PubMed

Recent Publications

Opinion: Independent third-party entities as a model for validation of commercial antibodies

N Biotechnol. 2021 Jul 8;65:1-8. doi: 10.1016/j.nbt.2021.07.001. Online ahead of print.

ABSTRACT

A vast array of commercial antibodies covers a large percentage of human gene products, but determining which among them is most appropriate for any given application is challenging. This leads to use of non-specific antibodies that contributes to issues with reproducibility. It is our opinion that the community of scientists who use commercial antibodies in their biomedical research would benefit from third-party antibody characterization entities that use standardized operating procedures to assess and compare antibody performance. Ideally, such entities would follow the principles of open science, such that all antibodies against any given protein target would be tested in parallel, and all data generated released to the public domain without bias. Furthermore, there should be no financial incentive for the entity beyond cost-recovery. Such non-profit organizations, combined with other scientific efforts, could catalyse new discoveries by providing scientists with better validated antibody tools.

PMID:34246180 | DOI:10.1016/j.nbt.2021.07.001



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Sphingosine-1-Phosphate Receptor 3 Potentiates Inflammatory Programs in Normal and Leukemia Stem Cells to Promote Differentiation

Cancer Discov. 2021 Jan;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 HSCs by activating stress myelopoiesis, such roles in LSCs are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator that drives myeloid differentiation and activates inflammatory programs in both HSCs and LSCs. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across cohorts of patients with AML, each with distinct phenotypic and clinical properties. S1PR3 was high in LSCs and blasts of mature myeloid samples with linkages to chemosensitivity, whereas 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. SIGNIFICANCE: S1PR3 is a novel regulator of myeloid fate in normal hematopoiesis that is heterogeneously expressed in AML. S1PR3 marks a subset of less primitive AML cases with a distinct inflammatory signature and therefore has clinical implications as both a therapeutic target and a biomarker to distinguish primitive from mature AML.See related commentary by Yang et al., p. 3.This article is highlighted in the In This Issue feature, p. 1.

PMID:34238756 | DOI:10.1158/2643-3230.BCD-20-0155



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A Colorimetric Test to Differentiate Patients Infected with Influenza from COVID-19

Small Struct. 2021 Jun 6:2100034. doi: 10.1002/sstr.202100034. Online ahead of print.

ABSTRACT

Patients infected with SARS-CoV-2 and influenza display similar symptoms, but treatment requirements are different. Clinicians need to accurately distinguish SARS-CoV-2 from influenza to provide appropriate treatment. Here, the authors develope a color-based technique to differentiate between patients infected with SARS-CoV-2 and influenza A using a nucleic acid enzyme-gold nanoparticle (GNP) molecular test requiring minimal equipment. The MNAzyme and GNP probes are designed to be robust to viral mutations. Conserved regions of the viral genomes are targeted, and two MNAzymes are created for each virus. The ability of the system to distinguish between SARS-CoV-2 and influenza A using 79 patient samples is tested. When detecting SARS-CoV-2 positive patients, the clinical sensitivity is 90%, and the specificity is 100%. When detecting influenza A, the clinical sensitivity and specificity are 93% and 100%, respectively. The high clinical performance of the MNAzyme-GNP assay shows that it can be used to help clinicians choose effective treatments.

PMID:34230923 | PMC:PMC8250260 | DOI:10.1002/sstr.202100034



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Province-Wide Analysis of Patient-Reported Outcomes for Stage IV Non-Small Cell Lung Cancer

Oncologist. 2021 Jul 3. doi: 10.1002/onco.13890. Online ahead of print.

ABSTRACT

BACKGROUND: In Ontario, Canada, patient-reported outcome (PRO) evaluation through the Edmonton Symptom Assessment System (ESAS) has been integrated into clinical workflow since 2007. As stage IV non-small cell lung cancer (NSCLC) is associated with substantial disease and treatment-related morbidity, this province-wide study investigated moderate to severe symptom burden in this population.

MATERIALS AND METHODS: ESAS collected from patients with stage IV NSCLC diagnosed between 2007 and 2018 linked to the Ontario provincial health care system database were studied. ESAS acquired within 12 months following diagnosis were analyzed and the proportion reporting moderate to severe scores (ESAS ≥4) in each domain was calculated. Predictors of moderate to severe scores were identified using multivariable Poisson regression models with robust error variance.

RESULTS: Of 22,799 patients, 13,289 (58.3%) completed ESAS (84,373 assessments) in the year following diagnosis. Patients with older age, with high comorbidity, and not receiving active cancer therapy had lower ESAS completion. The majority (94.4%) reported at least one moderate to severe symptom. The most prevalent were tiredness (84.1%), low well-being (80.7%), low appetite (71.7%), and shortness of breath (67.8%). Most symptoms peaked at diagnosis and, while declining, remained high in the following year. On multivariable analyses, comorbidity, low income, nonimmigrants, and urban residency were associated with moderate to severe symptoms. Moderate to severe scores in all ESAS domains aside from anxiety were associated with radiotherapy within 2 weeks prior, whereas drowsiness, low appetite and well-being, nausea, and tiredness were associated with systemic therapy within 2 weeks prior.

CONCLUSION: This province-wide PRO analysis showed moderate to severe symptoms were prevalent and persistent among patients with metastatic NSCLC, underscoring the need to address supportive measures in this population especially around treatments.

IMPLICATIONS FOR PRACTICE: In this largest study of lung cancer patient-reported outcomes (PROs), stage IV non-small cell lung cancer patients had worse moderate-to-severe symptoms than other metastatic malignancies such as breast or gastrointestinal cancers when assessed with similar methodology. Prevalence of moderate-to-severe symptoms peaked early and remained high during the first year of follow-up. Symptom burden was associated with recent radiation and systemic treatments. Early and sustained PRO collection is important to detect actionable symptom progression, especially around treatments. Vulnerable patients (e.g., older, high comorbidity) who face barriers in attending in-person clinic visits had lower PRO completion. Virtual PRO collection may improve completion.

PMID:34216415 | DOI:10.1002/onco.13890



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Shifting landscapes of human MTHFR missense-variant effects

Am J Hum Genet. 2021 Jul 1;108(7):1283-1300. doi: 10.1016/j.ajhg.2021.05.009.

ABSTRACT

Most rare clinical missense variants cannot currently be classified as pathogenic or benign. Deficiency in human 5,10-methylenetetrahydrofolate reductase (MTHFR), the most common inherited disorder of folate metabolism, is caused primarily by rare missense variants. Further complicating variant interpretation, variant impacts often depend on environment. An important example of this phenomenon is the MTHFR variant p.Ala222Val (c.665C>T), which is carried by half of all humans and has a phenotypic impact that depends on dietary folate. Here we describe the results of 98,336 variant functional-impact assays, covering nearly all possible MTHFR amino acid substitutions in four folinate environments, each in the presence and absence of p.Ala222Val. The resulting atlas of MTHFR variant effects reveals many complex dependencies on both folinate and p.Ala222Val. MTHFR atlas scores can distinguish pathogenic from benign variants and, among individuals with severe MTHFR deficiency, correlate with age of disease onset. Providing a powerful tool for understanding structure-function relationships, the atlas suggests a role for a disordered loop in retaining cofactor at the active site and identifies variants that enable escape of inhibition by S-adenosylmethionine. Thus, a model based on eight MTHFR variant effect maps illustrates how shifting landscapes of environment- and genetic-background-dependent missense variation can inform our clinical, structural, and functional understanding of MTHFR deficiency.

PMID:34214447 | PMC:PMC8322931 | DOI:10.1016/j.ajhg.2021.05.009



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Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering

Elife. 2021 Jul 2;10:e64951. doi: 10.7554/eLife.64951.

ABSTRACT

Cell cycle duration changes dramatically during development, starting out fast to generate cells quickly and slowing down over time as the organism matures. The cell cycle can also act as a transcriptional filter to control the expression of long gene transcripts, which are partially transcribed in short cycles. Using mathematical simulations of cell proliferation, we identify an emergent property that this filter can act as a tuning knob to control gene transcript expression, cell diversity, and the number and proportion of different cell types in a tissue. Our predictions are supported by comparison to single-cell RNA-seq data captured over embryonic development. Additionally, evolutionary genome analysis shows that fast-developing organisms have a narrow genomic distribution of gene lengths while slower developers have an expanded number of long genes. Our results support the idea that cell cycle dynamics may be important across multicellular animals for controlling gene transcript expression and cell fate.

PMID:34212855 | PMC:PMC8279763 | DOI:10.7554/eLife.64951



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A T cell redirection platform for co-targeting dual antigens on solid tumors

MAbs. 2021 Jan-Dec;13(1):1933690. doi: 10.1080/19420862.2021.1933690.

ABSTRACT

In order to direct T cells to specific features of solid cancer cells, we engineered a bispecific antibody format, named Dual Antigen T cell Engager (DATE), by fusing a single-chain variable fragment targeting CD3 to a tumor-targeting antigen-binding fragment. In this format, multiple novel paratopes against different tumor antigens were able to recruit T-cell cytotoxicity to tumor cells in vitro and in an in vivo pancreatic ductal adenocarcinoma xenograft model. Since unique surface antigens in solid tumors are limited, in order to enhance selectivity, we further engineered "double-DATEs" targeting two tumor antigens simultaneously. The double-DATE contains an additional autonomous variable heavy-chain domain, which binds a second tumor antigen without itself eliciting a cytotoxic response. This novel modality provides a strategy to enhance the selectivity of immune redirection through binary targeting of native tumor antigens. The modularity and use of a common, stable human framework for all components enables a pipeline approach to rapidly develop a broad repertoire of tailored DATEs and double-DATEs with favorable biophysical properties and high potencies and selectivities.

PMID:34190031 | PMC:PMC8253144 | DOI:10.1080/19420862.2021.1933690



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Comprehensive Assessment of the Relationship Between Site<sup>-2</sup> Specificity and Helix α2 in the Erbin PDZ Domain

J Mol Biol. 2021 Jun 24;433(18):167115. doi: 10.1016/j.jmb.2021.167115. Online ahead of print.

ABSTRACT

PDZ domains are key players in signalling pathways. These modular domains generally recognize short linear C-terminal stretches of sequences in proteins that organize the formation of complex multi-component assemblies. The development of new methodologies for the characterization of the molecular principles governing these interactions is critical to fully understand the functional diversity of the family and to elucidate biological functions for family members. Here, we applied an in vitro evolution strategy to explore comprehensively the capacity of PDZ domains for specific recognition of different amino acids at a key position in C-terminal peptide ligands. We constructed a phage-displayed library of the Erbin PDZ domain by randomizing the binding site-2 and adjacent residues, which are all contained in helix α2, and we selected for variants binding to a panel of peptides representing all possible position-2 residues. This approach generated insights into the basis for the common natural class I and II specificities, demonstrated an alternative basis for a rare natural class III specificity for Asp-2, and revealed a novel specificity for Arg-2 that has not been reported in natural PDZ domains. A structure of a PDZ-peptide complex explained the minimum requirement for switching specificity from class I ligands containing Thr/Ser-2 to class II ligands containing hydrophobic residues at position-2. A second structure explained the molecular basis for the specificity for ligands containing Arg-2. Overall, the evolved PDZ variants greatly expand our understanding of site-2 specificities and the variants themselves may prove useful as building blocks for synthetic biology.

PMID:34171344 | DOI:10.1016/j.jmb.2021.167115



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Understanding Carbon Nanotube-Based Ionic Diodes: Design and Mechanism

Small. 2021 Jun 25:e2100383. doi: 10.1002/smll.202100383. Online ahead of print.

ABSTRACT

The rectification of ion transport through biological ion channels has attracted much attention and inspired the thriving invention and applications of ionic diodes. However, the development of high-performance ionic diodes is still challenging, and the working mechanisms of ionic diodes constructed by 1D ionic nanochannels have not been fully understood. This work reports the systematic investigation of the design and mechanism of a new type of ionic diode constructed from horizontally aligned multi-walled carbon nanotubes (MWCNTs) with oppositely charged polyelectrolytes decorated at their two entrances. The major design and working parameters of the MWCNT-based ionic diode, including the ion channel size, the driven voltage, the properties of working fluids, and the quantity and length of charge modification, are extensively investigated through numerical simulations and/or experiments. An optimized ionic current rectification (ICR) ratio of 1481.5 is experimentally achieved on the MWCNT-based ionic diode. These results promise potential applications of the MWCNT-based ionic diode in biosensing and biocomputing. As a proof-of-concept, DNA detection and HIV-1 diagnosis is demonstrated on the ionic diode. This work provides a comprehensive understanding of the working principle of the MWCNT-based ionic diodes and will allow rational device design and optimization.

PMID:34171160 | DOI:10.1002/smll.202100383



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A defined subset of clonal retinal stem cell spheres is biased to RPE differentiation

iScience. 2021 May 21;24(6):102574. doi: 10.1016/j.isci.2021.102574. eCollection 2021 Jun 25.

ABSTRACT

Retinal stem cells (RSCs) are rare pigmented cells found in the pigmented ciliary layer of the mammalian retina. Studies show that RSCs can replicate to maintain the stem cell pool and produce retinal progenitors that differentiate into all retinal cell types. We classified RSCs based on their level and distribution of pigment into heavily pigmented (HP), lightly pigmented (LP), and centrally pigmented (CP) spheres. We report that CP spheres are capable of generating large cobblestone lawns of retinal pigment epithelial (RPE) cells. The other clonal sphere types (HP and LP) primarily produce cells with neural morphology and fewer RPE cells. The RSCs are homogeneous, but their downstream progenitors are different. We found that CP spheres contain highly proliferative populations of early RPE progenitors that respond to proliferative signals from the surrounding non-pigmented cells. HP and LP spheres contain late RPE progenitors which are not affected by proliferative signals.

PMID:34151227 | PMC:PMC8188557 | DOI:10.1016/j.isci.2021.102574



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