PubMed

Recent Publications

Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations

Cell Syst. 2021 Jun 16;12(6):608-621. doi: 10.1016/j.cels.2021.05.010.

ABSTRACT

Single-cell image analysis provides a powerful approach for studying cell-to-cell heterogeneity, which is an important attribute of isogenic cell populations, from microbial cultures to individual cells in multicellular organisms. This phenotypic variability must be explained at a mechanistic level if biologists are to fully understand cellular function and address the genotype-to-phenotype relationship. Variability in single-cell phenotypes is obscured by bulk readouts or averaging of phenotypes from individual cells in a sample; thus, single-cell image analysis enables a higher resolution view of cellular function. Here, we consider examples of both small- and large-scale studies carried out with isogenic cell populations assessed by fluorescence microscopy, and we illustrate the advantages, challenges, and the promise of quantitative single-cell image analysis.

PMID:34139168 | DOI:10.1016/j.cels.2021.05.010



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Production of Phenotypically Uniform Human Cerebral Organoids from Pluripotent Stem Cells

Bio Protoc. 2021 Apr 20;11(8):e3985. doi: 10.21769/BioProtoc.3985. eCollection 2021 Apr 20.

ABSTRACT

Recent advances in stem cell technology have allowed researchers to generate 3D cerebral organoids (COs) from human pluripotent stem cells (hPSCs). Indeed, COs have provided an unprecedented opportunity to model the developing human brain in a 3D context, and in turn, are suitable for addressing complex neurological questions by leveraging advancements in genetic engineering, high resolution microscopy, and tissue transcriptomics. However, the use of this model is limited by substantial variations in the overall morphology and cellular composition of organoids derived from the same pluripotent cell line. To address these limitations, we established a robust, high-efficiency protocol for the production of consistent COs by optimizing the initial phase of embryoid body (EB) formation and neural induction. Using this protocol, COs can be reproducibly generated with a uniform size, shape, and cellular composition across multiple batches. Furthermore, organoids that developed over extended periods of time (3-6 months) showed the establishment of relatively mature features, including electrophysiologically active neurons, and the emergence of oligodendrocyte progenitors. Thus, this platform provides a robust experimental model that can be used to study human brain development and associated disorders. Graphic abstract: Overview of cerebral organoid development from pluripotent stem cells.

PMID:34124288 | PMC:PMC8160534 | DOI:10.21769/BioProtoc.3985



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Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device

Nano Lett. 2021 Jun 23;21(12):5209-5216. doi: 10.1021/acs.nanolett.1c01280. Epub 2021 Jun 10.

ABSTRACT

The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.

PMID:34110166 | DOI:10.1021/acs.nanolett.1c01280



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A Norrin/Wnt surrogate antibody stimulates endothelial cell barrier function and rescues retinopathy

EMBO Mol Med. 2021 Jul 7;13(7):e13977. doi: 10.15252/emmm.202113977. Epub 2021 Jun 9.

ABSTRACT

The FZD4:LRP5:TSPAN12 receptor complex is activated by the secreted protein Norrin in retinal endothelial cells and leads to βcatenin-dependent formation of the blood-retina-barrier during development and its homeostasis in adults. Mutations disrupting Norrin signaling have been identified in several congenital diseases leading to hypovascularization of the retina and blindness. Here, we developed F4L5.13, a tetravalent antibody designed to induce FZD4 and LRP5 proximity in such a way as to trigger βcatenin signaling. Treatment of cultured endothelial cells with F4L5.13 rescued permeability induced by VEGF in part by promoting surface expression of junction proteins. Treatment of Tspan12-/- mice with F4L5.13 restored retinal angiogenesis and barrier function. F4L5.13 treatment also significantly normalized neovascularization in an oxygen-induced retinopathy model revealing a novel therapeutic strategy for diseases characterized by abnormal angiogenesis and/or barrier dysfunction.

PMID:34105895 | PMC:PMC8261507 | DOI:10.15252/emmm.202113977



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Known sequence features can explain half of all human gene ends

NAR Genom Bioinform. 2021 Jun 4;3(2):lqab042. doi: 10.1093/nargab/lqab042. eCollection 2021 Jun.

ABSTRACT

Cleavage and polyadenylation (CPA) sites define eukaryotic gene ends. CPA sites are associated with five key sequence recognition elements: the upstream UGUA, the polyadenylation signal (PAS), and U-rich sequences; the CA/UA dinucleotide where cleavage occurs; and GU-rich downstream elements (DSEs). Currently, it is not clear whether these sequences are sufficient to delineate CPA sites. Additionally, numerous other sequences and factors have been described, often in the context of promoting alternative CPA sites and preventing cryptic CPA site usage. Here, we dissect the contributions of individual sequence features to CPA using standard discriminative models. We show that models comprised only of the five primary CPA sequence features give highest probability scores to constitutive CPA sites at the ends of coding genes, relative to the entire pre-mRNA sequence, for 41% of all human genes. U1-hybridizing sequences provide a small boost in performance. The addition of all known RBP RNA binding motifs to the model, however, increases this figure to 49%, and suggests an involvement of both known and suspected CPA regulators as well as potential new factors in delineating constitutive CPA sites. To our knowledge, this high effectiveness of established features to predict human gene ends has not previously been documented.

PMID:34104882 | PMC:PMC8176999 | DOI:10.1093/nargab/lqab042



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A genome-scale yeast library with inducible expression of individual genes

Mol Syst Biol. 2021 Jun;17(6):e10207. doi: 10.15252/msb.202110207.

ABSTRACT

The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which > 5,600 yeast genes are engineered for transcriptional inducibility with single-gene precision at their native loci and without plasmids. Each strain contains SGA screening markers and a unique barcode, enabling high-throughput genetics. We characterized YETI using growth phenotyping and BAR-seq screens, and we used a YETI allele to identify the regulon of Rof1, showing that it acts to repress transcription. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from eukaryotic and prokaryotic systems shows that native expression is a variable that can bias promoter-perturbing screens, including CRISPRi. We engineered a second expression system, Z3 EB42, that gives lower expression than Z3 EV, a feature enabling conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.

PMID:34096681 | PMC:PMC8182650 | DOI:10.15252/msb.202110207



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Inhibition of Cancer Cell Adhesion, Migration and Proliferation by a Bispecific Antibody that Targets two Distinct Epitopes on αv Integrins

J Mol Biol. 2021 Jul 23;433(15):167090. doi: 10.1016/j.jmb.2021.167090. Epub 2021 Jun 4.

ABSTRACT

Members of the αv family of integrins regulate activation of transforming growth factor beta (TGFβ) and are directly involved in pro-tumorigenic phenotypes. Thus, αv integrins may be therapeutic targets for fibrosis and cancer, yet the isolation of selective inhibitors is currently a challenge. We generated synthetic antibodies selective for αv integrins by phage display selections on cell lines that displayed integrin heterodimers. We identified antibodies that targeted two distinct epitopes on cell-surface αv integrins and partially inhibited cell adhesion mediated by interactions between integrins and the latency-associated peptide, part of the pro-form of TGFβ. Using the isolated antibody paratope sequences we engineered a bispecific antibody capable of binding to both epitopes simultaneously; this antibody potently and completely inhibited cell adhesion mediated by integrins αvβ1, αvβ3 and αvβ5. In addition, the bispecific antibody inhibited proliferation and migration of lung carcinoma lines, where the highest and lowest potencies observed correlated with integrin-αv cell surface expression levels. Taken together, our results demonstrate that phage display selections with live cells can yield high quality anti-integrin antibodies, which we used as biparatopic building blocks to construct a bispecific antibody that strongly inhibited integrin function and may be a therapeutic candidate for cancer and fibrosis.

PMID:34090922 | DOI:10.1016/j.jmb.2021.167090



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Methacrylic acid-based hydrogels enhance skeletal muscle regeneration after volumetric muscle loss in mice

Biomaterials. 2021 Aug;275:120909. doi: 10.1016/j.biomaterials.2021.120909. Epub 2021 May 24.

ABSTRACT

Volumetric muscle loss (VML) impairs the regenerative ability of skeletal muscle resulting in scar tissue formation and loss of function. Current treatments are of limited efficacy as they do not fully restore function, i.e., force generation. Regenerative biomaterials, such as those containing methacrylic-acid (MAA), are proposed as a novel approach to enhancing muscle regeneration without added cells, growth factors or drugs. Here, the regenerative effects of two hydrogels were investigated: MAA-poly(ethylene glycol) (MAA-PEG) and MAA-collagen. These hydrogels were used to treat VML injuries in murine tibialis anterior muscles. The MAA-collagen hydrogel significantly increased regenerating muscle fiber size and muscle force production. While both hydrogels increased vascularization, only the MAA-collagen hydrogel increased apparent muscle innervation. The MAA-collagen hydrogel also significantly reduced a pro-inflammatory macrophage (MHCII+CD206-) population. Furthermore, the hydrogels had distinct gene expression profiles indicating that their regenerative abilities were carrier dependent. Overall, this study suggests MAA-collagen as a cell-free and drug-free approach to enhancing skeletal muscle regeneration after traumatic injury.

PMID:34087582 | DOI:10.1016/j.biomaterials.2021.120909



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Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila

Nucleic Acids Res. 2021 Jun 21;49(11):6196-6212. doi: 10.1093/nar/gkab413.

ABSTRACT

Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links for Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion inhibited cellular growth and reduced the expression levels of Anqa1 and Lin9. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.

PMID:34086947 | PMC:PMC8216455 | DOI:10.1093/nar/gkab413



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LRRC8A-containing chloride channel is crucial for cell volume recovery and survival under hypertonic conditions

Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2025013118. doi: 10.1073/pnas.2025013118.

ABSTRACT

Regulation of cell volume is essential for tissue homeostasis and cell viability. In response to hypertonic stress, cells need rapid electrolyte influx to compensate water loss and to prevent cell death in a process known as regulatory volume increase (RVI). However, the molecular component able to trigger such a process was unknown to date. Using a genome-wide CRISPR/Cas9 screen, we identified LRRC8A, which encodes a chloride channel subunit, as the gene most associated with cell survival under hypertonic conditions. Hypertonicity activates the p38 stress-activated protein kinase pathway and its downstream MSK1 kinase, which phosphorylates and activates LRRC8A. LRRC8A-mediated Cl- efflux facilitates activation of the with-no-lysine (WNK) kinase pathway, which in turn, promotes electrolyte influx via Na+/K+/2Cl- cotransporter (NKCC) and RVI under hypertonic stress. LRRC8A-S217A mutation impairs channel activation by MSK1, resulting in reduced RVI and cell survival. In summary, LRRC8A is key to bidirectional osmotic stress responses and cell survival under hypertonic conditions.

PMID:34083438 | PMC:PMC8201826 | DOI:10.1073/pnas.2025013118



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