The art and science of selecting graduate students in the biomedical sciences: Performance in doctoral study of the foundational sciences.

The goal of this study was to investigate associations between admissions criteria and performance in Ph.D. programs at Boston University School of Medicine. The initial phase of this project examined student performance in the classroom component of a newly established curriculum named "Foundations in Biomedical Sciences (FiBS)". Quantitative measures including undergraduate grade point average (GPA), graduate record examination (GRE; a standardized, computer-based test) scores for the verbal (assessment of test takers' ability to analyze, evaluate, and synthesize information and concepts provided in writing) and quantitative (assessment of test takers' problem-solving ability) components of the examination, previous research experience, and competitiveness of previous research institution were used in the study. These criteria were compared with competencies in the program defined as students who pass the curriculum as well as students categorized as High Performers. These data indicated that there is a significant positive correlation between FiBS performance and undergraduate GPA, GRE scores, and competitiveness of undergraduate institution. No significant correlations were found between FiBS performance and research background. By taking a data-driven approach to examine admissions and performance, we hope to refine our admissions criteria to facilitate an unbiased approach to recruitment of students in the life sciences and to share our strategy to support similar goals at other institutions.

Vertical integration of biochemistry and clinical medicine using a near-peer learning model.

Vertical integration has been extensively implemented across medical school curricula but has not been widely attempted in the field of biochemistry. We describe a novel curricular innovation in which a near-peer learning model was used to implement vertical integration in our medical school biochemistry course. Senior medical students developed and facilitated a case-based small group session for first year biochemistry students. Students were surveyed before and after the session on their attitudes about biochemistry, as well as the effectiveness of the session. Prior to the session, the students believed biochemistry was more important to understanding the basic science of medicine than it was to understanding clinical medicine or becoming a good physician. The session improved students' attitudes about the importance of biochemistry in clinical medicine, and after the session they now believe that understanding biochemistry is equally important to the basic sciences as clinical medicine. Students would like more sessions and believe the senior student facilitators were knowledgeable and effective teachers. The facilitators believe they improved their teaching skills. This novel combination of near-peer learning and vertical integration in biochemistry provided great benefit to both first year and senior medical students, and can serve as a model for other institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):507-516, 2016.

Leading change: curriculum reform in graduate education in the biomedical sciences.

The Division of Graduate Medical Sciences at the Boston University School of Medicine houses numerous dynamic graduate programs. Doctoral students began their studies with laboratory rotations and classroom training in a variety of fundamental disciplines. Importantly, with 15 unique pathways of admission to these doctoral programs, there were also 15 unique curricula. Departments and programs offered courses independently, and students participated in curricula that were overlapping combinations of these courses. This system created curricula that were not coordinated and that had redundant course content as well as content gaps. A partnership of key stakeholders began a curriculum reform process to completely restructure doctoral education at the Boston University School of Medicine. The key pedagogical goals, objectives, and elements designed into the new curriculum through this reform process created a curriculum designed to foster the interdisciplinary thinking that students are ultimately asked to utilize in their research endeavors. We implemented comprehensive student and peer evaluation of the new Foundations in Biomedical Sciences integrated curriculum to assess the new curriculum. Furthermore, we detail how this process served as a gateway toward creating a more fully integrated graduate experience, under the umbrella of the Program in Biomedical Sciences.

SHP-2/PTPN11 mediates gliomagenesis driven by PDGFRA and INK4A/ARF aberrations in mice and humans.

Recent collaborative efforts have subclassified malignant glioblastomas into 4 clinical relevant subtypes based on their signature genetic lesions. Platelet-derived growth factor receptor α (PDGFRA) overexpression is concomitant with a loss of cyclin-dependent kinase inhibitor 2A (CDKN2A) locus (encoding P16INK4A and P14ARF) in a large number of tumors within one subtype of glioblastomas. Here we report that activation of PDGFRα conferred tumorigenicity to Ink4a/Arf-deficient mouse astrocytes and human glioma cells in the brain. Restoration of p16INK4a but not p19ARF suppressed PDGFRα-promoted glioma formation. Mechanistically, abrogation of signaling modules in PDGFRα that lost capacity to bind to SHP-2 or PI3K significantly diminished PDGFRα-promoted tumorigenesis. Furthermore, inhibition of SHP-2 by shRNAs or pharmacological inhibitors disrupted the interaction of PI3K with PDGFRα, suppressed downstream AKT/mTOR activation, and impaired tumorigenesis of Ink4a/Arf-null cells, whereas expression of an activated PI3K mutant rescued the effect of SHP-2 inhibition on tumorigenicity. PDGFRα and PDGF-A are coexpressed in clinical glioblastoma specimens, and such co-expression is linked with activation of SHP-2/AKT/mTOR signaling. Together, our data suggest that in glioblastomas with Ink4a/Arf deficiency, overexpressed PDGFRα promotes tumorigenesis through the PI3K/AKT/mTOR-mediated pathway regulated by SHP-2 activity. These findings functionally validate the genomic analysis of glioblastomas and identify SHP-2 as a potential target for treatment of glioblastomas.

Sweet cues: How heparan sulfate modification of fibronectin enables growth factor guided migration of embryonic cells.

Growth factors regulate a diverse array of cellular functions including proliferation, survival, movement, and the ability to do this often involves interactions with the extracellular matrix (ECM) and particularly heparan sulfate proteoglycans (HSPGs). HSPGs have been shown to sequester growth factors, and to act as growth factor co-receptors or receptors themselves. Recent studies, however, have revealed a new role for HSPGs in mediating the interactions of growth factors with the ECM. Specifically, heparan sulfate has been shown to modulate fibronectin structure to reveal previously masked growth factor binding sites. In vivo, this mechanism appears to control the guidance of migrating cells during embryonic development as HSPG-modification of fibronectin enables direct platelet derived growth factor-fibronectin interactions necessary for this process. A model based on this observation is discussed here as well as the possibility that other growth factors/morphogens utilize similar mechanisms involving fibronectin or additional ECM proteins.

PDGF-A interactions with fibronectin reveal a critical role for heparan sulfate in directed cell migration during Xenopus gastrulation.

Platelet-derived growth factor (PDGF) signaling is essential for processes involving cell motility and differentiation during embryonic development in a wide variety of organisms including the mouse, frog, zebrafish, and sea urchin. In early Xenopus laevis embryos, PDGF-AA provides guidance cues for the migration of anterior mesendoderm cells as they move across a fibronectin-rich extracellular matrix. The long form of PDGF-A includes a positively charged carboxyl-terminal retention motif that can interact with the extracellular matrix and heparan sulfate proteoglycans (HSPGs). In this study we demonstrate that PDGF-AA binds directly to fibronectin and that this association is greatly enhanced by heparin. The PDGF-AA-fibronectin binding occurs across a broad range of pHs (5.5-9), which is significant because the PDGF-guided migration of Xenopus mesendoderm cells occurs under basic extracellular conditions (pH 8.4). We further demonstrate that endogenous HSPG's are required for the PDGF-AA-guided mesendoderm movement, suggesting an in vivo role for HSPGs in mediating the interaction between PDGF-AA and fibronectin.

Threonine 393 of beta-catenin regulates interaction with Axin.

CK2 is a regulatory kinase implicated in embryonic development and in cancer. Among the CK2 substrates is beta-catenin, a protein with dual function in Wnt signaling and cell adhesion. Previously, we reported that CK2 activity is required for beta-catenin stability and we identified threonine (T) 393 as a major CK2 phosphorylation site in beta-catenin. However, it is not known whether phosphorylation at T393 increases beta-catenin stability and if so, what is the mechanism. In this study we investigate the molecular mechanism of beta-catenin stabilization through phosphorylation at T393. We found that pseudophosphorylation of beta-catenin at T393 resulted in a stable activated form of beta-catenin with decreased affinity for Axin in vitro. This phosphomimetic mutant also displayed decreased regulation by Axin in vivo in a bioassay in Xenopus laevis embryos. In contrast, the binding of T393 pseudophosphorylated beta-catenin to E-cadherin was unaffected. Further analysis showed that pseudophosphorylation at T393 did not prevent beta-catenin phosphorylation by GSK3beta. Interestingly, we found that in the presence of pseudophophorylated beta-catenin and another activated form of beta-catenin, the recruitment of GSK3beta to Axin is enhanced. These findings indicate that phosphorylation of T393 by CK2 may affect the stability of beta-catenin through decreased binding to Axin. In addition, the increased recruitment of GSK3beta to the destruction complex in the presence of activated beta-catenin mutants could be a feedback mechanism to suppress overactive Wnt signaling.

Apoptosis regulates notochord development in Xenopus.

The notochord is the defining characteristic of the chordate embryo and plays critical roles as a signaling center and as the primitive skeleton. In this study we show that early notochord development in Xenopus embryos is regulated by apoptosis. We find apoptotic cells in the notochord beginning at the neural groove stage and increasing in number as the embryo develops. These dying cells are distributed in an anterior to posterior pattern that is correlated with notochord extension through vacuolization. In axial mesoderm explants, inhibition of this apoptosis causes the length of the notochord to approximately double compared to controls. In embryos, however, inhibition of apoptosis decreases the length of the notochord and it is severely kinked. This kinking also spreads from the anterior with developmental stage such that, by the tadpole stage, the notochord lacks any recognizable structure, although notochord markers are expressed in a normal temporal pattern. Extension of the somites and neural plate mirrors that of the notochord in these embryos, and the somites are severely disorganized. These data indicate that apoptosis is required for normal notochord development during the formation of the anterior-posterior axis, and its role in this process is discussed.

Migrating anterior mesoderm cells and intercalating trunk mesoderm cells have distinct responses to Rho and Rac during Xenopus gastrulation.

Rho GTPases have been shown recently to be important for cell polarity and motility of the trunk mesoderm during gastrulation in Xenopus embryos. This work demonstrated that Rho and Rac have both distinct and overlapping roles in regulating cell shape, and the dynamic properties, polarity, and type of protrusive activity of these cells. Overexpression of activated or inhibitory versions of these GTPases also disrupts development of the head in Xenopus embryos. In this study, we have undertaken a detailed analysis of Rho and Rac function in migrating anterior mesendoderm cells. Scanning electron micrographs of these cells in situ revealed that their normal shingle arrangement is disrupted and both the cells and their lamellipodia are disoriented. Anterior mesendoderm explants plated on their natural blastocoel roof matrix, however, still migrated towards the animal pole, although the tendency to move in this direction is reduced compared to controls. Analysis of a number of parameters in time-lapse recordings of dissociated cells indicated that Rho and Rac also have both distinct and overlapping roles in the motility of the prospective head mesoderm; however, their effects differ to those previously seen in the trunk mesoderm. Both GTPases appear to modulate cell polarization, migration, and protrusive activity. Rho alone, however, regulates the retraction of the lagging edge of the cell. We propose that within the gastrulating Xenopus embryo, two types of mesoderm cells that undergo different motilities have distinct responses to Rho GTPases.

A role for CK2alpha/beta in Xenopus early embryonic development.

CK2 is expressed widely in early embryonic development in several animal models, however its developmental role is unclear. One of the substrates of CK2 that is important in embryonic development is beta-catenin, the transcriptional co-activator of the canonical Wnt signaling pathway. This pathway has been implicated in diverse aspects of embryonic development, including one of the earliest events in embryonic development, the establishment of the dorso-ventral embryonic axis. In Xenopus laevis, dorso-ventral axis formation is dependent upon stabilization of beta-catenin in the future dorsal side of the embryo. Since CK2 phosphorylation of beta-catenin stabilizes it, we hypothesized that CK2 might be critical to upregulation of beta-catenin in Xenopus embryos and to the process of axis establishment. Our results demonstrate that CK2 is required for dorsal axis formation and is for normal upregulation of Wnt signaling genes and targets. Thus, CK2 is a regulator of endogenous axis formation in vertebrates.

Distinct effectors of platelet-derived growth factor receptor-alpha signaling are required for cell survival during embryogenesis.

Platelet-derived growth factor receptor (PDGFR) signaling is essential for normal embryonic development in many organisms, including frog, mouse, zebrafish, and sea urchin. The mode of action of PDGFR signaling during early development is poorly understood, however, mostly because inhibition of signaling through either the PDGFRalpha or PDGFRbeta is embryonic lethal. In Xenopus embryos, disruption of PDGFRalpha signaling causes migrating anterior mesoderm cells to lose direction and undergo apoptosis through the mitochondrial pathway. To understand the mechanism of PDGFRalpha function in this process, we have analyzed all known effector-binding sites in vivo. By using a chemical inducer of dimerization to activate chimera PDGFRalphas, we have identified a role for phospholipase Cgamma (PLCgamma) in protecting cells from death. PDGFRalpha-mediated cell survival requires PLCgamma and phosphatidylinositol 3-kinase signaling, and that PDGFRalpha with binding sites for these two signaling factors is sufficient for this activity. Other effectors of PDGFRalpha signaling, Shf, SHP-2, and Crk, are not required for this process. Thus, our findings show that PDGFRalpha signaling through PLCgamma and phosphatidylinositol 3-kinase has a protective role in preventing apoptosis in early development. Furthermore, we demonstrate that small molecule inducers of dimerization provide a powerful system to manipulate receptor function in developing embryos.

Protein kinase CK2 is required for dorsal axis formation in Xenopus embryos.

Dorsal axis formation in Xenopus embryos is dependent upon asymmetrical localization of beta-catenin, a transducer of the canonical Wnt signaling pathway. Recent biochemical experiments have implicated protein kinase CK2 as a regulator of members of the Wnt pathway including beta-catenin. Here, we have examined the role of CK2 in dorsal axis formation. CK2 was present in the developing embryo at an appropriate time and place to participate in dorsal axis formation. Overexpression of mRNA encoding CK2 in ventral blastomeres was sufficient to induce a complete ectopic axis, mimicking Wnt signaling. A kinase-inactive mutant of CK2alpha was able to block ectopic axis formation induced by XWnt8 and beta-catenin and was capable of suppressing endogenous axis formation when overexpressed dorsally. Taken together, these studies demonstrate that CK2 is a bona fide member of the Wnt pathway and has a critical role in the establishment of the dorsal embryonic axis.

Guidance of mesoderm cell migration in the Xenopus gastrula requires PDGF signaling.

In vertebrates, PDGFA and its receptor, PDGFRalpha, are expressed in the early embryo. Impairing their function causes an array of developmental defects, but the underlying target processes that are directly controlled by these factors are not well known. We show that in the Xenopus gastrula, PDGFA/PDGFRalpha signaling is required for the directional migration of mesodermal cells on the extracellular matrix of the blastocoel roof. Blocking PDGFRalpha function in the mesoderm does not inhibit migration per se, but results in movement that is randomized and no longer directed towards the animal pole. Likewise, compromising PDGFA function in the blastocoel roof substratum abolishes directionality of movement. Overexpression of wild-type PDGFA, or inhibition of PDGFA both lead to randomized migration, disorientation of polarized mesodermal cells, decreased movement towards the animal pole, and reduced head formation and axis elongation. This is consistent with an instructive role for PDGFA in the guidance of mesoderm migration.

The mitochondrial-apoptotic pathway is triggered in Xenopus mesoderm cells deprived of PDGF receptor signaling during gastrulation.

Platelet-derived growth factor receptor (PDGFR) signaling is required for normal gastrulation in Xenopus laevis. Embryos deprived of PDGFR signaling develop with a range of gastrulation-specific defects including spina bifida, shortened anteroposterior axis, and reduced anterior structures. These defects arise because the involuting mesoderm fails to move appropriately. In this study, we determine that inhibition of PDGFR signaling causes prospective head mesoderm cells to appear in the blastocoel cavity at the onset of gastrulation, stage 10. These aberrant cells undergo apoptosis via the caspase 3 pathway at an embryonic checkpoint called the early gastrula transition (EGT). They are TUNEL-positive and have increased levels of caspase 3 activity compared to control embryos. Apoptotic death of these mesoderm cells can be prevented by co-injection of mRNA encoding Bcl-2 or by injection of either a general caspase inhibitor or a caspase 3-specific inhibitor. Prevention of cell death, however, is not sufficient to rescue gastrulation defects in these embryos. Based on these data, we propose that PDGFR signaling is necessary for survival of prospective head mesoderm cells, and also plays an essential role in the control of their cell movement during gastrulation.

Distinct functions of Rho and Rac are required for convergent extension during Xenopus gastrulation.

We have undertaken the first detailed analysis of Rho GTPase function during vertebrate development by analyzing how RhoA and Rac1 control convergent extension of axial mesoderm during Xenopus gastrulation. Monitoring of a number of parameters in time-lapse recordings of mesoderm explants revealed that Rac and Rho have both distinct and overlapping roles in regulating the motility of axial mesoderm cells. The cell behaviors revealed by activated or inhibitory versions of these GTPases in native tissue were clearly distinct from those previously documented in cultured fibroblasts. The dynamic properties and polarity of protrusive activity, along with lamellipodia formation, were controlled by the two GTPases operating in a partially redundant manner, while Rho and Rac contributed separately to cell shape and filopodia formation. We propose that Rho and Rac operate in distinct signaling pathways that are integrated to control cell motility during convergent extension.