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1.
Fly (Austin) ; 18(1): 2409968, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39351922

RESUMEN

In situ hybridization techniques are powerful methods for exploring gene expression in a wide range of biological contexts, providing spatial information that is most often lost in traditional biochemical techniques. However, many in situ hybridization methods are costly and time-inefficient, particularly for screening-based projects that follow on from single-cell RNA sequencing data, which rely on of tens of custom-synthetized probes against each specific RNA of interest. Here we provide an optimized pipeline for Hybridization Chain Reaction (HCR)-based RNA visualization, including an open-source code for optimized probe design. Our method achieves high specificity and sensitivity with the option of multiplexing using only five pairs of probes, which greatly lowers the cost and time of the experiment. These features of our HCR protocol are particularly useful and convenient for projects involving screening several genes at medium throughput, especially as the method include an amplification step, which makes the signal readily visible at low magnification imaging.


Asunto(s)
Larva , ARN , Animales , Larva/genética , Larva/metabolismo , ARN/genética , Drosophila/genética , Hibridación in Situ/métodos , Drosophila melanogaster/genética
2.
Development ; 151(16)2024 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-39099456

RESUMEN

Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.


Asunto(s)
Perfilación de la Expresión Génica , Animales , Perfilación de la Expresión Génica/métodos , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transcriptoma/genética , Humanos , Hibridación in Situ/métodos , Ratones , Biología Evolutiva/métodos
3.
Virchows Arch ; 485(3): 519-526, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39120655

RESUMEN

This study describes the external quality assessment (EQA) scheme for molecular testing of RET alterations in non-small cell lung cancer (NSCLC), medullary thyroid carcinomas (MTC), and non-MTC. The lead panel institute and Quality Assurance Initiative in Pathology (Qualitätssicherungs-Initiative Pathologie [QuIP] GmbH) selected formalin-fixed paraffin-embedded (FFPE) tissue from MTC for RET mutation testing by next-generation sequencing (NGS) methods and FFPE tissue from NSCLC and non-MTC for RET gene fusion testing using either in situ hybridisation (ISH) or NGS methods, forming 3 sub-schemes of the EQA scheme. Tissue material underwent an internal validation phase followed by an external testing phase. The internal validation phase served as a cross-validation step conducted by panel institutes. In the external testing phase, the number of participating institutes in the RET point mutation sub-scheme, RET fusion (ISH) sub-scheme, and RET fusion (NGS) sub-scheme was 32, 24, and 38, respectively. The reported success rates for external testing were 96.0%, 89.5%, and 93.5% for the RET point mutation, the ISH RET fusion, and the NGS RET fusion EQA sub-schemes, respectively. These findings confirm the reliability of the NGS method in detecting RET alterations and align with current screening recommendations. Overall, 31 institutes were certified for RET point mutation testing by NGS methods, 22 institutes were certified for RET fusion testing by ISH, and 36 institutes were certified for RET fusion testing by NGS methods. Results can be employed to inform real-world diagnostic decisions in Germany, Austria, and Switzerland.


Asunto(s)
Carcinoma Neuroendocrino , Secuenciación de Nucleótidos de Alto Rendimiento , Neoplasias Pulmonares , Mutación , Proteínas Proto-Oncogénicas c-ret , Neoplasias de la Tiroides , Humanos , Proteínas Proto-Oncogénicas c-ret/genética , Neoplasias de la Tiroides/genética , Neoplasias de la Tiroides/patología , Neoplasias de la Tiroides/diagnóstico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/patología , Carcinoma Neuroendocrino/genética , Carcinoma Neuroendocrino/patología , Carcinoma Neuroendocrino/diagnóstico , Ensayos de Aptitud de Laboratorios , Carcinoma de Pulmón de Células no Pequeñas/genética , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Reproducibilidad de los Resultados , Análisis Mutacional de ADN/métodos , Fusión Génica , Hibridación in Situ/métodos
4.
PLoS One ; 19(7): e0305977, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39052564

RESUMEN

Profiling gene expression while preserving cell locations aids in the comprehensive understanding of cell fates in multicellular organisms. However, simple and flexible isolation of microregions of interest (mROIs) for spatial transcriptomics is still challenging. We present a laser-induced forward transfer (LIFT)-based method combined with a full-length mRNA-sequencing protocol (LIFT-seq) for profiling region-specific tissues. LIFT-seq demonstrated that mROIs from two adjacent sections could reliably and sensitively detect and display gene expression. In addition, LIFT-seq can identify region-specific mROIs in the mouse cortex and hippocampus. Finally, LIFT-seq identified marker genes in different layers of the cortex with very similar expression patterns. These genes were then validated using in situ hybridization (ISH) results. Therefore, LIFT-seq will be a valuable and efficient technique for profiling the spatial transcriptome in various tissues.


Asunto(s)
Perfilación de la Expresión Génica , Transcriptoma , Animales , Perfilación de la Expresión Génica/métodos , Ratones , Rayos Láser , Hipocampo/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Hibridación in Situ/métodos , Corteza Cerebral/metabolismo , Análisis de Secuencia de ARN/métodos
5.
Methods Mol Biol ; 2837: 137-148, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39044081

RESUMEN

Hepatitis B virus (HBV) developed highly intricates mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. With the aid of a series of classical analytical methods such as ultrafiltration, and Southern and Northern blots, a general framework of HBV life cycle has been established. However, this picture still lacks many key histological contexts which involves pathophysiological changes of hepatocytes, non-parenchymal cells, infiltrated leukocytes, and associated extracellular matrix. Here, we describe a CISH protocol modified from the ViewRNA assay that allows direct visualization of HBV RNA, DNA, and cccDNA in liver tissue of chronic hepatitis B patients. By coupling it with immunohistochemistry and other histological stains, much richer information regarding the HBV-induced pathological changes can be harvested.


Asunto(s)
ADN Viral , Virus de la Hepatitis B , Hibridación in Situ , Hígado , ARN Viral , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/aislamiento & purificación , Humanos , Hibridación in Situ/métodos , Hígado/virología , Hígado/metabolismo , ADN Viral/genética , ARN Viral/genética , Hepatitis B Crónica/virología , Compuestos Cromogénicos , Inmunohistoquímica/métodos , ADN Circular/genética , ADN Circular/análisis
6.
J Mol Diagn ; 26(10): 931-942, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39068989

RESUMEN

Gene expression analysis is pivotal in cancer research and clinical practice. Although traditional methods lack spatial context, RNA in situ hybridization (RNA-ISH) is a powerful technique that retains spatial tissue information. Here, RNAscope score, RT-droplet digital PCR, and automated QuantISH and QuPath were used for quantifying RNA-ISH expression values from formalin-fixed, paraffin-embedded samples. The methods were compared using high-grade serous ovarian carcinoma samples, focusing on CCNE1, WFDC2, and PPIB genes. The findings demonstrate good concordance between automated methods and RNAscope, with RT-droplet digital PCR showing less concordance. Additionally, QuantISH exhibits robust performance, even for low-expressed genes like CCNE1, showcasing its modular design and enhancing accessibility as a viable alternative for gene expression analysis.


Asunto(s)
Perfilación de la Expresión Génica , Hibridación in Situ , Neoplasias Ováricas , Humanos , Hibridación in Situ/métodos , Femenino , Perfilación de la Expresión Génica/métodos , Neoplasias Ováricas/genética , ARN/genética , Ciclina E/genética
7.
Nat Protoc ; 19(10): 3085-3137, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-38906985

RESUMEN

Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2-3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3-4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.


Asunto(s)
Tracto Gastrointestinal , Proteómica , Animales , Ratones , Tracto Gastrointestinal/metabolismo , Proteómica/métodos , Perfilación de la Expresión Génica/métodos , Transcriptoma , Inmunohistoquímica/métodos , Hibridación in Situ/métodos
8.
Head Neck Pathol ; 18(1): 51, 2024 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-38896376

RESUMEN

BACKGROUND: MYB RNA in situ hybridization (ISH) has emerged as a reliable and accessible marker to support adenoid cystic carcinoma (ACC) diagnosis, though still not well studied. Here, we report our results in a validation and prospective cohort to improve MYB RNA ISH diagnostic accuracy. METHODS: 79 cases (23 retrospective and 56 prospective) underwent MYB RNA ISH testing (44 ACC and 35 non-ACC). MYB RNA ISH results were initially interpreted based on previously established (original) scoring criteria. Weighted "i-scores", percent positive tumor cells, percent tumor cells with large signals (% LS), and staining pattern (abluminal, diffuse, focal non-patterned, or negative) were inputs for logistic regression models. Final model performance characteristics were compared with original scoring criteria and MYB::NFIB FISH results. RESULTS: An abluminal pattern was characteristic and exclusive to ACC. All i-scores, % LS, and percent positive were significantly higher in ACC. Original scoring criteria yielded a 95.5% sensitivity (Sn), 68.6% specificity (Sp), and 83.5% accuracy. MYB::NFIB FISH yielded a 42.9% sensitivity, 100% specificity, and 60% accuracy. Optimizing for performance, simplicity, and minimal collinearity, our final model was defined as: abluminal pattern and/or % LS > 16.5%, which resulted in a 93.2% Sn, 97.1% Sp, and 94.9% accuracy for ACC diagnosis. False negatives included an ACC with striking tubular eosinophilia and a MYBL1::NFIB translocated ACC. One false positive exclusive to the final model was a nasopharyngeal carcinoma with MYB amplification. CONCLUSIONS: MYB RNA ISH has a higher Sn than MYB::NFIB FISH while retaining high Sp. Our model provides improvements to specificity compared to original scoring criteria and highlight the importance of abluminal staining pattern and % LS. Nonetheless, alternate fusions remain key false negatives while rare non-ACC with other mechanisms of MYB activation may present as false positives.


Asunto(s)
Biomarcadores de Tumor , Carcinoma Adenoide Quístico , Proteínas Proto-Oncogénicas c-myb , Sensibilidad y Especificidad , Humanos , Carcinoma Adenoide Quístico/diagnóstico , Carcinoma Adenoide Quístico/genética , Carcinoma Adenoide Quístico/patología , Proteínas Proto-Oncogénicas c-myb/genética , Femenino , Persona de Mediana Edad , Masculino , Anciano , Adulto , Biomarcadores de Tumor/análisis , Biomarcadores de Tumor/genética , Estudios Retrospectivos , Hibridación in Situ/métodos , Estudios Prospectivos , Anciano de 80 o más Años , Hibridación Fluorescente in Situ/métodos , Adulto Joven
9.
Methods Mol Biol ; 2822: 143-156, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38907917

RESUMEN

RNA in situ hybridization reveals the abundance and location of gene expression in cells or tissues, providing a technical basis for the clinical diagnosis of diseases. In this chapter, we show a "V" shape probe-mediated single-molecule chromogenic in situ hybridization (vsmCISH) technique for bright-field visualization of individual RNA molecules. In our method, several pairs of target hybridization probes are hybridized to RNA molecules and each probe pair forms a "V" shape overhang. The overhang oligonucleotides then mediated the proximity ligation to form DNA circles, followed by rolling circle amplification for signal enhancement and enzyme-catalyzed chromogenic reaction-based readout. The colorimetric assay avoids problems such as photobleaching and autofluorescence of current fluorescent in situ hybridization-based single-molecule RNA detection techniques. Furthermore, the relatively straightforward protocol makes the method useful for biological research and clinical diagnosis applications.


Asunto(s)
Hibridación in Situ , ARN , Hibridación in Situ/métodos , ARN/genética , ARN/análisis , Humanos , Compuestos Cromogénicos/química , Colorimetría/métodos , Imagen Individual de Molécula/métodos
10.
Neurosci Lett ; 836: 137869, 2024 Jul 27.
Artículo en Inglés | MEDLINE | ID: mdl-38852766

RESUMEN

Dietary administration of a copper chelator, cuprizone (CPZ), has long been reported to induce intense and reproducible demyelination of several brain structures such as the corpus callosum. Despite the widespread use of CPZ as an animal model for demyelinating diseases such as multiple sclerosis (MS), the mechanism by which it induces demyelination and then allows robust remyelination is still unclear. An intensive mapping of the cell dynamics of oligodendrocyte (OL) lineage during the de- and remyelination course would be particularly important for a deeper understanding of this model. Here, using a panel of OL lineage cell markers as in situ hybridization (ISH) probes, including Pdgfra, Plp, Mbp, Mog, Enpp6, combined with immunofluorescence staining of CC1, SOX10, we provide a detailed dynamic profile of OL lineage cells during the entire course of the model from 1, 2, 3.5 days, 1, 2, 3, 4,5 weeks of CPZ treatment, as well as after 1, 2, 3, 4 weeks of recovery from CPZ treatment. The result showed an unexpected early death of mature OLs and response of OL progenitor cells (OPCs) in vivo upon CPZ challenge, and a prolonged upregulation of myelin-forming OLs compared to the intact control even 4 weeks after CPZ withdrawal. These data may serve as a basic reference system for future studies of the effects of any intervention on de- and remyelination using the CPZ model, and imply the need to optimize the timing windows for the introduction of pro-remyelination therapies in demyelinating diseases such as MS.


Asunto(s)
Linaje de la Célula , Cuprizona , Enfermedades Desmielinizantes , Oligodendroglía , Cuprizona/toxicidad , Animales , Enfermedades Desmielinizantes/inducido químicamente , Enfermedades Desmielinizantes/patología , Oligodendroglía/efectos de los fármacos , Oligodendroglía/patología , Oligodendroglía/metabolismo , Modelos Animales de Enfermedad , Hibridación in Situ/métodos , Ratones Endogámicos C57BL , Ratones , Remielinización/efectos de los fármacos , Remielinización/fisiología , Masculino , Quelantes/toxicidad , Quelantes/farmacología , Vaina de Mielina/patología , Vaina de Mielina/efectos de los fármacos , Vaina de Mielina/metabolismo
11.
Annu Rev Biomed Data Sci ; 7(1): 131-153, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38768396

RESUMEN

Overlaying omics data onto spatial biological dimensions has been a promising technology to provide high-resolution insights into the interactome and cellular heterogeneity relative to the organization of the molecular microenvironment of tissue samples in normal and disease states. Spatial omics can be categorized into three major modalities: (a) next-generation sequencing-based assays, (b) imaging-based spatially resolved transcriptomics approaches including in situ hybridization/in situ sequencing, and (c) imaging-based spatial proteomics. These modalities allow assessment of transcripts and proteins at a cellular level, generating large and computationally challenging datasets. The lack of standardized computational pipelines to analyze and integrate these nonuniform structured data has made it necessary to apply artificial intelligence and machine learning strategies to best visualize and translate their complexity. In this review, we summarize the currently available techniques and computational strategies, highlight their advantages and limitations, and discuss their future prospects in the scientific field.


Asunto(s)
Proteómica , Análisis de la Célula Individual , Análisis de la Célula Individual/métodos , Humanos , Proteómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Biología Computacional/métodos , Aprendizaje Automático , Genómica/métodos , Hibridación in Situ/métodos , Transcriptoma
12.
Plant J ; 119(3): 1627-1642, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38723112

RESUMEN

Gene expression analysis is essential for understanding the mechanisms involved in plant development. Here, we developed M2WISH, a protocol based on MicroWave treatment for Wholemount mRNA In Situ Hybridization in Arabidopsis. By permeabilizing tissues without damaging cellular organization this protocol results in high and homogeneous hybridization yields that enable systematic analysis of gene expression dynamics. Moreover, when combined with cellular histochemical staining, M2WISH successfully provides a cellular resolution of gene expression. Thus, we demonstrate the robustness of M2WISH with 10 genes on roots, aerial meristems, leaves, and embryos in the seed. We applied M2WISH to study the spatial dynamics of WUSCHEL (WUS) and CLAVATA3 (CLV3) expression during in vitro meristematic conversion of roots into shoot apical meristems. Thus, we showed that shoot apical meristems could arise from two different types of root structures that differed by their CLV3 gene expression patterns. We constructed 3D cellular representations of WUS and CLV3 gene co-expression pattern and stressed the variability inherent to meristem conversion. Thus, this protocol generates a large amount of data on the localization of gene expression, which can be used to model complex systems.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Regulación de la Expresión Génica de las Plantas , Hibridación in Situ , Meristema , Raíces de Plantas , ARN Mensajero , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Meristema/genética , Hibridación in Situ/métodos , ARN Mensajero/genética , ARN Mensajero/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Proteínas de Homeodominio/genética , Proteínas de Homeodominio/metabolismo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo
13.
PLoS One ; 19(5): e0304802, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38820371

RESUMEN

The yellow fever mosquito Aedes aegypti is a major disease vector and an increasingly popular emerging model research organism. We present here an improved protocol for the collection, fixation, and preparation of A. aegypti embryos for immunohistochemical and in situ hybridization studies. The processing of A. aegypti embryos for such studies is complicated by the inability to easily remove the vitelline membrane, which prevents the reagents needed for staining from reaching their targets, and which furthermore obscures visualization of the embryo since the membrane is highly sclerotized. Previously described protocols for removal of the vitelline membrane are very low throughput, limiting the capacity of work that can be accomplished in a reasonable timeframe. Our adapted protocol increases the throughput capacity of embryos by an individual user, with experienced users able to prepare an average of 100-150 embryos per hour. The protocol provides high-quality intact embryos that can be used for morphological, immunohistochemical, and in situ hybridization studies. The protocol has been successfully tested on embryos of ages ranging from 14h after egg laying (AEL) at 27°C through to 55h AEL. Critical to the success of the optimized protocol is the selection, fabrication, and description of the tools required. To this end, a video-demonstrated protocol has been placed at protocols.io to clarify the protocol and provide easy access and training to anyone interested in the preparation of A. aegypti embryos for biological studies.


Asunto(s)
Aedes , Hibridación in Situ , Animales , Aedes/embriología , Hibridación in Situ/métodos , Embrión no Mamífero , Fijación del Tejido/métodos , Inmunohistoquímica , Femenino
14.
Microsc Res Tech ; 87(8): 1926-1932, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38558482

RESUMEN

Detecting RNA molecules within their natural environment inside intact arthropods has long been challenging, particularly in small organisms covered by a tanned and pigmented cuticle. Here, we have developed a methodology that enables high-resolution analysis of the spatial distribution of transcripts of interest without having to dissect tiny organs or tissues, thereby preserving their integrity. We have combined an in situ amplification approach based on hybridization chain reaction, which enhances the signal-to-noise ratio, and a clearing approach that allows the visualization of inner organs beneath the cuticle. We have implemented this methodology for the first time in Hemiptera, mapping two salivary aphid (Acyrthosiphon pisum) transcripts, the effector c002 and the salivary sheath protein SHP. With a multiplex approach, we could simultaneously detect different mRNAs in mounted pea aphid head-thorax samples and show that they were distributed in distinct secretory cells of salivary glands. RESEARCH HIGHLIGHTS: Combining hybridisation chain reaction and clearing allows the detection of transcripts in intact aphids heads. The transcripts of the two salivary proteins c002 and SHP are compartmentalized in distinct secretory cells of the principal glands.


Asunto(s)
Áfidos , Cabeza , Animales , Áfidos/genética , Áfidos/metabolismo , Glándulas Salivales/metabolismo , ARN Mensajero/genética , Hibridación in Situ/métodos , Proteínas de Insectos/genética , Proteínas de Insectos/metabolismo , Expresión Génica , Proteínas y Péptidos Salivales/genética , Proteínas y Péptidos Salivales/metabolismo
15.
J Vet Diagn Invest ; 36(4): 498-505, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38650110

RESUMEN

RNAscope in situ hybridization (ISH) detects target RNA in formalin-fixed, paraffin-embedded (FFPE) tissues. Protocols suggest that prolonged FFPE storage and formalin fixation may impact signal detection, potentially limiting the utility of RNAscope ISH in retrospective studies. To develop parameters for RNAscope use with archived specimens, we evaluated the effect of formalin-fixation time by measuring the signal of a reference gene (16srRNA) in selected tissues fixed in 10% neutral-buffered formalin for 1, 2, 3, 5, 7, 10, 14, 21, 28, 60, 90, 180, and 270 d. The signal intensity and percent area of signal decreased after 180 d. Tissues had detectable signal at 180 d but not at 270 d of formalin fixation. To assess target detection in paraffin blocks, we qualitatively compared the signal of canine distemper virus (CDV) antigen via immunohistochemistry and CDV RNA via RNAscope ISH in replicate sections from blocks stored at room temperature for 6 mo, 1, 3, 6, 8, 11, 13, and 15 y; RNA was detected in FFPE tissues stored for up to 15 y. Our results demonstrate that RNAscope ISH can detect targets in tissues with prolonged paraffin storage intervals and formalin-fixation times.


Asunto(s)
Formaldehído , Hibridación in Situ , Adhesión en Parafina , Fijación del Tejido , Adhesión en Parafina/veterinaria , Hibridación in Situ/veterinaria , Hibridación in Situ/métodos , Animales , Fijación del Tejido/veterinaria , Fijación del Tejido/métodos , Perros , ARN Viral/análisis , Factores de Tiempo
16.
Methods Mol Biol ; 2757: 215-237, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38668969

RESUMEN

In situ hybridization is a powerful and precise tool for revealing cell- and tissue-specific gene expression and a critical approach to validating single-cell RNA-seq (scRNA-seq). However, applying it to highly fragile animals such as ctenophores is challenging. Here, we present an in situ hybridization protocol for adult Pleurobrachia bachei (Cydippida)-a notable reference species representing the earliest-branching metazoan lineage, Ctenophora, sister to the rest of Metazoa. We provided expression patterns for several markers of cell phenotypes, as illustrated examples. The list includes predicted small secretory molecules/neuropeptides, WntX, genes encoding RNA-binding proteins (Musashi, Elav, Dicer, Argonaut), Neuroglobin, and selected transcription factors such as BarX. Both cell- and organ-specific expression of these genes further support the convergent evolution of many ctenophore innovations, which are remarkably distinct from tissue and organ specification in other basal metazoan lineages.


Asunto(s)
Ctenóforos , Hibridación in Situ , Animales , Hibridación in Situ/métodos , Ctenóforos/genética , Ctenóforos/metabolismo , Perfilación de la Expresión Génica/métodos
17.
Mod Pathol ; 37(5): 100464, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38447752

RESUMEN

Extraskeletal myxoid chondrosarcoma (EMC) is an uncommon mesenchymal neoplasm characteristically composed of uniform-appearing round to spindle-shaped cells with eosinophilic cytoplasm and abundant myxoid extracellular matrix. Although the majority of cases harbor a pathognomonic t(9;22) translocation that fuses EWSR1 with the orphan nuclear receptor NR4A3, there are less common variants that partner NR4A3 with TAF15, TCF12, or TFG. By immunohistochemistry, EMC has features of both cartilaginous and neuroendocrine differentiation, as evidenced by inconsistent expression of S100 protein and synaptophysin or INSM1, respectively, in a subset of cases. Given the limitations of available immunohistochemical stains for the diagnosis of EMC, we analyzed genome-wide gene expression microarray data to identify candidate biomarkers based on differential expression in EMC in comparison with other mesenchymal neoplasms. This analysis pointed to CHRNA6 as the gene with the highest relative expression in EMC (96-fold; P = 8.2 × 10-26) and the only gene with >50-fold increased expression in EMC compared with other tumors. Using RNA chromogenic in situ hybridization, we observed strong and diffuse expression of CHRNA6 in 25 cases of EMC, including both EWSR1-rearranged and TAF15-rearranged variants. All examined cases of histologic mimics were negative for CHRNA6 overexpression; however, limited CHRNA6 expression, not reaching a threshold of >5 puncta or 1 aggregate of chromogen in >25% of cells, was observed in 69 of 685 mimics (10.1%), spanning an array of mesenchymal tumors. Taken together, these findings suggest that, with careful interpretation and the use of appropriate thresholds, CHRNA6 RNA chromogenic in situ hybridization is a potentially useful ancillary histologic tool for the diagnosis of EMC.


Asunto(s)
Biomarcadores de Tumor , Condrosarcoma , Hibridación in Situ , Neoplasias de los Tejidos Conjuntivo y Blando , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Humanos , Masculino , Persona de Mediana Edad , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/análisis , Condrosarcoma/genética , Condrosarcoma/patología , Condrosarcoma/diagnóstico , Condrosarcoma/metabolismo , Inmunohistoquímica , Hibridación in Situ/métodos , Neoplasias de los Tejidos Conjuntivo y Blando/genética , Neoplasias de los Tejidos Conjuntivo y Blando/patología , Neoplasias de los Tejidos Conjuntivo y Blando/diagnóstico , Neoplasias de Tejido Conjuntivo/genética , Neoplasias de Tejido Conjuntivo/patología , Neoplasias de Tejido Conjuntivo/diagnóstico , Receptores Nicotínicos/genética , Receptores Nicotínicos/metabolismo
18.
STAR Protoc ; 5(2): 102951, 2024 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-38492224

RESUMEN

Fertilized eggs initiate translation of stored mRNAs in spatially and temporally controlled manners. Here, we present a protocol for visualizing spatial and temporal translation in zebrafish embryos by fluorescence in situ hybridization and proximity ligation assay. We describe steps for labeling newly synthesized proteins and mRNA, visualizing mRNA translation and mRNA, sample mounting, and observation. Coupling detection of mRNA molecules with their translation sites is useful for understanding the molecular and cellular mechanisms that drive embryo development. For complete details on the use and execution of this protocol, please refer to Sato et al.1 and Takada et al.2.


Asunto(s)
Embrión no Mamífero , Hibridación Fluorescente in Situ , Biosíntesis de Proteínas , ARN Mensajero , Pez Cebra , Animales , Pez Cebra/embriología , Pez Cebra/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Embrión no Mamífero/metabolismo , Hibridación Fluorescente in Situ/métodos , Biosíntesis de Proteínas/genética , Hibridación in Situ/métodos , Desarrollo Embrionario/genética
19.
Am J Clin Pathol ; 161(6): 570-578, 2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38349613

RESUMEN

OBJECTIVES: In this feasibility study, we explored the combined use of circulating tumor human papillomavirus (HPV) DNA (ctHPVDNA) and HPV serology as diagnostic tests for HPV-associated oropharyngeal squamous cell carcinoma (OPSCC). METHODS: Among patients with research-banked serum or plasma at diagnosis, IgG antibodies to oncoproteins from HPV types 16, 18, 31, 33, 35, 45, 52, and 58 were detected with multiplex serology. Positivity for HPV 16 was defined based on detection of combinations of anti-E6, E1, E2, and E7 and for other high-risk types on detection of anti-E6 and anti-E7. Circulating tumor HPV DNA was detected by custom digital droplet polymerase chain reaction (ddPCR) assays for HPV types 16, 18, 33, 35, and 45. p16 immunohistochemistry and high-risk HPV RNA in situ hybridization (ISH) using a cocktail of 18 high-risk HPV types were performed on tissue. RESULTS: Of 75 patients, 67 (89.3%) were HPV-associated (p16 and HPV RNA ISH positive) and 8 (10.7%) were HPV-independent. All 8 HPV-independent patients were seronegative and negative for ctHPVDNA (100% specificity). Serology was positive in 53 (79.1%) of 67 HPV-associated patients, while ddPCR was positive for ctHPVDNA in 59 (88.6%) of 67 HPV-associated patients. Requiring both tests to be positive resulted in a sensitivity of 50 (74.6%) of 67 while combining assays (either positive) improved sensitivity to 62 (92.6%) of 67. CONCLUSIONS: Compared to HPV RNA ISH, HPV serology and ctHPVDNA are sensitive and highly specific biomarkers for HPV-associated OPSCC at the time of presentation.


Asunto(s)
ADN Viral , Estudios de Factibilidad , Neoplasias Orofaríngeas , Infecciones por Papillomavirus , Humanos , Femenino , Infecciones por Papillomavirus/diagnóstico , Infecciones por Papillomavirus/virología , Masculino , Neoplasias Orofaríngeas/virología , Neoplasias Orofaríngeas/diagnóstico , Persona de Mediana Edad , Biopsia Líquida/métodos , Anciano , ADN Viral/análisis , Carcinoma de Células Escamosas de Cabeza y Cuello/virología , Carcinoma de Células Escamosas de Cabeza y Cuello/diagnóstico , Adulto , Papillomaviridae/genética , Papillomaviridae/aislamiento & purificación , Carcinoma de Células Escamosas/virología , Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/patología , Anciano de 80 o más Años , Hibridación in Situ/métodos , Sensibilidad y Especificidad
20.
Curr Protein Pept Sci ; 25(4): 326-338, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38243942

RESUMEN

BACKGROUND: Neuropeptide pedal peptide (PP) and orcokinin (OK), which are structurally related active peptides, have been widely discovered in invertebrates and constitute the PP/OK neuropeptide family. They have complex structures and play myriad roles in physiological processes. To date, there have been no related reports of PP/OK-type neuropeptide in cephalopods, which possess a highly differentiated multi-lobular brain. METHODS: Rapid Amplification of cDNA Ends (RACE) was employed to obtain the open reading frame (ORF) of PP/OK-type neuropeptide in Sepiella japonica (termed as Sj-PP/OK). Various software were used for sequence analysis. Semi-quantitative PCR was applied to analyze the tissue distribution profile, quantitative real-time PCR (qRT-PCR) was used to study spatio-temporal expression throughout the entire growth and development period, and in situ hybridization (ISH) was employed to observe the tissue location of Sj-PP/OK. RESULTS: in the present study, we identified the ORF of Sj-PP/OK. The putative precursor of Sj-PP/ OK encodes 22 mature peptides, of which only tridecapeptides could undergo post-translationally amidated at C-terminus. Each of these tridecapeptides possesses the most conserved and frequent N-terminus Asp-Ser-Ile (DSI). Sequence analysis revealed that Sj-PP/OK shared comparatively low identity with other invertebrates PP or OK. The tissue distribution profile showed differences in the expression level of Sj-PP/OK between male and female. qRT-PCR data demonstrated that Sj-PP/OK was widely distributed in various tissues, with its expression level increasing continuously in the brain, optic lobe, liver, and nidamental gland throughout the entire growth and development stages until gonad maturation. ISH detected that Sj-PP/OK positive signals existed in almost all regions of the optic lobe except the plexiform zone, the outer edge of all functional lobes in the brain, epithelial cells and the outer membrane layer of the accessory nidamental gland. These findings suggest that Sj-PP/OK might play a role in the regulation of reproduction, such as vitellogenin synthesis, restoration, and ova encapsulation. CONCLUSION: The study indicated that Sj-PP/OK may be involved in the neuroendocrine regulation in cephalopods, providing primary theoretical basis for further studies of its regulation role in reproduction.


Asunto(s)
Secuencia de Aminoácidos , Decapodiformes , Hibridación in Situ , Neuropéptidos , Animales , Neuropéptidos/genética , Neuropéptidos/metabolismo , Neuropéptidos/química , Decapodiformes/genética , Decapodiformes/metabolismo , Hibridación in Situ/métodos , Filogenia , Sistemas de Lectura Abierta , Clonación Molecular , Secuencia de Bases , Femenino
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