Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

ImmuneQuest: Assessment of a Video Game as a Supplement to an Undergraduate Immunology Course

The study of immunology, particularly in this day and age, is an integral aspect of the training of future biologists, especially health professionals. Unfortunately, many students lose interest in or lack true comprehension of immunology due to the jargon of the field, preventing them from gaining a true conceptual understanding that is essential to all biological learning. To that end, a new video game, ImmuneQuest, has been developed that allows undergraduate students to “be” cells in the immune system, finding and attacking pathogens, while answering questions to earn additional abilities. The ultimate goal of ImmuneQuest is to allow students to understand how the major cells in the immune system work together to fight disease, rather than focusing on them as separate entities as is more commonly done in lecture material. This work provides the first assessment of ImmuneQuest in an upper-level immunology course. Students had significant gains in learning of information presented in ImmuneQuest compared with information discussed in lecture only. Furthermore, while students found the game “frustrating” at times, they agreed that the game aided their learning and recommended it for future courses. Taken together, these results suggest that ImmuneQuest appears to be a useful tool to supplement lecture material and increase student learning and comprehension

When Do Students “Learn-to-Comprehend” Scientific Sources?: Evaluation of a Critical Skill in Undergraduates Progressing through a Science Major

In response to the publication of <em>Vision and Change</em>, the biology department at Elmhurst College revised our curriculum to better prepare students for a career in science with the addition of various writing assignments in every course.<em> </em>One commonality among all of the assignments is the ability to comprehend and critically evaluate scientific literature to determine relevancy and possible future research. Several previous reports have analyzed specific methodologies to improve student comprehension of scientific writing and critical thinking skills, yet none of these examined student growth over an undergraduate career. In this study, we hypothesized upper-level students would be better able to comprehend and critically analyze scientific literature than introductory biology majors. Biology students enrolled in an introductory (200-level), mid- (300-level), or late-career (400-level) course were tasked with reading and responding to questions regarding a common scientific article and rating their comfort and confidence in reading published literature. As predicted, upper-level (mid- and late-career) students showed increases in comprehension and critical analysis relative to their first-year peers. Interestingly, we observed that upper-level students read articles differently than introductory students, leading to significant gains in understanding and confidence. However, the observed gains were modest overall, indicating that further pedagogical change is necessary to improve student skills and confidence in reading scientific articles while fulfilling the <em>Vision and Change </em>recommendations

A one-year introductory biology majors’ lab sequence incorporating Vision & Change

The introduction of Vision and Change by AAAS and the recommendation that biology departments amend their curricula to focus on key concepts and skills necessary for graduates has led to a re-envisioning of introductory curricula across the nation.  Many of the “standard” biology textbooks have realigned their focus with Vision and Change while new texts have emerged that completely revise how we teach introductory biology majors.  One such textbook is Integrating Concepts in Biology (ICB) by Campbell, Heyer, and Paradise.  Many departments, including ours, have adopted this text as a novel way to teach biology majors, focusing on active-learning, the scientific method, and specifically, understanding data.  However, with all of these revisions to biology textbooks, there have been no revisions or insights into corresponding labs for a typical 1-year introductory course sequence.  Here we provide a description of our 1-year lab sequence, emphasizing the scientific method and novel research, with a focus on the 5 “Big Ideas” presented in ICB.  By removing the “cookbook” labs typical of most introductory labs, we found that this system better emphasized the focus of Vision and Change and, concomitantly, students appeared to enjoy the lab experience and see the relevance to class material better compared to previous years.  We believe that this lab organization is a simple design that is not resource-intensive and can be utilized at schools of any size or budget.

Aberrant DNMT3B7 expression correlates to tissue type, stage, and survival across cancers.

Cancer cells are known for aberrant methylation patterns leading to altered gene expression and tumor progression. DNA methyltransferases (DNMTs) are responsible for regulating DNA methylation in normal cells. However, many aberrant versions of DNMTs have been identified to date and their role in cancer continues to be elucidated. It has been previously shown that an aberrant version of a de novo methylase, DNMT3B7, is expressed in many cancer cell lines and has a functional role in the progression of breast cancer, neuroblastoma, and lymphoma. It is clear that DNMT3B7 is important to tumor development in vitro and in vivo, but it is unknown if expression of the transcript in all of these cell lines translates to relevant clinical results. In this study, a bioinformatics approach was utilized to test the hypothesis that DNMT3B7 expression corresponds to tumor progression in patient samples across cancer types. Gene expression and clinical data were obtained from the Genomic Data Commons for the 33 cancer types available and analyzed for DNMT3B7 expression with relation to tissue type in matched and unmatched samples, staging of tumors, and patient survival. Here we present the results of this analysis indicating a role for DNMT3B7 in tumor progression of many additional cancer types. Based on these data, future in vitro and in vivo studies can be prioritized to examine DNMT3B7 in cancer and, hopefully, develop novel therapeutics to target this aberrant transcript across multiple tumor types

<i>DNMT3B7</i> Expression Promotes Tumor Progression to a More Aggressive Phenotype in Breast Cancer Cells

Epigenetic changes, such as DNA methylation, have been shown to promote breast cancer progression. However, the mechanism by which cancer cells acquire and maintain abnormal DNA methylation is not well understood. We have previously identified an aberrant splice form of a DNA methyltransferase, DNMT3B7, expressed in virtually all cancer cell lines but at very low levels in normal cells. Furthermore, aggressive MDA-MB-231 breast cancer cells have been shown to express increased levels of DNMT3B7 compared to poorly invasive MCF-7 cells, indicating that DNMT3B7 may have a role in promoting a more invasive phenotype. Using data gathered from The Cancer Genome Atlas, we show that DNMT3B7 expression is increased in breast cancer patient tissues compared to normal tissue. To determine the mechanism by which DNMT3B7 was functioning in breast cancer cells, two poorly invasive breast cancer cell lines, MCF-7 and T-47D, were stably transfected with a DNMT3B7 expression construct. Expression of DNMT3B7 led to hypermethylation and down-regulation of E-cadherin, altered localization of β-catenin, as well as increased adhesion turnover, cell proliferation, and anchorage-independent growth. The novel results presented in this study suggest a role for DNMT3B7 in the progression of breast cancer to a more aggressive state and the potential for future development of novel therapeutics.</p

Polo-Like Kinase 4 (PLK4) Is Overexpressed in Central Nervous System Neuroblastoma (CNS-NB)

Neuroblastoma (NB) is the most common extracranial solid tumor in pediatrics, with rare occurrences of primary and metastatic tumors in the central nervous system (CNS). We previously reported the overexpression of the polo-like kinase 4 (PLK4) in embryonal brain tumors. PLK4 has also been found to be overexpressed in a variety of peripheral adult tumors and recently in peripheral NB. Here, we investigated PLK4 expression in NBs of the CNS (CNS-NB) and validated our findings by performing a multi-platform transcriptomic meta-analysis using publicly available data. We evaluated the PLK4 expression by quantitative real-time PCR (qRT-PCR) on the CNS-NB samples and compared the relative expression levels among other embryonal and non-embryonal brain tumors. The relative PLK4 expression levels of the NB samples were found to be significantly higher than the non-embryonal brain tumors (p-value &lt; 0.0001 in both our samples and in public databases). Here, we expand upon our previous work that detected PLK4 overexpression in pediatric embryonal tumors to include CNS-NB. As we previously reported, inhibiting PLK4 in embryonal tumors led to decreased tumor cell proliferation, survival, invasion and migration in vitro and tumor growth in vivo, and therefore PLK4 may be a potential new therapeutic approach to CNS-NB

DNMT3B7 expression promotes tumor progression to a more aggressive phenotype in breast cancer cells.

Epigenetic changes, such as DNA methylation, have been shown to promote breast cancer progression. However, the mechanism by which cancer cells acquire and maintain abnormal DNA methylation is not well understood. We have previously identified an aberrant splice form of a DNA methyltransferase, DNMT3B7, expressed in virtually all cancer cell lines but at very low levels in normal cells. Furthermore, aggressive MDA-MB-231 breast cancer cells have been shown to express increased levels of DNMT3B7 compared to poorly invasive MCF-7 cells, indicating that DNMT3B7 may have a role in promoting a more invasive phenotype. Using data gathered from The Cancer Genome Atlas, we show that DNMT3B7 expression is increased in breast cancer patient tissues compared to normal tissue. To determine the mechanism by which DNMT3B7 was functioning in breast cancer cells, two poorly invasive breast cancer cell lines, MCF-7 and T-47D, were stably transfected with a DNMT3B7 expression construct. Expression of DNMT3B7 led to hypermethylation and down-regulation of E-cadherin, altered localization of β-catenin, as well as increased adhesion turnover, cell proliferation, and anchorage-independent growth. The novel results presented in this study suggest a role for DNMT3B7 in the progression of breast cancer to a more aggressive state and the potential for future development of novel therapeutics

Expression of <i>DNMT3B7</i> in normal and tumor patient samples.

<p>Representative graphs of 6 different tumor samples showing relative <i>DNMT3B7</i> expression, as measured by reads per kilobase per million (RPKM) or RNA-Seq by Expectation Maximization (RSEM), in unmatched normal and tumor tissues in (A) HNSC, (B) UCEC, and (C) THCA. Expression of <i>DNMT3B7</i> in matched patient samples is shown in (D) LIHC and (E) LUAD. <i>DNMT3B7</i> expression in primary and recurrent tissues in (F) LGG (<i>p</i> = 0.005) was assessed when normal samples were not available. All samples shown here were significant, <i>p</i> < 0.001, unless otherwise stated.</p