Donnelly Centre for Cellular and Biomolecular Research

PubMed

Recent Publications

Global Genetic Networks and the Genotype-to-Phenotype Relationship.

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Global Genetic Networks and the Genotype-to-Phenotype Relationship.

Cell. 2019 Mar 21;177(1):85-100

Authors: Costanzo M, Kuzmin E, van Leeuwen J, Mair B, Moffat J, Boone C, Andrews B

Abstract
Genetic interactions identify combinations of genetic variants that impinge on phenotype. With whole-genome sequence information available for thousands of individuals within a species, a major outstanding issue concerns the interpretation of allelic combinations of genes underlying inherited traits. In this Review, we discuss how large-scale analyses in model systems have illuminated the general principles and phenotypic impact of genetic interactions. We focus on studies in budding yeast, including the mapping of a global genetic network. We emphasize how information gained from work in yeast translates to other systems, and how a global genetic network not only annotates gene function but also provides new insights into the genotype-to-phenotype relationship.

PMID: 30901552 [PubMed - in process]



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Cell competition during reprogramming gives rise to dominant clones.

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Cell competition during reprogramming gives rise to dominant clones.

Science. 2019 Mar 21;:

Authors: Shakiba N, Fahmy A, Jayakumaran G, McGibbon S, David L, Trcka D, Elbaz J, Puri MC, Nagy A, van der Kooy D, Goyal S, Wrana JL, Zandstra PW

Abstract
The ability to generate induced pluripotent stem cells from differentiated cell types has enabled researchers to engineer cell states. Although studies have identifed molecular networks that reprogram cells to pluripotency, the cellular dynamics of these processes remain poorly understood. Here, by combining cellular barcoding, mathematical modelling, and lineage tracing approaches, we demonstrate that reprogramming dynamics in heterogeneous populations are driven by dominant "elite" clones. Clones arise a priori from a population of poised mouse embryonic fibroblasts (MEFs) derived from Wnt1-expressing cells that may represent a neural crest population. This work highlights the importance of cellular dynamics in fate programming outcomes and uncovers cell competition as a mechanism by which cells with context-specific eliteness emerge to occupy and dominate the reprogramming niche.

PMID: 30898844 [PubMed - as supplied by publisher]



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A Hyaluronan/Methylcellulose-Based Hydrogel for Local Cell and Biomolecule Delivery to the Central Nervous System.

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A Hyaluronan/Methylcellulose-Based Hydrogel for Local Cell and Biomolecule Delivery to the Central Nervous System.

Brain Res Bull. 2019 Mar 18;:

Authors: Ho MT, Teal CJ, Shoichet MS

Abstract
Regenerative medicine strategies rely on exogenous cell transplantation and/or endogenous cell stimulation. Biomaterials can help to increase the regenerative potential of cells and biomolecules by controlling transplanted cell fate and provide a local, sustained release of biomolecules. In this review, we describe the use of a hyaluronan/methylcellulose (HAMC)-based hydrogel as a delivery vehicle to the brain, spinal cord, and retina to promote cellular survival and tissue repair. We discuss various controlled release strategies to prolong the delivery of factors for neuroprotection. The versatility of this hydrogel for a diversity of applications highlights its potential to enhance cell- and biomolecule-based treatment strategies.

PMID: 30898580 [PubMed - as supplied by publisher]



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Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies.

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Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies.

Proc Natl Acad Sci U S A. 2019 04 02;116(14):6812-6817

Authors: Raman S, Beilschmidt M, To M, Lin K, Lui F, Jmeian Y, Ng M, Fernandez M, Fu Y, Mascall K, Duque A, Wang X, Pan G, Angers S, Moffat J, Sidhu SS, Magram J, Sinclair AM, Fransson J, Julien JP

Abstract
Aberrant activation of Wnt/β-catenin signaling occurs frequently in cancer. However, therapeutic targeting of this pathway is complicated by the role of Wnt in stem cell maintenance and tissue homeostasis. Here, we evaluated antibodies blocking 6 of the 10 human Wnt/Frizzled (FZD) receptors as potential therapeutics. Crystal structures revealed a common binding site for these monoclonal antibodies (mAbs) on FZD, blocking the interaction with the Wnt palmitoleic acid moiety. However, these mAbs displayed gastrointestinal toxicity or poor plasma exposure in vivo. Structure-guided engineering was used to refine the binding of each mAb for FZD receptors, resulting in antibody variants with improved in vivo tolerability and developability. Importantly, the lead variant mAb significantly inhibited tumor growth in the HPAF-II pancreatic tumor xenograft model. Taken together, our data demonstrate that anti-FZD cancer therapeutic antibodies with broad specificity can be fine-tuned to navigate in vivo exposure and tolerability while driving therapeutic efficacy.

PMID: 30894493 [PubMed - indexed for MEDLINE]



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Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic.

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Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic.

PLoS Genet. 2019 03;15(3):e1007530

Authors: Sun R, Hui S, Bader GD, Lin X, Kraft P

Abstract
A common complementary strategy in Genome-Wide Association Studies (GWAS) is to perform Gene Set Analysis (GSA), which tests for the association between one phenotype of interest and an entire set of Single Nucleotide Polymorphisms (SNPs) residing in selected genes. While there exist many tools for performing GSA, popular methods often include a number of ad-hoc steps that are difficult to justify statistically, provide complicated interpretations based on permutation inference, and demonstrate poor operating characteristics. Additionally, the lack of gold standard gene set lists can produce misleading results and create difficulties in comparing analyses even across the same phenotype. We introduce the Generalized Berk-Jones (GBJ) statistic for GSA, a permutation-free parametric framework that offers asymptotic power guarantees in certain set-based testing settings. To adjust for confounding introduced by different gene set lists, we further develop a GBJ step-down inference technique that can discriminate between gene sets driven to significance by single genes and those demonstrating group-level effects. We compare GBJ to popular alternatives through simulation and re-analysis of summary statistics from a large breast cancer GWAS, and we show how GBJ can increase power by incorporating information from multiple signals in the same gene. In addition, we illustrate how breast cancer pathway analysis can be confounded by the frequency of FGFR2 in pathway lists. Our approach is further validated on two other datasets of summary statistics generated from GWAS of height and schizophrenia.

PMID: 30875371 [PubMed - indexed for MEDLINE]



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netDx: interpretable patient classification using integrated patient similarity networks.

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netDx: interpretable patient classification using integrated patient similarity networks.

Mol Syst Biol. 2019 Mar 14;15(3):e8497

Authors: Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD

Abstract
Patient classification has widespread biomedical and clinical applications, including diagnosis, prognosis, and treatment response prediction. A clinically useful prediction algorithm should be accurate, generalizable, be able to integrate diverse data types, and handle sparse data. A clinical predictor based on genomic data needs to be interpretable to drive hypothesis-driven research into new treatments. We describe netDx, a novel supervised patient classification framework based on patient similarity networks, which meets these criteria. In a cancer survival benchmark dataset integrating up to six data types in four cancer types, netDx significantly outperforms most other machine-learning approaches across most cancer types. Compared to traditional machine-learning-based patient classifiers, netDx results are more interpretable, visualizing the decision boundary in the context of patient similarity space. When patient similarity is defined by pathway-level gene expression, netDx identifies biological pathways important for outcome prediction, as demonstrated in breast cancer and asthma. netDx can serve as a patient classifier and as a tool for discovery of biological features characteristic of disease. We provide a free software implementation of netDx with automation workflows.

PMID: 30872331 [PubMed - in process]



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The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency.

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The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency.

Sci Rep. 2019 Mar 11;9(1):4119

Authors: Manczyk N, Veggiani G, Teyra J, Strilchuk AW, Sidhu SS, Sicheri F

Abstract
USP37 is a deubiquitinase (DUB) with roles in the regulation of DNA damage repair and the cohesion of sister chromatids during mitosis. USP37 contains a unique insert of three ubiquitin interacting motifs (UIMs) within its catalytic DUB domain. We investigated the role of the three UIMs in the ability of USP37 to cleave di-ubiquitin chains. We found that the third UIM of USP37 recognizes the proximal ubiquitin moiety of K48 di-Ub to potentiate cleavage activity and posit that this mechanism of action may be generalizable to other chain types. In the case of K48-linked ubiquitin chains this potentiation stemmed largely from a dramatic increase in catalytic rate (kcat). We also developed and characterized three ubiquitin variant (UbV) inhibitors that selectively engage distinct binding sites in USP37. In addition to validating the deduced functional roles of the three UIMs in catalysis, the UbVs highlight a novel and effective means to selectively inhibit members of the difficult to drug DUB family.

PMID: 30858488 [PubMed - in process]



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Emerging drug development technologies targeting Ubiquitination for Cancer therapeutics.

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Emerging drug development technologies targeting Ubiquitination for Cancer therapeutics.

Pharmacol Ther. 2019 Mar 06;:

Authors: Veggiani G, Gerpe MCR, Sidhu SS, Zhang W

Abstract
Development of effective cancer therapeutic strategies relies on our ability to interfere with cellular processes that are dysregulated in tumors. Given the essential role of the ubiquitin proteasome system (UPS) in regulating a myriad of cellular processes, it is not surprising that malfunction of UPS components is implicated in numerous human diseases, including many types of cancer. The clinical success of proteasome inhibitors in treating multiple myeloma has further stimulated enthusiasm for targeting UPS proteins for pharmacological intervention in cancer treatment, particularly in the precision medicine era. Unfortunately, despite tremendous efforts, the paucity of potent and selective UPS inhibitors has severely hampered attempts to exploit the UPS for therapeutic benefits. To tackle this problem, many groups have been working on technology advancement to rapidly and effectively screen for potent and specific UPS modulators as intracellular probes or early-phase therapeutic agents. Here, we review several emerging technologies for developing chemical- and protein-based molecules to manipulate UPS enzymatic activity, with the aim of providing an overview of strategies available to target ubiquitination for cancer therapy.

PMID: 30851297 [PubMed - as supplied by publisher]



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Innate Control of Tissue-Reparative Human Regulatory T Cells.

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Innate Control of Tissue-Reparative Human Regulatory T Cells.

J Immunol. 2019 Mar 08;:

Authors: Lam AJ, MacDonald KN, Pesenacker AM, Juvet SC, Morishita KA, Bressler B, iGenoMed Consortium, Pan JG, Sidhu SS, Rioux JD, Levings MK

Abstract
Regulatory T cell (Treg) therapy is a potential curative approach for a variety of immune-mediated conditions, including autoimmunity and transplantation, in which there is pathological tissue damage. In mice, IL-33R (ST2)-expressing Tregs mediate tissue repair by producing the growth factor amphiregulin, but whether similar tissue-reparative Tregs exist in humans remains unclear. We show that human Tregs in blood and multiple tissue types produced amphiregulin, but this was neither a unique feature of Tregs nor selectively upregulated in tissues. Human Tregs in blood, tonsil, synovial fluid, colon, and lung tissues did not express ST2, so ST2+ Tregs were engineered via lentiviral-mediated overexpression, and their therapeutic potential for cell therapy was examined. Engineered ST2+ Tregs exhibited TCR-independent, IL-33-stimulated amphiregulin expression and a heightened ability to induce M2-like macrophages. The finding that amphiregulin-producing Tregs have a noneffector phenotype and are progressively lost upon TCR-induced proliferation and differentiation suggests that the tissue repair capacity of human Tregs may be an innate function that operates independently from their classical suppressive function.

PMID: 30850479 [PubMed - as supplied by publisher]



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Modulated Protein Delivery to Engineer Tissue Repair.

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Modulated Protein Delivery to Engineer Tissue Repair.

Tissue Eng Part A. 2019 Mar 08;:

Authors: Shoichet MS, Hettiaratchi MH

Abstract
Protein delivery presents a powerful strategy to stimulate regeneration of damaged tissues. However, the clinical translation of many promising therapeutic proteins in the research pipeline has been hindered by the inability to localize and control their release within the injury site. The only biomaterials-based strategies that have been approved for controlled protein release clinically are the absorbable collagen sponge for bone morphogenetic protein-2 (BMP-2) delivery to repair large bone defects (Medtronic's Infuse Bone Graft) and poly(lactic-co-glycolic) acid (PLGA) microparticles for sustained human growth hormone (hGH) delivery (Genentech's Nutropin Depot). Despite their clinical approval, even these products possess inherent limitations that curb their widespread use: the collagen sponge exhibits rapid BMP-2 release that has been linked with numerous undesirable side effects [1], while commercialization of the long-acting hGH formulation was eventually halted due to manufacturing concerns over the low protein loading capacity of the PLGA particles [2]. Notwithstanding substantive research over the past 25 years, achieving effective control over protein delivery remains an ongoing challenge.

PMID: 30848169 [PubMed - as supplied by publisher]



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