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.
Imagine this scenario: You are working on a high profile scientific finding (for example the Nevada SARS-CoV-2 reinfection case), and you need to 1) perform a bioinformatics analysis; 2) provide detailed methods of the exact analysis for publication; 3) share those methods so that others could recreate your analysis; 4) provide publication-quality images. What’s more, you needed this all done yesterday. What do you do? Dr. Joel R. Sevinsky, Ph.D., recently found himself in this situation while working with the Nevada State Public Health Laboratory on a potential SARS-CoV-2 reinfection case (published The Lancet Infectious Diseases; access the article here). He had numerous analysis software options to choose from and decided upon QIAGEN CLC Genomics Workbench. The main reason for doing so is it satisfied all the requirements mentioned above and enabled high productivity during a time of limited bandwidth.
Dr. Sevinsky developed an analysis pipeline for SARS-CoV-2 using ARTIC amplicons and the Illumina DNA Prep library preparation kit. He had designed a workflow in QIAGEN CLC Genomics Workbench and was preparing a tutorial (access tutorial here). Given the modularity of the designed workflow, he was able to modify the pipeline in just a few minutes to accept metagenomics data as input, rather than amplicons, and perform the analysis. No coding, no command line. All he had to do was point and click in the workflow diagram, remove one step, redirect a couple of outputs, and the new pipeline was ready. When the analysis was done, he had a complete visualization of the variant differences between the two SARS-CoV-2 strains, confirming their hypothesis that this was a clear case of SARS-CoV-2 reinfection supported by genomic data. This visualization could be shared and viewed with anyone that has QIAGEN CLC Genomics Workbench installed, even without a license. Furthermore, Dr. Sevinsky and his team were able to compare the results with other bioinformatics platforms because the software allowed the export of results files in many standard open formats (.bam, .vcf and others).
According to many researchers, the most important aspect of a scientific publication is the methods section. This section should document in exact detail how an experiment and analysis were accomplished so that other scientists can replicate the findings. The bioinformatics results from Dr. Sevinsky’s analysis were accompanied by a full history of algorithms, workflows, reference files and input files, all with version documentation, used to generate the results. This detailed history was included as supplemental data in their publication.
Sometimes, especially in bioinformatics, the most detailed methods can still provide obstacles to recreating an analysis. Unless a documented workflow uses containers and workflow managers, which require significant bioinformatics expertise to maintain, getting the environment correct to recreate the analysis can be difficult. It can also be very time consuming to set up. Fortunately, the entire workflow with input data, references and parameters can be packaged in a single file, exported and shared with the scientific community. Dr. Sevinsky’s journal article will include this file as supplemental data, and for the SARS-CoV-2 tutorial mentioned above you can find a package that includes input fastq files, reference files, primer files and workflows at this resource center here.
Lastly, to get his findings published in a top-tier journal, Dr. Sevinsky and his team needed high-quality images that clearly communicated their findings. QIAGEN CLC Genomics Workbench provided advanced visualization tools that could easily be exported into editable formats for publication. Moreover, the visualization settings can be saved, so you can further refine your analysis without having to recreate the format of the final figure, which is an enormous time saver.
Overall, QIAGEN CLC Genomics Workbench allowed Dr. Sevinsky and his team to communicate their results as quickly as possible. No github sites to create, no Docker containers to manage. Just efficient analysis and publication of results.
If your scientific position utilizes NGS data and requires a lot of “getting things done”, QIAGEN CLC Genomics Workbench is an invaluable tool for your laboratory.
Ready to ramp up your NGS productivity? Take QIAGEN CLC Genomics Workbench for a spin. Start your free trial, or request a consultation 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.
