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1.
Cell ; 171(7): 1573-1588.e28, 2017 Dec 14.
Article in English | MEDLINE | ID: mdl-29224777

ABSTRACT

There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not employ this structural protein. Here, we show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements and forms dimers that facilitate the interaction of these DNA elements. Deletion of YY1 binding sites or depletion of YY1 protein disrupts enhancer-promoter looping and gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.


Subject(s)
Enhancer Elements, Genetic , Promoter Regions, Genetic , YY1 Transcription Factor/metabolism , Animals , CCCTC-Binding Factor/metabolism , Embryonic Stem Cells/metabolism , Humans , Mice
2.
Nature ; 624(7991): 366-377, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38092913

ABSTRACT

Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq)1 technologies to generate 301,626 methylomes and 176,003 chromatin conformation-methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 cross-modality-annotated subclasses. We identified 2.6 million differentially methylated regions across the genome that represent potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide spatial transcriptomics data validated the association of spatial epigenetic diversity with transcription and improved the anatomical mapping of our epigenetic datasets. Furthermore, chromatin conformation diversities occurred in important neuronal genes and were highly associated with DNA methylation and transcription changes. Brain-wide cell-type comparisons enabled the construction of regulatory networks that incorporate transcription factors, regulatory elements and their potential downstream gene targets. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a whole-brain SMART-seq2 dataset. Our study establishes a brain-wide, single-cell DNA methylome and 3D multi-omic atlas and provides a valuable resource for comprehending the cellular-spatial and regulatory genome diversity of the mouse brain.


Subject(s)
Brain , DNA Methylation , Epigenome , Multiomics , Single-Cell Analysis , Animals , Mice , Brain/cytology , Brain/metabolism , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Cytosine/metabolism , Datasets as Topic , Transcription Factors/metabolism , Transcription, Genetic
3.
Nature ; 624(7991): 390-402, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38092918

ABSTRACT

Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.


Subject(s)
Conserved Sequence , Evolution, Molecular , Gene Expression Regulation , Gene Regulatory Networks , Mammals , Neocortex , Animals , Humans , Mice , Callithrix/genetics , Chromatin/genetics , Chromatin/metabolism , Conserved Sequence/genetics , DNA Methylation , DNA Transposable Elements/genetics , Epigenome , Gene Expression Regulation/genetics , Macaca/genetics , Mammals/genetics , Motor Cortex/cytology , Motor Cortex/metabolism , Multiomics , Neocortex/cytology , Neocortex/metabolism , Regulatory Sequences, Nucleic Acid/genetics , Single-Cell Analysis , Transcription Factors/metabolism , Genetic Variation/genetics
4.
Nature ; 624(7991): 378-389, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38092917

ABSTRACT

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs-specifically, those identified from a subset of cortical excitatory neurons-are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.


Subject(s)
Brain , Chromatin , Single-Cell Analysis , Animals , Humans , Mice , Brain/cytology , Brain/metabolism , Cerebral Cortex/cytology , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Deep Learning , DNA Transposable Elements/genetics , Gene Regulatory Networks/genetics , Neurons/metabolism
5.
Nature ; 598(7879): 120-128, 2021 10.
Article in English | MEDLINE | ID: mdl-34616061

ABSTRACT

Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing1,2 to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data3 enabled prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments4. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.


Subject(s)
Brain/cytology , DNA Methylation , Epigenome , Epigenomics , Neurons/classification , Neurons/metabolism , Single-Cell Analysis , Animals , Atlases as Topic , Brain/metabolism , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Cytosine/chemistry , Cytosine/metabolism , Datasets as Topic , Dentate Gyrus/cytology , Enhancer Elements, Genetic/genetics , Gene Expression Profiling , Hippocampus/cytology , Hippocampus/metabolism , Male , Mice , Mice, Inbred C57BL , Models, Biological , Neural Pathways , Neurons/cytology
6.
Nature ; 598(7879): 129-136, 2021 10.
Article in English | MEDLINE | ID: mdl-34616068

ABSTRACT

The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.


Subject(s)
Cerebrum/cytology , Cerebrum/metabolism , Regulatory Sequences, Nucleic Acid/genetics , Animals , Atlases as Topic , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Chromatin Assembly and Disassembly , Gene Expression Regulation , Genetic Predisposition to Disease/genetics , Humans , Male , Mice , Mice, Inbred C57BL , Nervous System Diseases/genetics , Neuroglia/classification , Neuroglia/metabolism , Neurons/classification , Neurons/metabolism , Sequence Analysis, DNA , Single-Cell Analysis
7.
Nature ; 598(7879): 111-119, 2021 10.
Article in English | MEDLINE | ID: mdl-34616062

ABSTRACT

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.


Subject(s)
Motor Cortex/cytology , Neurons/classification , Single-Cell Analysis , Animals , Atlases as Topic , Callithrix/genetics , Epigenesis, Genetic , Epigenomics , Female , GABAergic Neurons/cytology , GABAergic Neurons/metabolism , Gene Expression Profiling , Glutamates/metabolism , Humans , In Situ Hybridization, Fluorescence , Male , Mice , Middle Aged , Motor Cortex/anatomy & histology , Neurons/cytology , Neurons/metabolism , Organ Specificity , Phylogeny , Species Specificity , Transcriptome
8.
Nature ; 598(7879): 103-110, 2021 10.
Article in English | MEDLINE | ID: mdl-34616066

ABSTRACT

Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.


Subject(s)
Epigenomics , Gene Expression Profiling , Motor Cortex/cytology , Neurons/classification , Single-Cell Analysis , Transcriptome , Animals , Atlases as Topic , Datasets as Topic , Epigenesis, Genetic , Female , Male , Mice , Motor Cortex/anatomy & histology , Neurons/cytology , Neurons/metabolism , Organ Specificity , Reproducibility of Results
9.
Proc Natl Acad Sci U S A ; 120(20): e2210991120, 2023 05 16.
Article in English | MEDLINE | ID: mdl-37155843

ABSTRACT

In 2021, the World Health Organization reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical samples of glioblastomas and G4 IDHm astrocytomas were analyzed at single-cell resolution. These profiles afforded resolution of intratumoral genetic heterogeneity, including delineation of cell-to-cell variations in distinct cell states, focal gene amplifications, as well as extrachromosomal circular DNAs. Despite differences in IDH mutation status and significant intratumoral heterogeneity, the profiled tumor cells shared a common chromatin structure defined by open regions enriched for nuclear factor 1 transcription factors (NFIA and NFIB). Silencing of NFIA or NFIB suppressed in vitro and in vivo growths of patient-derived glioblastomas and G4 IDHm astrocytoma models. These findings suggest that despite distinct genotypes and cell states, glioblastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intratumoral heterogeneity.


Subject(s)
Astrocytoma , Brain Neoplasms , Glioblastoma , Adult , Humans , Glioblastoma/genetics , Glioblastoma/pathology , Chromatin/genetics , Transcriptome , Astrocytoma/genetics , Astrocytoma/pathology , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Mutation , Isocitrate Dehydrogenase/genetics , Isocitrate Dehydrogenase/metabolism
10.
Circulation ; 149(16): e1113-e1127, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38465648

ABSTRACT

Hematopoietic stem cell transplantation can cure various disorders but poses cardiovascular risks, especially for elderly patients and those with cardiovascular diseases. Cardiovascular evaluations are crucial in pretransplantation assessments, but guidelines are lacking. This American Heart Association scientific statement summarizes the data on transplantation-related complications and provides guidance for the cardiovascular management throughout transplantation. Hematopoietic stem cell transplantation consists of 4 phases: pretransplantation workup, conditioning therapy and infusion, immediate posttransplantation period, and long-term survivorship. Complications can occur during each phase, with long-term survivors facing increased risks for late effects such as cardiovascular disease, secondary malignancies, and endocrinopathies. In adults, arrhythmias such as atrial fibrillation and flutter are the most frequent acute cardiovascular complication. Acute heart failure has an incidence ranging from 0.4% to 2.2%. In pediatric patients, left ventricular systolic dysfunction and pericardial effusion are the most common cardiovascular complications. Factors influencing the incidence and risk of complications include pretransplantation therapies, transplantation type (autologous versus allogeneic), conditioning regimen, comorbid conditions, and patient age. The pretransplantation cardiovascular evaluation consists of 4 steps: (1) initial risk stratification, (2) exclusion of high-risk cardiovascular disease, (3) assessment of cardiac reserve, and (4) optimization of cardiovascular reserve. Clinical risk scores could be useful tools for the risk stratification of adult patients. Long-term cardiovascular management of hematopoietic stem cell transplantation survivors includes optimizing risk factors, monitoring, and maintaining a low threshold for evaluating cardiovascular causes of symptoms. Future research should prioritize refining risk stratification and creating evidence-based guidelines and strategies to optimize outcomes in this growing patient population.


Subject(s)
Cardiovascular Diseases , Heart Diseases , Hematopoietic Stem Cell Transplantation , Adult , Humans , Child , Aged , Cardiovascular Diseases/diagnosis , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/therapy , Survivorship , American Heart Association , Transplantation Conditioning/adverse effects , Hematopoietic Stem Cell Transplantation/adverse effects , Heart Diseases/etiology
11.
Nature ; 572(7770): 543-548, 2019 08.
Article in English | MEDLINE | ID: mdl-31391587

ABSTRACT

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex1-4. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus5,6. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain7-12. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers7,8, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites9-12. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference.


Subject(s)
Mediator Complex/chemistry , Mediator Complex/metabolism , RNA Polymerase II/chemistry , RNA Polymerase II/metabolism , RNA Splicing , Transcription, Genetic , Animals , Cell Line , Enhancer Elements, Genetic/genetics , Gene Expression Regulation/genetics , Humans , Mediator Complex/genetics , Mice , Phosphorylation , Protein Domains , RNA Polymerase II/genetics , RNA Splicing Factors/chemistry , RNA Splicing Factors/genetics , RNA Splicing Factors/metabolism
13.
Circulation ; 148(3): 297-308, 2023 07 18.
Article in English | MEDLINE | ID: mdl-37377045

ABSTRACT

Advances in cancer therapeutics have revolutionized survival outcomes in patients with cancer. However, cardiovascular toxicities associated with specific cancer therapeutics adversely affect the outcomes of patients with cancer. Recent studies have uncovered excess risks of these cardiotoxic events, especially in traditionally underrepresented populations. Despite advances in strategies to limit the risks of cardiovascular events among cancer survivors, relatively limited guidance is available to address the rapidly growing problem of disparate cardiotoxic risks among women and underrepresented patient populations. Previously decentralized and sporadic evaluations have led to a lack of consensus on the definitions, investigation, and potential optimal strategies to address disparate cardiotoxicity in contemporary cancer care (eg, with immunotherapy, biologic, or cytotoxic therapies) settings. This scientific statement aims to define the current state of evidence for disparate cardiotoxicity while proposing uniform and novel methodological approaches to inform the identification and mitigation of disparate cardio-oncology outcomes in future clinical trials, registries, and daily clinical care settings. We also propose an evidence-based integrated approach to identify and mitigate disparities in the routine clinical setting. This consensus scientific statement summarizes and clarifies available evidence while providing guidance on addressing inequities in the era of emerging anticancer therapies.


Subject(s)
Cardiovascular System , Neoplasms , United States , Humans , Female , Cardiotoxicity/therapy , American Heart Association , Neoplasms/drug therapy , Medical Oncology
14.
Circulation ; 148(16): 1271-1286, 2023 10 17.
Article in English | MEDLINE | ID: mdl-37732422

ABSTRACT

Advances in cancer therapeutics have led to dramatic improvements in survival, now inclusive of nearly 20 million patients and rising. However, cardiovascular toxicities associated with specific cancer therapeutics adversely affect the outcomes of patients with cancer. Advances in cardiovascular imaging have solidified the critical role for robust methods for detecting, monitoring, and prognosticating cardiac risk among patients with cancer. However, decentralized evaluations have led to a lack of consensus on the optimal uses of imaging in contemporary cancer treatment (eg, immunotherapy, targeted, or biological therapy) settings. Similarly, available isolated preclinical and clinical studies have provided incomplete insights into the effectiveness of multiple modalities for cardiovascular imaging in cancer care. The aims of this scientific statement are to define the current state of evidence for cardiovascular imaging in the cancer treatment and survivorship settings and to propose novel methodological approaches to inform the optimal application of cardiovascular imaging in future clinical trials and registries. We also propose an evidence-based integrated approach to the use of cardiovascular imaging in routine clinical settings. This scientific statement summarizes and clarifies available evidence while providing guidance on the optimal uses of multimodality cardiovascular imaging in the era of emerging anticancer therapies.


Subject(s)
Cardiovascular Diseases , Neoplasms , United States , Humans , American Heart Association , Neoplasms/diagnostic imaging , Neoplasms/therapy , Medical Oncology , Multimodal Imaging/methods , Cardiovascular Diseases/diagnostic imaging , Cardiovascular Diseases/therapy
15.
J Am Chem Soc ; 146(6): 3609-3614, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38290427

ABSTRACT

We introduce the arsenido ligand onto the TiIV ion, yielding a remarkably covalent Ti≡As bond and the parent arsinidene Ti═AsH moiety. An anionic arsenido ligand is assembled via reductive decarbonylation involving the discrete TiII salt [K(cryptand)][(PN)2TiCl] (1) (cryptand = 222-Kryptofix) and Na(OCAs)(dioxane)1.5 in thf/toluene to produce the mixed alkali ate-complex [(PN)2Ti(As)]2(µ2-KNa(thf)2) (2) and the discrete salt [K(cryptand)][(PN)2Ti≡As] (3) featuring a terminal Ti≡As ligand. Protonation of 2 or 3 with various weak acids cleanly forms the parent arsinidene [(PN)2Ti═AsH] (4), which upon deprotonation with KCH2Ph in thf generates the more symmetric anionic arsenido [(PN)2Ti(As){µ2-K(thf)2}]2 (5). Experimental and computational studies suggest the pKa of 4 to be ∼23, and the bond orders in 2, 3, and 5 are all in the range of a Ti≡As triple bond, with decreasing bond order in 4.

16.
Anal Chem ; 96(26): 10569-10576, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38877973

ABSTRACT

The high prevalence and economic burden of heart failure remain a challenge to global health. This lifelong disease leads to a buildup of permanent heart damage, making early detection and frequent monitoring crucial for effective treatment. N-terminal proBNP (NT-proBNP) is an important biomarker for monitoring the disease state, but current commercial and research NT-proBNP assays require phlebotomy and bulky equipment or do not satisfy clinical requirements such as sensitivity and detection thresholds. Here, we report a point-of-care (POC) compatible microfluidic digital immunoassay that can quantify the NT-proBNP concentration in a small volume of whole blood. Our automated microfluidic device takes whole blood samples mixed with biotinylated detection antibodies and passes through a plasma filter to react with a capture antibody-functionalized sensor surface. Streptavidin-coated gold nanoparticles (GNPs) are then released to mark the surface-bound single NT-proBNP immunocomplexes and recorded with bright-field microscopy. NT-proBNP concentrations in the sample are quantified via a hybrid digital/analog calibration curve. Digital counts of bound GNPs are used as readout signal at low concentrations for high sensitivity detection, and GNP pixel occupancies are used at high concentrations for extended dynamic range. With this approach, we detected NT-proBNP in the range of 8.24-10 000 pg/mL from 7 µL of whole blood in 10 min, with a limit of detection of 0.94 pg/mL. Finally, the method was validated with 15 clinical serum samples, showing excellent linear correlation (r = 0.998) with Roche's Elecsys proBNP II assay. This evidence indicates that this method holds promise for decentralized monitoring of heart failure.


Subject(s)
Natriuretic Peptide, Brain , Peptide Fragments , Point-of-Care Systems , Natriuretic Peptide, Brain/blood , Humans , Immunoassay/methods , Peptide Fragments/blood , Gold/chemistry , Metal Nanoparticles/chemistry , Microfluidic Analytical Techniques/instrumentation , Lab-On-A-Chip Devices , Limit of Detection
17.
Nat Methods ; 18(3): 283-292, 2021 03.
Article in English | MEDLINE | ID: mdl-33589836

ABSTRACT

Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissues lack single-cell resolution. Here we describe an ultra-high-throughput method, Paired-Tag, for joint profiling of histone modifications and transcriptome in single cells to produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our single-cell multiomics approach enables comprehensive analysis of chromatin state and gene regulation in complex tissues and characterization of gene regulatory programs in the constituent cell types.


Subject(s)
Frontal Lobe/metabolism , Gene Expression Regulation/genetics , Hippocampus/metabolism , Histone Code/genetics , Regulatory Sequences, Nucleic Acid/genetics , Animals , Cell Line, Tumor , Chromatin/metabolism , Epigenesis, Genetic/genetics , Frontal Lobe/cytology , Gene Expression Profiling , HeLa Cells , Hippocampus/cytology , Humans , Male , Mice , Mice, Inbred C57BL , Protein Processing, Post-Translational , Single-Cell Analysis , Transcriptome/genetics
18.
Mod Pathol ; 37(6): 100493, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38615709

ABSTRACT

Demand for anal cancer screening is expected to rise following the recent publication of the Anal Cancer-HSIL Outcomes Research trial, which showed that treatment of high-grade squamous intraepithelial lesions significantly reduces the rate of progression to anal cancer. While screening for human papillomavirus-associated squamous lesions in the cervix is well established and effective, this is less true for other sites in the lower anogenital tract. Current anal cancer screening and prevention rely on high-resolution anoscopy with biopsies. This procedure has a steep learning curve for providers and may cause patient discomfort. Scattering-based light-sheet microscopy (sLSM) is a novel imaging modality with the potential to mitigate these challenges through real-time, microscopic visualization of disease-susceptible tissue. Here, we report a proof-of-principle study that establishes feasibility of dysplasia detection using an sLSM device. We imaged 110 anal biopsy specimens collected prospectively at our institution's dysplasia clinic (including 30 nondysplastic, 40 low-grade squamous intraepithelial lesion, and 40 high-grade squamous intraepithelial lesion specimens) and found that these optical images are highly interpretable and accurately recapitulate histopathologic features traditionally used for the diagnosis of human papillomavirus-associated squamous dysplasia. A reader study to assess diagnostic accuracy suggests that sLSM images are noninferior to hematoxylin and eosin images for the detection of anal dysplasia (sLSM accuracy = 0.87; hematoxylin and eosin accuracy = 0.80; P = .066). Given these results, we believe that sLSM technology holds great potential to enhance the efficacy of anal cancer screening by allowing accurate sampling of diagnostic tissue at the time of anoscopy. While the current imaging study was performed on ex vivo biopsy specimens, we are currently developing a handheld device for in vivo imaging that will provide immediate microscopic guidance to high-resolution anoscopy providers.


Subject(s)
Anus Neoplasms , Papillomavirus Infections , Proof of Concept Study , Humans , Papillomavirus Infections/complications , Papillomavirus Infections/pathology , Anus Neoplasms/virology , Anus Neoplasms/pathology , Anus Neoplasms/diagnostic imaging , Female , Anal Canal/virology , Anal Canal/pathology , Anal Canal/diagnostic imaging , Squamous Intraepithelial Lesions/virology , Squamous Intraepithelial Lesions/pathology , Microscopy/methods , Male , Biopsy , Middle Aged , Papillomaviridae , Human Papillomavirus Viruses
19.
Histopathology ; 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38859768

ABSTRACT

AIMS: Molecular classification according to The Cancer Genome Atlas (TCGA) improves endometrial endometrioid carcinoma (EEC) prognostication and has specific treatment implications; however, original data were skewed towards low-grade and low-stage tumours. Herein, we molecularly classify EECs metastatic at the time of diagnosis or with subsequently documented recurrent/metastatic disease to examine correlation with clinical outcomes. METHODS: TCGA categories include POLE-mutated, microsatellite instability (MSI), p53 abnormal (p53 abnl) and no specific molecular profile (NSMP). POLE targeted sequencing at exons 9, 11, 13 and 14 and immunohistochemistry (IHC) for PMS2, MSH6 and p53 were performed to establish molecular classification. RESULTS: The distribution in our cohort of 141 EECs was similar to that generally reported in EEC, with nine POLE-mutated (6%), 45 MSI (32%), 16 p53 abnl (11%) and 71 NSMP (50%), with similar distributions between low- and high-stage cohorts. We demonstrate that when stratified by molecular subtype, disease-specific survival from the time of high-stage (stages III-IV) presentation or time of recurrence in low-stage (stages I-II) disease among metastatic and/or recurrent EEC is strongly associated with TCGA classification (high-stage P = 0.02, low-stage P = 0.017). Discordant molecular classification between primary and metastatic/recurrent tumours occurred in four of 105 (3.8%) patients, two related to PMS2/MSH6 IHC and two related to p53 IHC. CONCLUSIONS: We demonstrate that molecular classification is prognostically relevant not only at the time of diagnosis, but also at the time of recurrence and in the metastatic setting. Rare subclonal alterations occur and suggest a role for confirming TCGA classification in recurrent/metastatic tumours.

20.
Chemistry ; : e202401736, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38845448

ABSTRACT

Reaction of a nucleophilic germylene Ge[CH(SiMe3)2]2 with the phosphanyl phosphaketene [{(H2C)(NDipp)}2P]PCO induces decarbonylation to form a phosphanyl phosphagermene [{(H2C)(NDipp)}2P]P=Ge[CH(SiMe3)2]2 (1; Dipp = 2,6-diisopropyl-phenyl). Addition of CO2 or MeCN to 1 results in [3+2]-cycloaddition reactions to afford five-membered heterocycles. This mode of reactivity is reminiscent of that observed for frustrated Lewis pairs, with the pendant phosphanyl group acting as a base and the germanium center as a Lewis acid. Contrastingly, 1,2-addition across the P=Ge bond was observed when using ammonia, small primary amines (NH2nPr, NH2iPr), or metal complexes (e.g. Au(PPh3)Cl and ZnEt2). These latter reactions allow for the one-step synthesis of metal phosphide complexes.

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