PubMed

Recent Publications

Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation

Blood Cancer Discov. 2021 Jan 1;2(1):32-53. doi: 10.1158/2643-3230.BCD-20-0155. Epub 2020 Dec 1.

ABSTRACT

Acute myeloid leukemia (AML) is a caricature of normal hematopoiesis, driven from leukemia stem cells (LSC) that share some hematopoietic stem cell (HSC) programs including responsiveness to inflammatory signaling. Although inflammation dysregulates mature myeloid cells and influences stemness programs and lineage determination in HSC by activating stress myelopoiesis, such roles in LSC are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator which drives myeloid differentiation and activates inflammatory programs in both HSC and LSC. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across AML patient cohorts, each with distinct phenotypic and clinical properties. S1PR3 was high in LSC and blasts of mature myeloid samples with linkages to chemosensitivity, while S1PR3 activation in primitive samples promoted LSC differentiation leading to eradication. Our studies open new avenues for therapeutic target identification specific for each AML subset.

PMID:33458693 | PMC:PMC7116590 | DOI:10.1158/2643-3230.BCD-20-0155



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Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways

J Biol Chem. 2020 Dec 11;295(50):16906-16919. doi: 10.1074/jbc.RA120.014831.

ABSTRACT

Kinases are critical components of intracellular signaling pathways and have been extensively investigated with regard to their roles in cancer. p21-activated kinase-1 (PAK1) is a serine/threonine kinase that has been previously implicated in numerous biological processes, such as cell migration, cell cycle progression, cell motility, invasion, and angiogenesis, in glioma and other cancers. However, the signaling network linked to PAK1 is not fully defined. We previously reported a large-scale yeast genetic interaction screen using toxicity as a readout to identify candidate PAK1 genetic interactions. En masse transformation of the PAK1 gene into 4,653 homozygous diploid Saccharomyces cerevisiae yeast deletion mutants identified ∼400 candidates that suppressed yeast toxicity. Here we selected 19 candidate PAK1 genetic interactions that had human orthologs and were expressed in glioma for further examination in mammalian cells, brain slice cultures, and orthotopic glioma models. RNAi and pharmacological inhibition of potential PAK1 interactors confirmed that DPP4, KIF11, mTOR, PKM2, SGPP1, TTK, and YWHAE regulate PAK1-induced cell migration and revealed the importance of genes related to the mitotic spindle, proteolysis, autophagy, and metabolism in PAK1-mediated glioma cell migration, drug resistance, and proliferation. AKT1 was further identified as a downstream mediator of the PAK1-TTK genetic interaction. Taken together, these data provide a global view of PAK1-mediated signal transduction pathways and point to potential new drug targets for glioma therapy.

PMID:33453946 | DOI:10.1074/jbc.RA120.014831



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ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations

J Mol Biol. 2021 Jan 13:166810. doi: 10.1016/j.jmb.2021.166810. Online ahead of print.

ABSTRACT

The ELASPIC web server allows users to evaluate the effect of mutations on protein folding and protein-protein interaction on a proteome-wide scale. It uses homology models of proteins and protein-protein interactions, which have been precalculated for several proteomes, and machine learning models, which integrate structural information with sequence conservation scores, in order to make its predictions. Since the original publication of the ELASPIC web server, several advances have motivated a revisiting of the problem of mutation effect prediction. First, progress in neural network architectures and self-supervised pre-trained has resulted in models which provide more informative embeddings of protein sequence and structure than those used by the original version of ELASPIC. Second, the amount of training data has increased several-fold, largely driven by advances in deep mutation scanning and other multiplexed assays of variant effect. Here, we describe two machine learning models which leverage the recent advances in order to achieve superior accuracy in predicting the effect of mutation on protein folding and protein-protein interaction. The models incorporate features generated using pre-trained transformer- and graph convolution-based neural networks, and are trained to optimize a ranking objective function, which permits the use of heterogeneous training data. The outputs from the new models have been incorporated into the ELASPIC web server, available at http://elaspic.kimlab.org.

PMID:33450251 | DOI:10.1016/j.jmb.2021.166810



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Poly-Methacrylic Acid Cross-Linked with Collagen Accelerates Diabetic Wound Closure

ACS Biomater Sci Eng. 2020 Nov 9;6(11):6368-6377. doi: 10.1021/acsbiomaterials.0c01222. Epub 2020 Oct 27.

ABSTRACT

Impaired blood vessel formation limits the healing of diabetic ulcers and leaves patients at high risk for amputation. Nonbiologic vascular regenerative materials made of methacrylic acid (MAA) copolymer, such as MAA-co-methyl methacrylate beads, have shown to enhance wound healing in a diabetic animal model, but their lack of biodegradability precludes their clinical implementation. Here, a new MAA-based gel was created by cross-linking polyMAA with collagen using carbodiimide chemistry. Using this gel on full-thickness wounds in diabetic db/db mice augmented vascularization of the wound bed, resulting in a faster closure compared to untreated or collagen-only treated wounds. After 21 days, almost all the wounds were closed and re-epithelialized in the polyMAA-collagen group compared to that in the other groups in which most wounds remained open. Histological and fluorescent gel tracking data suggested that the gel resorbed during the phase of tissue remodeling, likely because of the action of macrophages that colonized the gel. We expect the addition of the polyMAA to commercially available collagen-based dressing to be a good candidate to treat diabetic ulcers.

PMID:33449665 | DOI:10.1021/acsbiomaterials.0c01222



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Large-scale survey and database of high affinity ligands for peptide recognition modules

Mol Syst Biol. 2020 Dec;16(12):e9310. doi: 10.15252/msb.20199310.

ABSTRACT

Many proteins involved in signal transduction contain peptide recognition modules (PRMs) that recognize short linear motifs (SLiMs) within their interaction partners. Here, we used large-scale peptide-phage display methods to derive optimal ligands for 163 unique PRMs representing 79 distinct structural families. We combined the new data with previous data that we collected for the large SH3, PDZ, and WW domain families to assemble a database containing 7,984 unique peptide ligands for 500 PRMs representing 82 structural families. For 74 PRMs, we acquired enough new data to map the specificity profiles in detail and derived position weight matrices and binding specificity logos based on multiple peptide ligands. These analyses showed that optimal peptide ligands resembled peptides observed in existing structures of PRM-ligand complexes, indicating that a large majority of the phage-derived peptides are likely to target natural peptide-binding sites and could thus act as inhibitors of natural protein-protein interactions. The complete dataset has been assembled in an online database (http://www.prm-db.org) that will enable many structural, functional, and biological studies of PRMs and SLiMs.

PMID:33438817 | PMC:PMC7724964 | DOI:10.15252/msb.20199310



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Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity

Nat Commun. 2021 Jan 12;12(1):335. doi: 10.1038/s41467-020-20483-8.

ABSTRACT

Previous transcriptomic profiling studies have typically focused on separately analyzing mRNA expression, alternative splicing and alternative polyadenylation differences between cell and tissue types. However, the relative contribution of these three transcriptomic regulatory layers to cell type specification is poorly understood. This question is particularly relevant to neurons, given their extensive heterogeneity associated with brain location, morphology and function. In the present study, we generated profiles for the three regulatory layers from developmentally and regionally distinct subpopulations of neurons from the mouse hippocampus and broader nervous system. Multi-omics factor analyses revealed differing contributions of each transcriptomic layer in the discrimination of neurons based on their stage of development, region, and function. Importantly, profiles of differential alternative splicing and polyadenylation better discriminated specific neuronal subtype populations than gene expression patterns. These results provide evidence for differential relative contributions of coordinated gene regulatory layers in the specification of neuronal subtypes.

PMID:33436550 | PMC:PMC7804943 | DOI:10.1038/s41467-020-20483-8



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Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival

Elife. 2021 Jan 11;10:e64090. doi: 10.7554/eLife.64090.

ABSTRACT

Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary human GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In-depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival, in line with the higher invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs as shown by in vitro and in vivo assays. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

PMID:33427645 | PMC:PMC7847307 | DOI:10.7554/eLife.64090



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Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy

Cell. 2021 Jan 7;184(1):226-242.e21. doi: 10.1016/j.cell.2020.11.018.

ABSTRACT

Cancer cells enter a reversible drug-tolerant persister (DTP) state to evade death from chemotherapy and targeted agents. It is increasingly appreciated that DTPs are important drivers of therapy failure and tumor relapse. We combined cellular barcoding and mathematical modeling in patient-derived colorectal cancer models to identify and characterize DTPs in response to chemotherapy. Barcode analysis revealed no loss of clonal complexity of tumors that entered the DTP state and recurred following treatment cessation. Our data fit a mathematical model where all cancer cells, and not a small subpopulation, possess an equipotent capacity to become DTPs. Mechanistically, we determined that DTPs display remarkable transcriptional and functional similarities to diapause, a reversible state of suspended embryonic development triggered by unfavorable environmental conditions. Our study provides insight into how cancer cells use a developmentally conserved mechanism to drive the DTP state, pointing to novel therapeutic opportunities to target DTPs.

PMID:33417860 | DOI:10.1016/j.cell.2020.11.018



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Molecular wayfinding: Mapping transport dynamics

APL Bioeng. 2021 Jan 4;5(1):010401. doi: 10.1063/5.0035333. eCollection 2021 Mar.

NO ABSTRACT

PMID:33415311 | PMC:PMC7785322 | DOI:10.1063/5.0035333



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A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa

Mol Cell. 2021 Feb 4;81(3):571-583.e6. doi: 10.1016/j.molcel.2020.12.011. Epub 2021 Jan 6.

ABSTRACT

The arms race between bacteria and phages has led to the evolution of diverse anti-phage defenses, several of which are controlled by quorum-sensing pathways. In this work, we characterize a quorum-sensing anti-activator protein, Aqs1, found in Pseudomonas phage DMS3. We show that Aqs1 inhibits LasR, the master regulator of quorum sensing, and present the crystal structure of the Aqs1-LasR complex. The 69-residue Aqs1 protein also inhibits PilB, the type IV pilus assembly ATPase protein, which blocks superinfection by phages that require the pilus for infection. This study highlights the remarkable ability of small phage proteins to bind multiple host proteins and disrupt key biological pathways. As quorum sensing influences various anti-phage defenses, Aqs1 provides a mechanism by which infecting phages might simultaneously dampen multiple defenses. Because quorum-sensing systems are broadly distributed across bacteria, this mechanism of phage counter-defense may play an important role in phage-host evolutionary dynamics.

PMID:33412111 | DOI:10.1016/j.molcel.2020.12.011



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