QIAGEN Digital Insights Publication Roundup (Winter 2019/2020)

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QIAGEN Digital Insights

QIAGEN Digital Insights Publication Roundup (Winter 2019/2020)

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. 

Selected publications:


QIAGEN IPA


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.

QIAGEN CLC


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.

QIAGEN OmicSoft Array Suite and Lands


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.