CLEC11A methylation is correlated to AML subtypes and cytogenetic risk factors but not patient demographics.

Acute myeloid leukemia (AML) is an aggressive and lethal cancer of the blood, which leads to the death of over 11,000 patients in the United States each year. Research on identifying, characterizing, and treating AML is crucial in the fight against this deadly disease. Recent studies have examined the role of CLEC11A in cancer, including AML. However, there have been conflicting reports related to tumor progression and survival. Because survival is based on a variety of factors, including classification of the tumor, genetic risk factors, and demographics, it is imperative that we determine what role CLEC11A may have in cancer survival. Therefore, utilizing data from the Genomic Data Commons, we analyzed CLEC11A methylation in 108 AML patients compared to FAB classification, cytogenetic risk factors, age, race, and gender. Our results show statistically significant correlations between methylation of CLEC11A and FAB classification as well as poor genetic risk factors. However, no difference was observed in CLEC11A methylation when compared to demographic data. Our results, matched with a known biological function of CLEC11A in early hematopoiesis, indicate that CLEC11A may be an important marker for AML diagnosis and prognosis and provide relevant data in the ongoing search for novel therapeutics to improve AML survival.

CURE in a Box: an Online CURE for Introductory Biology Majors That Incorporates Vision and Change.

Course-based undergraduate research experiences (CUREs) help fulfill the recommendation of Vision and Change for biology curricula to focus on key concepts and skills to better prepare students for careers in the sciences. However, the COVID-19 pandemic has forced many schools to move instruction online, highlighting the dearth of resources available for offering a CURE for introductory biology outside of the traditional laboratory-based setting. Here, we present a revision of our first-semester General Biology laboratory for a synchronous online setting where students perform a research-based wet lab component at home using an affordable preassembled kit while still meeting the CURE learning objectives. This template can be utilized by other colleges and universities that are looking to offer a safe, reliable, and affordable CURE in their introductory biology courses whether in a virtual or face-to-face environment.

Science Bootcamp Goes Virtual: a Compressed, Interdisciplinary Online CURE Promotes Psychosocial Gains in STEM Transfer Students.

Course-based undergraduate research experiences (CUREs) are well-documented as high-impact practices that can broaden participation and success in STEM. Drawing primarily from a community of practice theoretical framework, we previously developed an interdisciplinary CURE course (Science Bootcamp) for STEM majors focused entirely on the scientific process. Among first-year students, Science Bootcamp leads to psychosocial gains and increased retention. In the current study, we test whether an online Science Bootcamp also improved outcomes for STEM transfer students-a group that faces "transfer shock," which can negatively impact GPA, psychosocial outcomes, and retention. To this end, we redesigned Science Bootcamp to a 2-week course for STEM transfer students to complete prior to beginning the fall semester at our 4-year institution. Due to the COVID-19 pandemic, the course was conducted in an entirely virtual format, using primarily synchronous instruction. Despite the course being virtual, the diverse group of STEM majors worked in small groups to conduct rigorous, novel empirical research projects from start to finish, even presenting their results in a poster symposium. Assessment data confirmed the compressed, online Science Bootcamp contained key CURE components-opportunities for collaboration, discovery and relevance, and iteration-and that students were highly satisfied with the course. Moreover, in line with our hypothesis, STEM transfer students who participated in the online Science Bootcamp experienced a range of psychosocial gains (e.g., belonging to STEM). In sum, these findings suggest our online Science Bootcamp promotes positive STEM outcomes, representing a highly flexible and affordable CURE that can be scaled for use at institutions of any size.

E-Cadherin, NFATC3, and PLP2 Are Differentially Methylated in Multiple Cancers.

It is well documented that cancer cells have abnormal methylation patterns often caused by faulty methylating machinery. Specifically, E-cadherin, NFATC3, and PLP2 are 3 genes known to be aberrantly methylated in cancer cells. These genes are well documented for their role in signaling pathways involved with cell proliferation, adhesion, migration, and other signs of tumor progression. Therefore, changes in gene expression of CDH1, NFATC3, and PLP2 due to aberrant methylation can lead to profound changes in cellular function and tumor formation. In order to ensure that previous in vitro and in vivo methylation studies match what is observed in the clinic, we utilized a bioinformatics approach to complete an extensive analysis of methylation patterns of these 3 genes, analyzing over 5000 patient samples, across all cancers for which both normal and tumor tissues were available. Specifically, we analyzed overall and site-specific methylation patterns, at CpG islands and shores, of all 3 genes across 14 cancer types. Furthermore, we compared these methylation levels in normal and tumor samples of both matched and unmatched patient samples in order to determine any differences between groups. Finally, we examined whether an aberrant DNA methyltransferase, DNMT3B7, known to be expressed in cancer cells and to alter methylation patterns in vitro correlated with altered overall and site-specific methylation of CDH1, NFATC3, and PLP2 in these patient samples. Our results indicate that methylation patterns of CDH1 and NFATC3 were unexpectedly varied across tumors, contrary to previous studies performed in vitro, while PLP2 showed the expected hypomethylation pattern in tumor tissues. We also observed some correlation between DNMT3B7 expression and methylation patterns of these genes, but patterns were inconsistent. Taken together, these results emphasize the necessity for in vivo and patient studies rather than a complete reliance on in vitro data and provide multiple areas of future research.

Does Repetition Matter? Analysis of Biology Majors' Ability to Comprehend Journal Articles Across a Major.

The ability to read and critically analyze the primary literature is a core skill necessary for future success in scientific fields. While many studies have described methodologies to teach journal reading, no studies examine how much practice and repetition is required before students learn how to comprehend a journal article. Here we assessed student journal reading and comprehension throughout an undergraduate biology major, analyzing students in six upper-level elective courses, some of which had no journal reading requirements while others had extensive requirements built into the course. We hypothesized that there would be a strong correlation between number of articles read in a semester and student ability to comprehend the articles, as well as their comfort and confidence with journal reading. Surprisingly, we found that the number of articles required for a class did not affect overall student reading comprehension and critical thinking even though students self-assessed that they gained comfort and confidence with articles as the number increased. Instead, we found that sophomore students in their first upper-level biology course showed significant gains in learning when the course activities include journal article readings. After this initial gain, there were no significant learning gains in future years, no matter the number of journals required in the course. Together, the results shown here indicate that it is not necessary to revise an entire curriculum to improve students' journal reading and critical thinking skills. Instead, early intervention and exposure to critical journal article reading is most important for this skill development.

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 have led to a re-envisioning of introductory curricula across the nation. Many of the "standard" biology text books 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 five "Big Ideas" presented in ICB. By removing the "cookbook" labs typical of most introductory laboratory courses, we found that this system better emphasized the focus of Vision and Change and, concomitantly, student appeared to enjoy the lab sequence 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.

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 < 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.

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.

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 Vision and Change, 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. 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 Vision and Change recommendations.

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 ß-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.

Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma.

Epigenetic changes in pediatric neuroblastoma may contribute to the aggressive pathophysiology of this disease, but little is known about the basis for such changes. In this study, we examined a role for the DNA methyltransferase DNMT3B, in particular, the truncated isoform DNMT3B7, which is generated frequently in cancer. To investigate if aberrant DNMT3B transcripts alter DNA methylation, gene expression, and phenotypic character in neuroblastoma, we measured DNMT3B expression in primary tumors. Higher levels of DNMT3B7 were detected in differentiated ganglioneuroblastomas compared to undifferentiated neuroblastomas, suggesting that expression of DNMT3B7 may induce a less aggressive clinical phenotype. To test this hypothesis, we investigated the effects of enforced DNMT3B7 expression in neuroblastoma cells, finding a significant inhibition of cell proliferation in vitro and angiogenesis and tumor growth in vivo. DNMT3B7-positive cells had higher levels of total genomic methylation and a dramatic decrease in expression of the FOS and JUN family members that comprise AP1 transcription factors. Consistent with an established antagonistic relationship between AP1 expression and retinoic acid receptor activity, increased differentiation was seen in the DNMT3B7-expressing neuroblastoma cells following treatment with all-trans retinoic acid (ATRA) compared to controls. Our results indicate that DNMT3B7 modifies the epigenome in neuroblastoma cells to induce changes in gene expression, inhibit tumor growth, and increase sensitivity to ATRA.