Xabier Martinez de Morentin Iribarren

Navarrabiomed · Department of Traslational Bioinformatics

Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scRNA-seq) datasets. As a result, we robustly identify for the...

Understanding the regulation of normal and malignant human hematopoiesis requires a comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Recent studies using scRNA-seq technologies have shed light on the organization of the hematopoietic regulatory microenvironment in the mouse. These studies have resolved some...

Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scRNA-seq) datasets. As a result, we robustly identify for the...

Monocytic and granulocytic myeloid-derived suppressor cells together with tumor-infiltrating macrophages constitute the main tumor-infiltrating immunosuppressive myeloid populations. Due to the phenotypic resemblance to conventional myeloid cells, their identification and purification from within the tumors is technically difficult and makes their...

During the last decade, extensive efforts have been made to comprehend cardiac cell genetic and functional diversity. Such knowledge allows for the definition of the cardiac cellular interactome as a reasonable strategy to increase our understanding of the normal and pathologic heart. Previous experimental approaches including cell lineage tracing,...

Background While programmed cell death receptor 1 (PD-1) blockade treatment has revolutionized treatment of patients with melanoma, clinical outcomes are highly variable, and only a fraction of patients show durable responses. Therefore, there is a clear need for predictive biomarkers to select patients who will benefit from the treatment. Method...

Biological systems are extremely complex and have emergent properties that cannot be explained or even predicted by studying their individual parts in isolation. The reductionist approach, although successful in the early days of molecular biology, underestimates this complexity. As the amount of available data grows, so it will become increasingly...

Recent progress in single-cell genomics has generated multiple tools for cell clustering, annotation, and trajectory inference; yet, inferring their associated regulatory mechanisms is unresolved. Here we present scMomentum, a model-based data-driven formulation to predict gene regulatory networks and energy landscapes from single-cell transcriptom...

Background: Cardiac fibroblasts (CFs) have a central role in the ventricular remodeling process associated with different types of fibrosis. Recent studies have shown that fibroblasts do not respond homogeneously to heart injury. Because of the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population heteroge...

Cardiac fibroblasts have a central role during the ventricular remodeling process associated with different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited se...

The benefits of mindfulness on human health are well-documented, but the mechanisms underlying these effects are not well-understood. Our aim was to identify molecular alterations related to mindfulness by profiling the epigenetic response in long-term meditators. We performed a genome-wide screen of DNA methylation by using the Illumina HumanMethy...

Protein S-nitrosylation is a cysteine post-translational modification mediated by nitric oxide. An increasing number of studies highlight S-nitrosylation as an important regulator of signaling involved in numerous cellular processes. Despite of the significant progress in the development of redox proteomic methods, identification and quantification...

Significance: Loss of smell is involved in early stages of Alzheimer's disease (AD), usually preceding classic disease symptoms. However, the mechanisms governing this dysfunction are still poorly understood, losing its potential as a useful tool for clinical diagnosis. Our study characterizes potential AD-associated molecular changes in APP/PS1 m...

Olfactory dysfunction is present in up to 90% of Alzheimer's disease (AD) patients. Although deposition of hyperphosphorylated tau and β-amyloid substrates are present in olfactory areas, the molecular mechanisms associated with decreased smell function are not completely understood. We have applied mass spectrometry-based quantitative proteomics t...

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells that are defined by their myeloid origin, immature state and ability to potently suppress T cell responses. They regulate immune responses and the population significantly increases in the tumor microenvironment of patients with glioma and other malignant tumors. For t...

Myeloid-derived suppressor cells (MDSCs) differentiate from bone marrow precursors, expand in cancer-bearing hosts and accelerate tumor progression. MDSCs have become attractive therapeutic targets, as their elimination strongly enhances anti-neoplastic treatments. Here, immature myeloid dendritic cells (DCs), MDSCs modeling tumor-infiltrating subs...

The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections which, in turn, define ∼ 900 neuroanatomically subdivisions in the adult brain (Hawrylycz MJ et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revea...