Faculty Bibliography

Biomolecular networks have already found great utility in characterizing complex biological systems arising from pairwise interactions amongst biomolecules. Here, we explore the important and hitherto neglected role of information asymmetry in the genesis and evolution of such pairwise biomolecular interactions. Information asymmetry between sender and receiver genes is identified as a key feature distinguishing early biochemical reactions from abiotic chemistry, and a driver of network topology as biomolecular systems become more complex. In this context, we review how graph theoretical approaches can be applied not only for a better understanding of various proximate (mechanistic) relations, but also, ultimate (evolutionary) structures encoded in such networks from among all types of variations they induce. Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory, whereby sender and receiver gene players accrue benefit from gene duplication, leading to a preferential attachment mode of network growth. The study of the resulting dynamics suggests many mathematical/computational problems, the majority of which are intractable yet yield to efficient approximation algorithms, when studied through an algebraic graph theoretic lens. We relegate for future work the role of other possible generalizations, additionally involving horizontal gene transfer, sexual recombination, endo-symbiosis, etc., which enrich the underlying graph theory even further.

Background and purpose: Dysfunction of the cardiac sodium channel Nav1.5 is associated with cardiac arrhythmias but therapeutic options to restore Nav1.5 are limited. Nav1.5 is transported to the cell membrane by the microtubule network and is differentially distributed around subcellular domains, with enrichment at the intercalated discs of cardiomyocytes. We have previously demonstrated that Nav1.5-based sodium current (INa) is modulated by the microtubule plus-end binding proteins CLIP-associating protein 2 (CLASP2) and End binding 1 (EB1), which are both enriched in the intercalated disc. Inhibition of Glycogen synthase kinase 3 beta (GSK3beta) by SB216763 (SB2) is known to enhance the interaction between CLASP2, EB1, and microtubules, thereby increasing microtubule recruitment and stability. We therefore hypothesise that GSK3beta inhibition by SB2 increases INa by enhancing Nav1.5 trafficking specifically to the intercalated disc.
Methods and Results: Cells were incubated with 5 M of the pharmacological GSK3beta inhibitor SB2 followed by whole-cell patch clamp measurements. In adult mouse cardiomyocytes, an increased whole-cell peak sodium current density (INa) was observed after subacute (2-4 hour) incubation with SB2, while INa kinetics remained unaffected. Macropatch experiments were performed on freshly isolated murine cardiomyocytes to investigate the effect of SB2 on INa in subcellular microdomains. These experiments revealed that SB2 specifically increased INa at the intercalated disc, while INa at the lateral membrane remained unaffected. To prove the central role of CLASP2 in these effects of SB2 on INa wholecell measurements were performed on cardiomyocytes from Clasp2-KO mice, showing that SB2 does not affect INa in the absence of CLASP2. Conclusion and perspectives: The GSK3beta inhibitor SB2 increased whole-cell peak INa in isolated murine cardiomyocytes. On the subcellular level, INa was specifically increased at the intercalated discs, while the current was unaffected at the lateral membrane of cardiomyocytes. Treatment with SB2 in cardiomyocytes lacking CLASP2 did not affect INa, showing that SB2 affects INa through CLASP2. Thus, the microtubule/EB1/CLASP2 complex constitutes a promising target for modulating INa in a microdomain-specific manner, which could be of particular relevance for diseases caused by a loss of Nav1.5 at the intercalated disc, such as arrhythmogenic right ventricular cardiomyopathy (ARVC)

Blockade of Ras activity by inhibiting its post-translational methylation catalyzed by isoprenylcysteine carboxylmethyltransferase (ICMT) has been suggested as a promising antitumor strategy. However, the paucity of inhibitors has precluded the clinical validation of this approach. In this work we report a potent ICMT inhibitor, compound 3 [UCM-1336, IC₅₀ = 2 μM], which is selective against the other enzymes involved in the post-translational modifications of Ras. Compound 3 significantly impairs the membrane association of the four Ras isoforms, leading to a decrease of Ras activity and to inhibition of Ras downstream signaling pathways. In addition, it induces cell death in a variety of Ras-mutated tumor cell lines and increases survival in an in vivo model of acute myeloid leukemia. Because ICMT inhibition impairs the activity of the four Ras isoforms regardless of its activating mutation, compound 3 surmounts many of the common limitations of available Ras inhibitors described so far. In addition, these results validate ICMT as a valuable target for the treatment of Ras-driven tumors.

Background: Nav1.5 is targeted to distinct subcellular microdomains of cardiomyocytes by the microtubule network, with sodium current being largest in the intercalated disc (ID) region. The microtubule plus-end tracking proteins End Binding 1 (EB1) and CLIP-associating protein 2 (CLASP2) are mainly located at the ID and regulate microtubule recruitment and stability. The small molecule SB216763 (SB2) acts on Glycogen synthase kinase 3 beta (GSK3beta) and is known to enhance the EB1-CLASP2 interaction, thereby increasing microtubule stability.
Objective(s): To investigate the effect of targeting EB1-CLASP2 on Nav1.5 localisation and sodium current density (INa) in subcellular microdomains.
Method(s): Patch clamp and Stochastic Optical Reconstruction Microscopy (STORM) imaging experiments were performed on human iPSC-derived cardiomyocytes (hiPSC-CMs) and freshly isolated murine ventricular cardiomyocytes.
Result(s): EB1 overexpression in hiPSC-CMs increased membrane Nav1.5 cluster density and consequently increased whole-cell INa and action potential (AP) upstroke velocity, without affecting INa kinetics or other AP parameters. Increased whole-cell INa was observed in murine cardiomyocytes after 2-4 hours of SB2 treatment (5micro M), while INa kinetics remained unaffected. Macropatch experiments revealed that SB2 specifically increased INa at the ID, while INa at the lateral membrane was unchanged. In contrast, SB2 did not affect INa or Nav1.5 cluster size or density in cardiomyocytes from mice Clasp2-deficient mice.
Conclusion(s): Targeting the plus-end tracking proteins EB1 and CLASP2 resulted in increased whole-cell peak INa in hiPSC-CMs and isolated murine cardiomyocytes. On the subcellular level, INa was specifically increased at the ID after pharmacologically enhancing the CLASP2-EB1 interaction by SB2. Treatment with SB2 in cardiomyocytes lacking CLASP2 did not affect INa or Nav1.5 distribution, demonstrating the central role for CLASP2 in the SB2-mediated effects. Thus, the microtubule-EB1-CLASP2 complex constitutes a promising target for modulating INa in a microdomain-specific manner.
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The long-term effectiveness of antibody responses relies on the development of humoral immune memory. Humoral immunity is maintained by long-lived plasma cells that secrete antigen-specific antibodies, and memory B cells that rapidly respond to antigen re-exposure by generating new plasma cells and memory B cells. Developing effective immunological memory is essential for protection against pathogens, and is the basis of successful vaccinations. IgE responses have evolved for protection against helminth parasites infections and against toxins, but IgE is also a potent mediator of allergic diseases. There has been a dramatic increase in the incidence of allergic diseases in recent decades and this has provided the impetus to study the nature of IgE antibody responses. As will be discussed in depth in this review, the IgE memory response has unique features that distinguish it from classical B cell memory.

Patients with pancreatic ductal adenocarcinoma do not benefit from checkpoint blockade. However, human tumors harbor evidence of adaptive immunity in clonally expanded T-cell populations. Immune intact modeling of human tumors identifies stromal sequestration as a mechanism of immune escape. Targeting the stroma combined with checkpoint blockade unleashes antitumor immunity.See related article by Seo et al., p. 3934.

Down syndrome (DS), a complex genetic disorder caused by chromosome 21 trisomy, is associated with mitochondrial dysfunction leading to the accumulation of damaged mitochondria. Here we report that mitophagy, a form of selective autophagy activated to clear damaged mitochondria is deficient in primary human fibroblasts derived from individuals with DS leading to accumulation of damaged mitochondria with consequent increases in oxidative stress. We identified two molecular bases for this mitophagy deficiency: PINK1/PARKIN impairment and abnormal suppression of macroautophagy. First, strongly downregulated PARKIN and the mitophagic adaptor protein SQSTM1/p62 delays PINK1 activation to impair mitophagy induction after mitochondrial depolarization by CCCP or antimycin A plus oligomycin. Secondly, mTOR is strongly hyper-activated, which globally suppresses macroautophagy induction and the transcriptional expression of proteins critical for autophagosome formation such as ATG7, ATG3 and FOXO1. Notably, inhibition of mTOR complex 1 (mTORC1) and complex 2 (mTORC2) using AZD8055 (AZD) restores autophagy flux, PARKIN/PINK initiation of mitophagy, and the clearance of damaged mitochondria by mitophagy. These results recommend mTORC1-mTORC2 inhibition as a promising candidate therapeutic strategy for Down Syndrome.

BACKGROUND/AIMS/OBJECTIVE:Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic form of kidney disease. High-throughput microarray analysis has been applied for elucidating key genes and pathways associated with ADPKD. Most genetic profiling data from ADPKD patients have been uploaded to public databases but not thoroughly analyzed. This study integrated 2 human microarray profile datasets to elucidate the potential pathways and protein-protein interactions (PPIs) involved in ADPKD via bioinformatics analysis in order to identify possible therapeutic targets. METHODS:The kidney tissue microarray data of ADPKD patients and normal individuals were searched and obtained from NCBI Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified, and enriched pathways and central node genes were elucidated using related websites and software according to bioinformatics analysis protocols. Seven DEGs were validated between polycystic kidney disease and control kidney samples by quantitative real-time polymerase chain reaction. RESULTS:Two original human microarray datasets, GSE7869 and GSE35831, were integrated and thoroughly analyzed. In total, 6,422 and 1,152 DEGs were extracted from GSE7869 and GSE35831, respectively, and of these, 561 DEGs were consistent between the databases (291 upregulated genes and 270 downregulated genes). From 421 nodes, 34 central node genes were obtained from a PPI network complex of DEGs. Two significant modules were selected from the PPI network complex by using Cytotype MCODE. Most of the identified genes are involved in protein binding, extracellular region or space, platelet degranulation, mitochondrion, and metabolic pathways. CONCLUSIONS:The DEGs and related enriched pathways in ADPKD identified through this integrated bioinformatics analysis provide insights into the molecular mechanisms of ADPKD and potential therapeutic strategies. Specifically, abnormal decorin expression in different stages of ADPKD may represent a new therapeutic target in ADPKD, and regulation of metabolism and mitochondrial function in ADPKD may become a focus of future research.

Background/UNASSIGNED:The purpose of this study is to evaluate the ability of preoperative and postoperative radiographic union scores for tibia fractures (RUST) to predict treatment success of tibia fracture nonunion. Materials and methods/UNASSIGNED:Patients presenting for operative treatment of tibia fracture nonunion were enrolled in a prospective data registry. Enrolled patients were followed at regular intervals for 12 months. Preoperative and 12 week postoperative radiographs were reviewed and scored using the RUST criteria. Postoperative time to union was determined by clinical and radiographic measures. Multivariate regressions were conducted to predict time to union using preoperative and postoperative RUST while controlling for treatment method. Receiver operating characteristic (ROC) curve was conducted to determine the accuracy of preoperative RUST in predicting failure of treatment. Results/UNASSIGNED:Sixty-eight patients with aseptic tibia fracture nonunion treated operatively were identified. Sixty-one patients achieved union. Mean preoperative RUST was 7.5 (SD 1.4). Mean postoperative RUST was 9.2 (SD 1.4). Multivariate linear regressions demonstrated that preoperative (p = 0.043) and postoperative (p = 0.007) RUST are significant predictors of time to union after tibia fracture nonunion surgery. ROC curve demonstrated preoperative RUST below 7 was a good predictor of developing persistent tibia fracture nonunion (AUC = 0.83, Sensitivity = 1.000, Specificity = 0.745). Conclusions/UNASSIGNED:RUST preoperatively and postoperatively predicts outcome after nonunion surgery. RUST can be used as part of the complete clinical picture to shape patient expectations and guide treatment.

PURPOSE/OBJECTIVE:To identify and characterize amyloid-like substance (ALS) in human and mouse oocytes and preimplantation embryos. METHODS:An experimental prospective pilot study. A total of 252 mouse oocytes and preimplantation embryos and 50 immature and in vitro matured human oocytes and parthenogenetic human embryos, from 11 consenting fertility patients, ages 18-45. Fluorescence intensity from immunofluorescent staining and data from confocal microscopy were quantified. Data were compared by one-way analysis of variance, with the least square-MEANS post-test, Pearson correlation coefficients (r), and bivariate analyses (t tests). ALS morphology was verified using transmission electron microscopy. RESULTS:Immunostaining for ALS appears throughout the zona pellucida, as well as in the cytoplasm and nucleus of mouse and human oocytes, polar bodies, and parthenogenetic embryos, and mouse preimplantation embryos. In mouse, 2-cell embryos exhibited the highest level of ALS (69000187.4 ± 6733098.07). Electron microscopy confirmed the presence of ALS. In humans, fresh germinal vesicle stage oocytes exhibited the highest level of ALS (4164.74088 ± 1573.46) followed by metaphase I and II stages (p = 0.008). There was a significant negative association between levels of ALS and patient body mass index, number of days of ovarian stimulation, dose of gonadotropin used, time between retrieval and fixation, and time after the hCG trigger. Significantly higher levels of ALS were found in patients with AMH between 1 and 3 ng/ml compared to < 1 ng/ml. CONCLUSION/CONCLUSIONS:We demonstrate for the first time the presence, distribution, and change in ALS throughout some stages of mouse and human oocyte maturation and embryonic development. We also determine associations between ALS in human oocytes with clinical characteristics.