary human fibroblasts. Read the full paper here.
To request information on the QIAGEN Digital Insight solutions, contact bioinformaticssales@qiagen.com.
Researchers across the world are using QIAGEN Digital Insights solutions to accelerate their work in a variety of applications
Powerful insights help innovate, integrate and translate scientific results into impactful discoveries. Many noteworthy papers cite QIAGEN Digital Insights solutions and demonstrate how our tools help drive research insights and discoveries. These papers use QIAGEN Ingenuity Pathway Analysis (IPA), QIAGEN CLC and/or QIAGEN OmicSoft to help drive success. The QIAGEN Digital Insights portfolio encompasses a comprehensive, easy-to-use toolbox that ensures continuity in NGS workflow. Here, we have curated a selection of just a few recent papers to offer a sense of the diversity of the research for which QIAGEN Digital Insights solutions makes a difference.
A novel panel of differentially-expressed microRNAs in breast cancer brain metastasis may predict patient survival
First Author: Athina Giannoudis
In honor of World Cancer Day, discover how Dr. Giannoudis and colleagues at the University of Liverpool investigate differentially expressed miRNAs in breast cancer that has metastasized to the brain. See how the team uses QIAGEN IPA to identify miRNA biomarkers that may be predictive of survival. Read the paper here.
CD4+ T cell help creates memory CD8+ T cells with innate and help-independent recall capacities
First Author: Tomasz Ahrends
Read about the exciting research by T. Ahrends and colleagues at Netherlands Cancer Institute who perform a whole genome analysis to study how CD4+ T cells help generate CD8+ cytotoxic T cells. In order to identify the function and subcellular localization of the genes, the team uses QIAGEN IPA to determine which genes are differentially expressed when support from CD4+ T cells is available. Read the entire paper here.
Mediator MED23 regulates inflammatory responses and liver fibrosis
First Author: Zhichao Wang
Dive into the details of new and noteworthy research by Z. Wang and colleagues at Fudan University who study the role of MED23 in the development of liver fibrosis. Read about how the team uses QIAGEN IPA to tease out the involvement of MED23 by predicting upstream regulators of upregulated genes in a MED23 knockout mouse model, and potential targets for therapeutic intervention in liver fibrosis. Delve into the team’s research here.
Changes in DNA methylation from pre- to post-adolescence are associated with pubertal exposures
First Author: Luhang Han
To recognize Reproductive Health Day, read fascinating research by L. Han and colleagues at the University of Memphis, who perform a longitudinal study to identify epigenetic changes from pre- to post-adolescence. See how the team uses QIAGEN IPA to investigate pathways affected by the DNA methylation changes associated with puberty and environmental factors. Explore the paper here.
Genetics of glucocorticoid-associated osteonecrosis in children with acute lymphoblastic leukemia
First author: Seth E. Karol
In honor of International Childhood Cancer Day (February 14, 2020), we are highlighting this previous paper from researchers at St. Jude. Seth Karol and colleagues performed a genome-wide association study with over 2000 children and use QIAGEN IPA to identify the genetic causes of osteonecrosis that occur during glucocorticoid therapy given to children with acute lymphoblastic leukemia. Read the full paper here.
A novel mouse model of enteric Vibrio parahaemolyticus infection reveals that the type III secretion system 2 effector VOPC plays a key role in tissue invasion and gastroenteritis
First author: Hyungiun Yang
Dig into this interesting study by H. Yang and colleagues from the University of British Columbia, which reveals how V. parahaemolyticus, a bacteria commonly found in contaminated seafood, causes gastroenteritis in humans. Read how the team uses QIAGEN IPA to study the T3SS2 secretion system to show that its effectors are necessary to cause gut infection. Access the full article here.
Loss of amyloid precursor protein exacerbates early inflammation in Niemann-Pick disease type C
First author: Samuel D. Shin
For Rare Disease Day, February 28, 2020, we are highlighting research by Samuel Shin and colleagues from Loma Linda University who are studying Niemann-Pick disease type C, a lethal neurodegenerative condition, affecting one in 100,000 thousand children. Find out how the team uses QIAGEN IPA to reveal how the loss of amyloid precursor protein contributes to the neuroinflammation observed in this disease. Access the paper here.
Expression of microRNA in follicular fluid in women with and without PCOS
First author: Alexandra E. Butler
Dr. A. Butler and colleagues from Hamad Bin Khalifa University (HBKU) look at the differences in miRNA expression in follicular fluid of women with polycystic ovary syndrome (PCOS). In this recent paper, the team used QIAGEN IPA to extensively look at the differential expression of these small non-coding RNAs and identified 12 miRNAs that are involved in reproductive pathways, 12 related to inflammatory disease and 6 implicated in benign pelvic disease.
Multi-omics approach for studying tears in treatment-naïve glaucoma patients
First author: Claudia Rossi
Researchers use QIAGEN IPA to analyze the tears of glaucoma patients in this multi-'omics study to understand primary open-angle glaucoma (PAOG). In the research paper, the team performed metabolomics and proteomics analyses to identify key differences that may result in new screening options for this disease, which is the leading cause of irreversible blindness.
Longitudinal multi-omics of host-microbe dynamics in prediabetes
First author: Wenyu Zhou
Zhou and colleagues from Stanford University perform a multi-'omics study looking into the connection between host-microbiome interaction and the predisposition to type-2 diabetes. In this Nature article, read how the team uses QIAGEN IPA to search for enriched pathways to understand how changes during respiratory viral infections can lead to the development of diabetes.
Trans-ethnic association study of blood pressure determinants in over 750,000 individuals
First author: Ayush Giri
Significant research by Dr. A. Giri and colleagues from Vanderbilt University who are involved in the investigation of over 750,000 individuals for genetic variants that affect blood pressure. Discover how the team uses QIAGEN IPA to identify enriched pathways involving the 840 genes predicted to be associated with blood pressure regulation.
Fibrogenic activity of MECP2 is regulated by phosphorylation in hepatic stellate cells
First author: Eva Moran-Salvador
Discover the research by Dr. E. Moran-Salvador and colleagues from Newcastle University who study the role of MECP2 expressed by hepatic stellate cells (HSCs) in liver fibrosis. See how the team uses QIAGEN IPA to identify enriched pathways where MECP2 is involved, and how the deletion of MECP2 leads to reduced fibrosis in mice.
Immunological observations and transcriptomic analysis of trimester‐specific full‐term placentas from three Zika virus-infected women
First author: Fok-Moon Lum
Dr. F Lum and colleagues from Agency for Science, Technology and Research, Singapore look at placental development during pregnancy after a Zika virus infection. In this paper, see how the team uses QIAGEN IPA to identify eIF2 as the major canonical pathway involved in the differential gene expression pattern when compared to healthy controls.
Proteomic profiling of extracellular vesicles isolated from cerebrospinal fluid of former national football league players at risk for chronic traumatic encephalopathy
First author: Satoshi Muraoka
Dr. S. Muraoka and colleagues look at the proteomic profile of cerebrospinal fluid samples from former NFL players to understand the biology of chronic traumatic encephalopathy, a condition that affects individuals with a history of repetitive mild traumatic brain injury. In this research paper, the team use QIAGEN IPA to look at upstream regulators, pathways and functional networks of the differentially expressed proteins to identify a plausible biomarker.
Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells
First author: Lei Tan
Crucial research by Dr. L. Tan and colleagues from Weill Cornell Medical College strives to reveal the outcomes of a Zika virus infection during the pre- and peri-implantation stage of pregnancy. Learn how the team used QIAGEN IPA to identify two key gene networks that are strongly affected by the virus.
Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior
First author: Zuzanna Misiewicz
Check out this interesting paper by Dr. Z. Misiewicz and colleagues from University of Helsinki who use a multi-'omics approach to understand the molecular mechanisms behind anxiety and stress disorders. Discover how the team use QIAGEN IPA to identify certain mitochondrial genes in blood cells related to these debilitating disorders.
Microbe-host interplay in atopic dermatitis and psoriasis
First author: Nanna Fyhrquist
Interesting research by Dr. N. Fyhrquist and colleagues from the Karolinska Institute who study the interplay between the skin microbiome and skin diseases such as dermatitis and psoriasis. The team use QIAGEN IPA to identify key regulators and pathway activation in host cells to identify transcriptomic signatures for skin barrier function, tryptophan metabolism and immune activation as a basis for plausible biomarkers and targeted therapies.
Zinc chelation specifically inhibits early stages of Dengue virus replication by activation of NF-κB and induction of antiviral response in epithelial cells
First author: Meenakashi Kar
Dr. M. Kar and colleagues from Translational Health Science and Technology Institute in Faridabad, India (THSTI) perform cutting-edge immunology research using QIAGEN IPAs to understand how zinc chelation can inhibit early stages of Dengue virus by activating NFkB to induce an antiviral response in epithelial cells.
Combined transcriptome and metabolome analysis identifies defense responses in spider mite-infested pepper (Capsicum annuum)
First Author: Yuanyuan Zhang
Researchers at Wageningen University use QIAGEN CLC Genomics Workbench to study the leaf transcriptomes and metabolomes of Capsicum peppers to identify how they fight spider mite infections. Read the full story here.
Hippocampal clock regulates memory retrieval via Dopamine and PKA-induced GluA1 phosphorylation
First author: Shunsuke Hasegawa
Intriguing research by S. Hasegawa and colleagues at Tokyo University who investigate the role of the circadian clock in memory retrieval. See how the team uses both QIAGEN CLC Genomics Workbench and QIAGEN IPA to understand how circadian-dependent transcription factor BMAL1 contributes to loss of memory retrieval in the late afternoon. Read the details here.
Rousette bat dendritic cells overcome Marburg virus-mediated antiviral responses by upregulation of interferon-related genes while downregulating proinflammatory disease mediators
First author: Joseph Prescott
Fascinating research by J. Prescott and colleagues from the US Centers for Disease Control and Prevention (CDC) which focuses on how the immune system of the rousette bat coexists with the Marburg virus. See how the team uses QIAGEN's CLC Genomics Workbench and QIAGEN IPA to understand how bat dendritic cells downregulate immune maturation while upregulating pathogen-sensing pathways during a viral infection. Explore the topic further here.
Coronary arterial development is regulated by a Dll4-Jag1-EphrinB2 signaling cascade
First author: Stanislao Igor Travisano
In honor of American Heart Month, we are highlighting research by S. Travisano and team from Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Spain, who investigate the role of the Notch signaling pathway in coronary arterial development. Learn how they use both QIAGEN CLC Genomics Workbench and QIAGEN IPA to show the importance of the Dll4-Jag1-EphrinB2 signaling cascade in coronary angiogenesis. Get the details by accessing the full paper here.
Screening identifies small molecules that enhance the maturation of human pluripotent stem cell-derived myotubes
First author: Sridhar Selvaraj
Exciting research from the University of Minnesota where Selvaraj et al. examine a combination of small molecules can help with the development of pluripotent stem cells into mature myotubules. Read how the team uses QIAGEN CLC Genomics Workbench and QIAGEN IPA to understand how these small molecules help with stem cell maturation.
PD-L1 blockade by atezolizumab downregulates signaling pathways associated with tumor growth, metastasis and hypoxia in human triple-negative breast cancer
First author: Reem Saleh
In this paper, read how researchers at HBKU use QIAGEN Genomics Workbench and QIAGEN IPA to understand how atezolizumab targets PD-L1 and helps in the treatment of triple-negative breast cancer, the most aggressive type of breast cancer.
Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering
First author: Shu-Ting You
Delve into this interesting research paper by You and colleagues from Academia Sinica in Taiwan where they study the role of methyltransferase Hmt1 in regulating noise buffering. See how the team uses QIAGEN CLC Genomics Workbench to identify Hmt-1 as a master regulator that adjusts protein noise levels in response to stressful environments.
Micro RNA transcriptome profile in canine oral melanoma
First author: Md. Mahfuzur Rahman
In this recent paper, researchers use QIAGEN CLC Genomics Workbench to understand the miRNA transcriptome profile in canine oral melanoma and how it plays a role in cancer pathogenesis. The team links their observations to three oncogenic miRNAs targets (miR-450b, 301a and 223) from a human study that were also down-regulated in canine oral melanoma and had a significant negative correlation with their respective miRNAs.
An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat
First author: Xiucheng Cui
Fascinating research out of the Ottawa Research and Development Centre where a team has developed a method to delete large segments of the genome using the CRISPR/Cas9 technique. See how they apply QIAGEN CLC Genomics Workbench to help them use an optimized Cas-9 plant codon to edit hexaploidic wheat genomes.
Genome sequence of a novel Enterococcus faecalis sequence type 922 strain isolated from a door handle in the intensive care unit of a district hospital in Durban, South Africa
First author: Christiana Shobo
December 1–7 is National Handwashing Awareness Week. Washing your hands is one of the easiest ways to prevent overuse of antibiotics and fight antimicrobial resistance. This work by Dr. C. Shobo and colleagues from the University of KwaZulu-Natal demonstrate this by using QIAGEN CLC Genomics Workbench to investigate the resistome of a novel Enterococcus faecalis found on the door handle of an intensive care unit (ICU) in South Africa. Check it out!
Human perivascular stem cell-derived extracellular vesicles mediate bone repair
First author: Jiajia Xu
Interesting research by Dr. J Xu and colleagues from Johns Hopkins University show how extracellular vesicles (EVs) derived from human perivascular stem cells (PSCs) are able to repair bone by stimulating osteoblasts just like PSCs. Discover how the team use QIAGEN CLC Genomics Server and Workbench to understand the transcriptomics of the EVs.
Comparative modulation of lncRNAs in wild-type and rag1-heterozygous mutant zebrafish exposed to immune challenge with spring viraemia of carp virus (SVCV)
First author: Valentina Valenzuela-Muñoz
Research by V. Valenzuela-Muñoz and colleagues from University of Concepción use QIAGEN CLC Genomics Workbench to discover the role of long non-coding RNAs (lncRNAs) in the infection of zebrafish with spring viraemia of carp virus.
Small extracellular vesicles convey the stress-induced adaptive responses of melanoma cells
First author: Maria Harmati
M. Harmati and colleagues from the University of Szeged use both QIAGEN CLC Genomics Workbench and QIAGEN Ingenuity Pathway Analysis to investigate how extracellular vesicles from melanoma cells convey adaptive stress responses. In their paper, they leverage these insights to illustrate how to predict different stress responses which could influence efficacy of treatments based on therapy-induced host responses.
Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients
First Author: David Michalovich
Discover this interesting and relevant research by a team at GSK who leverage QIAGEN OmicSoft Array Studio to investigate the connection between obesity and asthma severity. They find the gut microbiome plays a significant role in these conditions. Check out the full paper here.
Reduced TRPM8 expression underpins reduced migraine risk and attenuated cold pain sensation in humans
First author: Narender R. Gavva
Researchers from Amgen use QIAGEN OmicSoft Array Studio in this study to understand how a specific allele in TRPM8 can act as a cold sensor to reduce migraine risk in humans located in colder climates.
Inhibition of mir-378a-3p by inflammation enhances IL-33 levels: A novel mechanism of alarmin modulation in ulcerative colitis
First author: Karen Dubois-Camacho
In this recent paper, researchers at the Universidad de Chile use QIAGEN OmicSoft Array Studio to study the role of miRNAs in regulating pro-inflammatory mediators such as IL-33 in ulcerative colitis, a form of inflammatory bowel disease.
PD-1hiCXCR5– T peripheral helper cells promote B cell responses in lupus via MAF and IL-21
First author: Alexandra Bocharnikov
Researchers from Harvard, Merck, Johns Hopkins and several other prominent institutions collaborate in this research paper and use QIAGEN OmicSoft Array Studio and QIAGEN IPA to understand how T peripheral helper cells contribute to B cell dysfunction in lupus.
The CSF-1-receptor inhibitor, JNJ-40346527 (PRV-6527), reduced inflammatory macrophage recruitment to the intestinal mucosa and suppressed murine T cell-mediated colitis
First author: Carl L Manthey
In this recent paper, read how researchers from Janssen Research and Development use QIAGEN OmicSoft Array Studio and QIAGEN IPA to demonstrate the involvement of macrophages in Crohn's disease and how inhibition of the CSF-1 pathway helped in attenuating the disease in mice.
Identification of predictive genetic signatures of Cytarabine responsiveness using a 3D acute myeloid leukaemia model
First author: Haiyan Xu
Dr. H. Xu and colleagues from Merck study the ability of bone marrow cells from acute myeloid leukaemia (AML) patients to resist cancer treatment in a 3D cell culture system. Read how the team use QIAGEN OmicSoft Studio to identify unique gene expression signatures and novel genetic mutations associated with sensitivity to Ara‐C treatment in proliferating AML cells. These unique signatures could potentially be used as predictive biomarkers to determine optimal treatment regimens.
Cell-autonomous and non-cell autonomous effects of neuronal BIN1 loss in vivo
First author: Kathleen M. McAvoy
Interesting research from Dr. K. McAvoy and colleagues from Biogen and Harvard Medical School who study the genetic contribution of neuronal-specific BIN1 isoforms in late onset Alzheimer's disease. Learn how the team use QIAGEN OmicSoft Array Studio and QIAGEN Ingenuity Pathway Analysis to look at gene enrichment and activated pathways in BIN1-knockout mice to better understand this disease.
To request information on the QIAGEN Digital Insight Solutions, contact bioinformaticssales@qiagen.com.
As a researcher, it’s an enormous task to acquire knowledge and insight from the sea of biological data and complex interactions involved in a specific research topic. With QIAGEN Bioinformatics’ Ingenuity Pathway Analysis (IPA), we make it easier.
With the comprehensive, manually curated content of the Ingenuity Knowledge Base, combined with powerful algorithms, IPA provides advanced analysis capabilities to help scientists understand the biological context of expression analysis experiments. With IPA, you can identify the most significant pathways, and discover novel regulatory networks and causal relationships associated with your experimental data.
In the past several months there have been over 500 citations for Ingenuity Pathway Analysis, demonstrating how this tool helps put biological data in context to gain insight. Here, we round up just a few of them to offer a sense of the diverse research for which Ingenuity Pathway Analysis makes a difference.
Increasing evidence indicates that miR-301a is a potential oncogenic microRNA and that its genetic ablation reduces Kras-driven lung tumorigenesis in mice. A recent Molecular Cancer paper describes how researchers from China studied the role of miR-301a on host antitumor immunity.
After differentially expressed genes (DEGs) of two mouse models (with or without miR-301a) were identified from RNA-seq data, IPA was used to identify gene networks. The five most highly implicated IPA networks related to cell cycle and immune response were merged, and it was discovered that IFNG (INF-γ) and CTNNB1 (β-catenin) were in the core modules within the entire network. This discovery led to further investigation of these genes, which enabled the researchers to find that miR-301a deficiency recruits immune cells to the tumor microenvironment, resulting in higher IFN-γ expression in early lung tumorigenesis. Additionally, miR-301a directly targets Runx3 mRNA, a negative regulator of the β-catenin pathway. After further experiments, the authors conclude that miR-301a facilitates antitumor immunity in the tumor microenvironment via Runx3 suppression during lung tumorigenesis.
In a Nature Communications paper, scientists from the Broad Institute and the Worchester Polytechnic Institute looked into transcriptional dynamics of macrophages infected with Candida albicans. IPA was used to investigate biological relationships, canonical pathways and upstream regulators of differentially expressed genes in macrophages either exposed to or infected with C. albicans.
Using IPA, the group was able to assess the overlap between significantly DEGs and an extensively curated database of target genes for each of several hundred known regulatory proteins. The researchers found that transcriptomes of infected macrophages and phagocytosed C. albicans displayed tightly coordinated shifts in gene expression, and they established an approach for studying host-pathogen trajectories to resolve heterogeneity in dynamic populations.
A group of collaborating researchers from China recently published their findings on the signaling pathway network profile of human ovarian cancers. They used IPA to mine signaling pathway networks with nearly 1200 differentially expressed mitochondrial proteins, and they compared the pathway and network changes between ovarian cancers and controls. Their results were experimentally validated using qRT-PCR and Western blot. The scientific data generated in this study may lead to the discovery of pathway- and network-based disease and treatment biomarkers for ovarian cancers, and potentially novel molecular mechanisms and therapeutic targets for this disease.
Metal oxide nanoparticles (NPs) are widely used in industry despite little knowledge about the cellular pathways involved in their potential toxicity. Collaborating scientists from France and Ireland published in Cell Biology and Toxicology results of their gene expression study, showing expression changes in rat macrophages upon exposure to metal oxide NPs. IPA was used to identify top canonical pathways influenced by the exposure, notably eIF2 signaling involved in protein homeostasis.
If QIAGEN’s IPA is helping you make strides in your research, we would love to hear about it. Please contact us to share your story, or just to request a free trial!
We recently announced an Ingenuity® Pathway Analysis (IPA®) update, which now includes more than 47,000 datasets available for Analysis Match. To mark the occasion, we’ve rounded up a few of the most interesting scientific studies that featured IPA. The teams we read about, and the work they accomplish, continues to impress us with their endless resourcefulness and creativity. We hope you’ll enjoy reading how IPA is helping scientists and researchers to generate deeper insights into their work.
Presymptomatic Change in MicroRNAs Modulates Tau Pathology
First author: Salil Sharma
Nature recently published a study by a cohort of Indiana University scientists who wanted to identify RNA changes that might contribute to tauopathy (a class of neurodegenerative diseases caused by misfolding of the tau protein). They used QIAGEN IPA throughout the stages of their process, leveraging its network analysis functionality to correlate observed transcriptomic changes, and analyzing miR-RNA pairing. They discovered that many canonical and disease associated pathways were altered at the presymptomatic stage of tauopathy, and that miR (MicroRNA) changes at an early stage of tauopathy are likely to contribute to disease progression. By invoking early miR changes triggered by Tau expression, they may impact disease progression by altering several key biological pathways.
Resveratrol Protects Mice Against SEB‐Induced Acute Lung Injury and Mortality by miR‐193a Modulation that Targets TGF‐β Signaling
First author: Hasan Alghetaa
A group of scientists from the University of South Carolina studied the impact of using Resveratrol—a phytoallexin—on mice with Staphylococcal enterotoxin B (SEB)-induced acute lung injury. They used QIAGEN IPA to analyze IDs and fold change quantities of 66 differentially regulated MiRNA to determine potentially affected gene targets and molecular pathways. They published their results in the March issue of Journal of Cellular and Molecular Medicine, in which they wrote, “our studies suggest that RES can effectively neutralize SEB‐mediated lung injury and mortality through potential regulation of miRNA that promote anti‐inflammatory activities”
Hodgkin Lymphoma-Derived Extracellular Vesicles Change the Secretome of Fibroblasts Toward a CAF Phenotype
First author: Bastian Dörsam
When a team of German researchers researched the extracellular vesicles (EV)-mediated interplay of Hodgkin Lymphoma (HL) cells and fibroblast, they used QIAGEN IPA to analyze pathway proteomic data. They found that HL cells and fibroblasts interact in a two-way manner, which not only changes migratory properties but also encourages the transition of a healthy fibroblast to a cancer-associated fibroblast (CAF) phenotype that is concomitant with the alteration of their inflammatory secretome. The team published their results in Frontiers in Immunology, with the conclusion that more in-depth study of the complex interactions in HL and the role of EVs might contribute to the development of novel therapeutic cancer-fighting tools.
Exploring Gene Expression Biomarker Candidates for Neurobehavioral Impairment from Total Sleep Deprivation
First author: Hilary A. Uyhelji
A recent report in Biomedical Genomics presented novel candidate biomarkers associated with lapses of attention during total sleep deprivation (TSD). The Oklahoma City-based team used QIAGEN IPA to explore molecular pathways and networks based on previously published gene interactions and found that 212 genes changed expression while responding to the TSD treatment. This supports previous TSD-associated findings, and also points to immune response and ion signaling. The report confirms that “analysis of these genes may aid fundamental understanding of the impact of TSD on neurobehavioral performance.”
Prostate Cancer Susceptibility Gene HIST1H1A is a Modulator of Androgen Receptor Signaling and Epithelial to Mesenchymal Transition
First author: Kendra A. Williams
Prostate cancer is one of the most commonly diagnosed male cancers. A cohort of scientists in Maryland set out to decipher the functional role of the HIST1H1A gene in the development of aggressive prostate cancer, using QIAGEN’s IPA to analyze omics data. This helped them to conclude that HIST1H1A expression is significantly suppressed in human prostate adenocarcinoma compared to its normal counterpart. They also determined that systems genetics can be used to show how hereditary variation influences the susceptibility to aggressive prostate cancer. The results of this study—published in Oncotarget—have provided a clearer understanding of the mechanisms that underlie aggressive development of prostate cancer, which in turn will aid researchers to develop better options for treatment.
If QIAGEN’s IPA is helping you make strides in your research, we would love to hear about it. Please contact us to share your story, or just to request a free trial!
Check out these recent articles citing Biomedical Genomics Workbench, a comprehensive, highly accurate NGS data analysis platform, providing researchers with a user-friendly, customizable human hereditary disease and cancer analysis solution for biomarker discovery and validation. Below are a few examples of how researchers from Pennsylvania to Japan are using Biomedical Genomics Workbench to accelerate their research.
Relaxin Reverses Inflammatory and Immune Signals in Aged Hearts
First author: Brian Martin
A team based out of the University of Pennsylvania studied the cardiovascular benefits of relaxin—a pregnancy hormone—on both young and old rats to determine its effects on the heart’s aging process. They extracted RNA and analyzed genomic changes, importing raw transcript data into Biomedical Genomics Workbench and mapping reads to the rat reference genome. The study, which ran in PLOS ONE, concluded that relaxin both alters gene transcription and suppresses inflammatory pathways and genes associated with heart failure and aging. This has therapeutic potential for cardiovascular and inflammation-related diseases, such as heart failure, diabetes and atrial fibrillation.
Comparison of Genetic Profiling of Primary Central Nervous System (CNS) Lymphoma Before and After Extra-CNS Relapse
First author: Kosuke Toyoda
In 2017, a team of Japanese scientists studied the mechanism of chemotherapy resistance in lymphomas of the CNS (central nervous system), which were previously identified as promising targets for immune checkpoint blockade therapy. They performed comprehensive genomic analysis in the hope of better understanding tumor oncogenic evolution and overcoming the immune privilege. The team compared the impact of extra-CNS relapse, using Biomedical Genomics Workbench to call variants. Their report, which ran in Blood Journal, suggested that the evolution of mutations enabled systemic disease progression with a breakthrough of immune privilege, characterized by immunological overpowering and the dysregulation of B-cell proliferation signaling.
Assessing the GeneRead SNP for Analysis of Low-Template and PCR-Inhibitory Samples
First author: Maja Sidstedt
When forensic DNA laboratories use massive parallel sequencing for human identification purposes, chances are good that the DNA samples are heterogeneous and of varying quality. SNP assays must therefore be able to handle impurities and low amounts of DNA. Using Biomedical Genomics Workbench to analyze sequencing data, a Swedish team evaluated the GeneRead Individual Identity SNP panel, which handled multiple extraction methods and withstood inhibitor solutions and was concluded to be satisfactory for casework-like samples. Read about the study, which ran in PLOS ONE in January this year.
To request your no-obligation trial of Biomedical Genomics Workbench, just click here.
Our recent Variant Analysis update includes several key features, most notably, improved data export (now completed offline to improve performance) and better handling of uploaded VCF files. The Allele Frequency Community (AFC) now features CentoMD data, with details about 155,000 sequenced individuals whose genotypes offer a more comprehensive view of population genomics. We also updated the statistics available in AFC, which contains summary statistics from public, private and users from QIAGEN’s community. These statistics are now based on more than 750,000 samples that were analyzed through our platforms—including more than 38,000 whole genomes, and more than 358,000 exome samples. The new Variant Analysis release inspired us to look at how our customers are putting it to use it in their workflows. Read on for more details—and possibly some inspiration!
Oligogenic genetic variation of neurodegenerative disease genes in 980 postmortem human brains
First author: Michael J. Keogh
The Journal of Neurology, Neurosurgery and Psychiatry recently published a study developed by an UK-based team that analyzed genetic variants of three neurodegenerative diseases in 980 postmortem human brains. They used Variant Analysis to study 49 genes known to be associated with three neurodegenerative disorders: Alzheimer’s disease (AD), Parkinson’s disease-dementia with Lewy bodies (PD-DLB), and frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS), and investigated whether synergistic interaction between two or more functional genetic variants contributed to increased likelihood of early onset. They determined that the presence of oligogenic variants did not influence the age of onset or disease severity, which they noted is an important a priori bias to guard against in future research.
Mutational landscape of radiation-associated angiosarcoma of the breast
First author: Bryan J. Thibodeau
A team of scientists from Michigan, California, and Alberta, Canada recently investigated genomic variation in biospecimens from radiation-associated breast angiosarcomas—a rare complication of radiation therapy for breast carcinoma. In their report, which was published in Oncotarget, the team mentioned using Variant Analysis to characterize variants and to investigate signaling pathways preferentially affected in radiation-association angiosarcomas. Due to the relative rarity of this type of tumor, the team recommended further investigation, using whole genome or exome sequencing, to further the discovery and confirmation of potential drug targets and to identify potential radiation-associated signatures.
Pediatric dilated cardiomyopathy‐associated LRRC10 (Leucine‐Rich Repeat–Containing 10) variant reveals LRRC10 as an auxiliary subunit of cardiac L‐type Ca2+ channels
First Author: Marites T. Woon
A group of researchers from Madison, Wisc., and Rochester, Minn. sought to further understand the genetic causes of dilated cardiomyopathy (DCM). Their report, published in the Journal of the American Heart Association, details their work and includes mention of Variant Analysis to analyze variant call format files. The team found a rare, homozygous variant in a cardiac‐specific protein, which provides evidence that variants in LRRC10 can serve as a genetic cause of DCM. This research deepens our burgeoning understanding of the condition and provides a potential link to its pathophysiology.
ARL6IP1 mutation causes congenital insensitivity to pain, acromutilation and spastic paraplegia
First Author: M. Nizon
A team from Nantes, France, reported in Clinical Genetics about their research on the role of ARL6IP1 in the pathophysiology of insensitivity to pain and spastic paraplegia, which are symptoms of hereditary sensory and autonomic neuropathies (HSAN) type II. They used Variant Analysis to generate variant annotation and interpretation analyses, enabling them to identify a homozygous variant in ARL6IP1, which they determined as a key factor in hereditary spastic paraplegia and sensorimotor neuropathy.
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