Biology subjects

Hernandez, J. M.

Publications and source records attributed to Hernandez, J. M..

3 recordsLinked to original sources

bioRxiv2021

FECAL MICROBIOME OF CHILDREN WITH NOROVIRUS GASTROENTERITIS

The human fecal microbiome is composed of endogenous bacteria, eukaryotic viruses, bacteriophages and retroviruses. Several pathological conditions, including gastroenteritis, may be characterized by imbalance of gastrointestinal functions, with alteration in the diversity and composition of the fecal microbiota. Were analyzed twenty-seven fecal microbiome in children hospitalized with gastroenteritis (norovirus positive) from northern region of Brazil. After sequencing, was verified the presence of the domains Bacteria (95%) and Eukaryota (3.1%), the viruses represented 1.9%. Among the pathogenic viruses were found in addition to noroviruses the picornaviruses, enterovirus and parechovirus. The bacteriophages detected were of Caudovirales order, families Siphoviridae, Podoviridae and Myoviridae. In 22.2% (6/27) of the samples was observed co-infection between norovirus, enterovirus B and echovirus. As for the others components of the microbiome, we can highlight the presence of the taxonomic groups: Terrabacteria (50.2%), composed mainly of Actinobacteria and Firmicutes; Proteobacteria (34.5%) represented by the Enterobacteriaceae family; and FCB group (22%) whose most abundant microorganisms were those of the phylum Bacterioidetes. We performed a metagenomic approach to analyze the fecal microbiota of children with viral gastroenteritis, it was observed that the bacterias (Enterobacteriaceae) deserve attention in a possible association with noroviruses, as they were found in large quantities in infections. In addition, other enteric viruses were observed, such as enteroviruses.

microbiology↗

bioRxiv2020

IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues

The diverse composition of mammalian tissues poses challenges for understanding the cell-cell interactions required for organ homeostasis and how spatial relationships are perturbed during disease. Existing methods such as single-cell genomics, lacking a spatial context, and traditional immunofluorescence, capturing only 2-6 molecular features, cannot resolve these issues. Imaging technologies have been developed to address these problems, but each possesses limitations that constrain widespread use. Here we report a new method that overcomes major impediments to highly multi-plex tissue imaging. Iterative Bleaching Extends multi-pleXity (IBEX) uses an iterative staining and chemical bleaching method to enable high resolution imaging of >65 parameters in the same tissue section without physical degradation. IBEX can be employed with various types of conventional microscopes and permits use of both commercially available and user-generated antibodies in an open system to allow easy adjustment of staining panels based on ongoing marker discovery efforts. We show how IBEX can also be used with amplified staining methods for imaging strongly fixed tissues with limited epitope retention and with oligonucleotide-based staining, allowing potential cross-referencing between flow cytometry, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and IBEX analysis of the same tissue. To facilitate data processing, we provide an open source platform for automated registration of iterative images. IBEX thus represents a technology that can be rapidly integrated into most current laboratory workflows to achieve high content imaging to reveal the complex cellular landscape of diverse organs and tissues. Significance StatementSingle cell flow cytometry and genomic methods are rapidly increasing our knowledge of the diversity of cell types in metazoan tissues. However, suitably robust methods for placing these cells in a spatial context that reveal how their localization and putative interactions contribute to tissue physiology and pathology are still lacking. Here we provide a readily accessible pipeline (IBEX) for highly multi-plex immunofluorescent imaging that enables a fine-grained analysis of cells in their tissue context. Additionally, we describe extensions of the IBEX workflow to handle hard to image tissue preparations and a method to facilitate direct integration of the imaging data with flow cytometry and sequencing technologies.

immunology↗

bioRxiv2020

Single-cell atlas of tumor clonal evolution in liver cancer

Tumor evolution is a key feature of tumorigenesis and plays a pivotal role in driving intratumor heterogeneity, treatment failure and patients prognosis. Here we performed single-cell transcriptome profiling of 46 primary liver cancers from 37 patients enrolled for interventional studies. We surveyed the landscape of ~57,000 malignant and non-malignant cells and determined tumor cell clonality by developing a machine learning-based consensus clustering method. We found evidence of tumor cell branching evolution using hierarchical clustering, RNA velocity as well as reverse graph embedding methods. Interestingly, an increasing tumor cell clonality was tightly linked to patients prognosis, accompanied by a polarized immune cell landscape. We identified osteopontin as a key player for tumor cell evolution and microenvironmental reprogramming. Our study offers insight into the collective behavior of tumor cell communities in liver cancer as well as potential drivers for tumor evolution in response to therapy.

cancer biology↗