Biology subjects

Etchevers, H. C.

Publications and source records attributed to Etchevers, H. C..

11 recordsLinked to original sources

bioRxiv2026

Spatially resolved diversity in molecular states underlies congenital melanocytic nevi and associated tumors

The congenital melanocytic nevus (CMN) is a developmental skin disorder characterized by prenatal melanocyte overgrowth, exhibiting heterogeneity in surface size, depth, and clinical behavior. Large/giant CMN carry an elevated, anticipatory melanoma risk relative to more common, small CMN. However, deeper insights into melanocytic states, genomic and epigenomic alterations, and microenvironmental cues governing disease progression are needed to predict lesions disposed to transformation. Although large/giant CMN melanocyte heterogeneity was recently established, spatial organization of these states and their niche interactions are unknown. Using advanced spatial and single-cell transcriptomics and bulk methylomics, we characterized ten CMN, seven CMN-associated proliferative nodules and three clinically diagnosed melanomas arising in CMN from children, integrating data from healthy skin references to contextualize melanocyte states in situ. CMN-specific melanocytic states, distinct in differentiation and proliferation, were spatially stratified, with immature melanocytes in deep dermis and more differentiated melanocytes approaching the epidermis. We then constructed a robust atlas of CMN cellular states by integrating single-cell transcriptomic data from five new large/giant CMN with published datasets, using it to deconvolute the spatial information. Cell-cell communication inference uncovered enhanced signaling (e.g. pleiotrophin, IGF1, periostin, semaphorin pathways) between CMN melanocytes, fibroblasts, and hair follicle-associated cells. Analysis of CMN-derived tumors, including longitudinal cases with [≥]2 samples, revealed divergent spatial melanocytic transcription distinguishing immune-enriched lesions from tumors with oncogenic/pro-invasive signatures. Collectively, these findings establish a spatially resolved framework linking melanocyte heterogeneity, signaling, and genomic instability in CMN, providing mechanistic insights to refine risk stratification and prognosis for CMN-associated tumors.

genetics↗

bioRxiv2025

RIPOR2 promotes multinucleation of melanoma cells downstream of the RAS/ERK oncogenic pathway

One-third of skin melanomas arise from melanocytic nevi, benign skin lesions composed of clustered melanocytes. Benign nevi are associated with overactivation of the mitogen-activated protein kinase RAS/ERK pathway, resulting from driver mutations, most commonly in the BRAF or NRAS gene. However, this overactivation in melanocytes is insufficient to induce melanoma formation, as only a minority of benign nevi give rise to melanoma. Overactivation of the RAS/ERK pathway promotes genetic and epigenetic alterations by inducing aneuploidy, but the processes by which nevi evolve into melanoma via RAS/ERK pathway-dependent aneuploidy are only partially understood. Using single-nucleus RNA sequencing after overactivation of the RAS/ERK pathway in the chicken embryo, we discovered that RIPOR2 is a positive transcriptional target of this pathway, including in melanocyte precursors. Similar transcriptional control of RIPOR2 by RAS/ERK is conserved in human melanoma cells. RIPOR2 emerged as an attractive target because it encodes an atypical RHOA inhibitory protein involved in the development of physiologically multinucleated cell types. Multinucleation in cancer has been shown to promote aneuploidy, which correlates with tumor aggressiveness. We found that RIPOR2 is ectopically expressed in human nevi and skin melanomas and functionally promotes multinucleation in both an animal model and human tumor-derived cells, including melanoma cell lines. Our results suggest that RIPOR2 expression, downstream of RAS/ERK overactivation in skin melanocytes, promotes the emergence of multinucleated cells, a previously overlooked step in melanoma formation.

cancer biology↗

bioRxiv2024

Multi-modal refinement of the human heart atlas during the first gestational trimester

1.Forty first-trimester human hearts were studied to lay groundwork for further studies of principles underlying congenital heart defects. We first sampled 49,227 cardiac nuclei from three fetuses at 8.6, 9.0, and 10.7 post-conceptional weeks (pcw) for single-nucleus RNA sequencing, enabling distinction of six classes comprising 21 cell types. Improved resolution led to identification of novel cardiomyocytes and minority autonomic and lymphatic endothelial transcriptomes, among others. After integration with 5-7 pcw heart single-cell RNAseq, we identified a human cardiomyofibroblast progenitor preceding diversification of cardiomyocyte and stromal lineages. Analysis of six Visium sections from two additional hearts was aided by deconvolution, and key spatial markers validated on sectioned and whole hearts in two- and three-dimensional space and over time. Altogether, anatomical-positional features including innervation, conduction and subdomains of the atrioventricular septum translate latent molecular identity into specialized cardiac functions. This atlas adds unprecedented spatial and temporal resolution to the characterization of human-specific aspects of early heart formation.

developmental biology↗

bioRxiv2024

Deconvoluted methylation profiles discriminate between closely related melanocytic nevi

Congenital melanocytic nevi (CMN) and common acquired melanocytic nevi (AMN) are melanoma-predisposing skin conditions presenting excessive numbers of melanocytes but arising at different times in life. Appropriately weighted whole-genome methylation analysis can be used as a basis for further research in dermatopathology and as applied here provides new insights into nevus biology.

cancer biology↗

bioRxiv2024

Braf-mutant Schwann cells divert to a repair phenotype to induce congenital demyelinating neuropathy

RASopathies, rare congenital syndromes affecting multiple organ systems, often include peripheral neuropathy of unknown origin. While RASopathy-associated gene variants are proto-oncogenic, the impact of timing and mosaicism on pathogenicity remains poorly understood. Here, we investigate the links between Braf, a key mitogen-activated protein kinase (MAPK) effector, and peripheral neuropathy. By targeting Braf p.V600E, an oncogenic variant found in mosaic RASopathies, to embryonic Mpz-expressing cells in mice, we induced a congenital Charcot-Marie-Tooth-like degenerative neuropathy. This phenotype was characterized by hyperplastic nerves, hindlimb weakness, and unexpectedly reduced body size. Constitutively active Braf expanded a Jun+ Schwann cell repair state, impairing myelination and nerve homeostasis. To examine relevance to RASopathies, we differentiated patient-derived stem cells bearing the cardio-facio-cutaneous syndrome-associated BRAF p.Q257R variant into Schwann cells. Compared to wild-type controls, CFC-derived cells failed to acquire mature phenotypes, instead exhibiting progenitor or repair-type transcriptional profiles. Our findings implicate somatic mosaicism in the unresolved genetic heterogeneity of neuropathies and expand the candidate gene list for peripheral nerve disorders. Moreover, they reveal a MAPK-dependent mechanism linking neural crest-derived Schwann cell dysfunction to both body growth and nerve homeostasis, providing new insights into the mechanisms in RASopathy-associated neuropathy and potential therapeutic targets.

developmental biology↗

bioRxiv2023

Modeling corticotroph deficiency with pituitary organoids supports the functional role of NFKB2 in human pituitary differentiation

BackgroundDeficient Anterior pituitary with common Variable Immune Deficiency (DAVID) syndrome, combining adrenocorticotropic hormone deficiency (ACTHD) and primary hypogammaglobulinemia, is caused by NFKB2 heterozygous mutations. Nuclear factor kappa B (NFKB) signaling is a key regulator of the immune system; however, the underlying mechanism of its association with endocrine symptoms remains unknown. The role of NFKB2 in the development of the human pituitary was called into question by Nfkb2-deficient Lym1 mice, which have normal pituitary functions. PurposeThe aim of this study was to create a human disease model to define the role of NFKB2 in human pituitary development. MethodsWe established pituitary organoids in three-dimensional (3D) culture after directed differentiation from CRISPR/Cas9-edited human induced pluripotent stem cells (hiPSC). First, we conducted a proof-of-concept study, introducing a homozygous TBX19K146R/K146R missense pathogenic variant in hiPSC, an allele found in patients with congenital isolated ACTHD. We then used the same method to produce NFKB2D865G/D865G mutant organoids, harboring the pathogenic missense variant previously identified in DAVID patients. This mutation causes a failure of NFKB2 p100 phosphorylation that blocks processing to form active NFKB2 p52. We further characterized pituitary organoid development with bulk RNA sequencing and validated findings with quantitative RT-PCR and by immunofluorescence in section and whole organoids. ResultsAnalysis of wild-type (WT) organoids demonstrated that this in vitro model recapitulates corticotroph cell differentiation. TBX19K146R/K146R organoids conserved early expression of HESX1, but had significantly decreased PITX1, TBX19, LHX3, and POMC transcription. NFKB2D865G/D865G organoids also had dramatically reduced corticotrophs. Furthermore, NFKB2D865G/D865G significantly perturbs the expression of 67 genes known to contribute to pituitary development, among which 39 transcription factors. Differential expression was found for several growth factor genes or genes associated with the epithelial-to-mesenchymal transition and terminal endocrine differentiation. ConclusionWe used a combination of CRISPR/Cas9 editing and refinement of a 3D organoid culture protocol to model human ACTHD due to TBX19 or NFKB2 mutations. The NFKB2 variant studied induced a significant decrease in corticotroph differentiation, confirming the causative role of NFKB2 in isolated or syndromic ACTHD and demonstrating for the first time a direct functional role of NFKB2 in human pituitary development.

developmental biology↗

bioRxiv2022

Multiple congenital malformations arise from somatic mosaicism for constitutively active Pik3ca signalling

Recurrent missense mutations of the PIK3CA oncogene are among the most frequent drivers of human cancers. These often lead to constitutive activation of its product p110, a phosphatidylinositol 3-kinase (PI3K) catalytic subunit. In addition to causing a broad range of cancers, the H1047R mutation is also found in affected tissues of a distinct set of congenital tumors and malformations. Collectively termed PIK3CA-related disorders (PRDs), these lead to overgrowth of brain, adipose, connective and musculoskeletal tissues and/or blood and lymphatic vessel components. Vascular malformations are frequently observed in PRD, due to cell-autonomous activation of PI3K signaling within endothelial cells. These, like most muscle, connective tissue and bone, are derived from the embryonic mesoderm. However, important organ systems affected in PRDs are neuroectodermal derivatives. To further examine their development, we drove the most common post-zygotic activating mutation of Pik3ca in neural crest and related embryonic lineages. Outcomes included macrocephaly, cleft secondary palate and more subtle skull anomalies. Surprisingly, Pik3ca-mutant subpopulations of neural crest origin were also associated with widespread cephalic vascular anomalies. Mesectodermal neural crest is a major source of non-endothelial connective tissue in the head, but not the body. To examine the response of vascular connective tissues of the body to constitutive Pik3ca activity during development, we expressed the mutation by way of an Egr2 (Krox20) Cre driver. Lineage tracing led us to observe new lineages that had normally once expressed Krox20 and that may be co-opted in pathogenesis, including vascular pericytes and perimysial fibroblasts. Finally, Schwann cell precursors having transcribed either Krox20 or Sox10 and induced to express constitutively active PI3K were associated with vascular and other tumors. These murine phenotypes may aid discovery of new candidate human PRDs affecting craniofacial and vascular smooth muscle development as well as the reciprocal paracrine signaling mechanisms leading to tissue overgrowth.

developmental biology↗

bioRxiv2021

Sustained experimental activation of FGF8/ERK in the developing chicken spinal cord reproducibly models early events in ERK-mediated tumorigenesis

Most human cancers demonstrate activated MAPK/ERK pathway signaling as a key tumor initiation step, but the immediate steps of further oncogenic progression are poorly understood due to a lack of appropriate models. Spinal cord differentiation follows caudal elongation in vertebrate embryos; both processes are regulated by a FGF8 gradient highest in neuromesodermal progenitors (NMP), where kinase effectors ERK1/2 maintain an undifferentiated state. FGF8/ERK signal attenuation is necessary for NMPs to progress to differentiation. We show that sustained ERK1/2 activity, using a constitutively active form of the kinase MEK1 (MEK1ca) in the chicken embryo, reproducibly provokes neopasia in the developing spinal cord. Transcriptomic data show that neoplasia not only relies on the maintenance of NMP gene expression, and the inhibition of genes expressed in the differentiating spinal cord, but also on a profound change in the transcriptional signature of the spinal cord cells leading to a complete loss of cell-type identity. MEK1ca expression in the developing spinal cord of the chicken embryo is therefore a tractable in vivo model to identify the critical factors fostering malignancy in ERK-induced tumorigenesis.

developmental biology↗

bioRxiv2018

Ectopic expression of Hoxb1 induces cardiac and craniofacial malformations

Members of the large family of Hox transcription factors are encoded by genes whose tightly regulated expression in development and in space within different embryonic tissues confer positional identity from the neck to the tips of the limbs. Many structures of the face, head and heart develop from cell populations expressing few or no Hox genes. Hoxb1 is the member of its chromosomal cluster expressed in the most rostral domain during vertebrate development, but never by the multipotent neural crest cell population anterior to the cerebellum. We have developed a novel floxed transgenic mouse line, CAG-Hoxb1,-EGFP (CAG-Hoxb1), which upon recombination by Cre recombinase conditionally induces robust Hoxb1 and eGFP over-expression. When induced within the neural crest lineage, pups die at birth. A variable phenotype develops from E11.5 on, associating frontonasal hypoplasia/aplasia, micrognathia/agnathia, major ocular and forebrain anomalies, and cardiovascular malformations. Neural crest derivatives in the body appear unaffected. Transcription of effectors of developmental signaling pathways (Bmp, Shh, Vegfa) and transcription factors (Pax3, Sox9) is altered in mutants. These outcomes emphasize that repression of Hoxb1, along with other paralog group 1 and 2 Hox genes, is strictly necessary in anterior cephalic NC for craniofacial, visual, auditory and cardiovascular development.

developmental biology↗

bioRxiv2017

Widespread dynamic and pleiotropic expression of the melanocortin-1-receptor (MC1R) system is conserved across chick, mouse and human embryonic development

BackgroundMC1R, a G-protein coupled receptor with high affinity for alpha-melanocyte stimulating hormone (MSH), modulates pigment production in melanocytes from many species and is associated with human melanoma risk. MC1R mutations affecting human skin and hair color also have pleiotropic effects on the immune response and analgesia. Variants affecting human pigmentation in utero alter the congenital phenotype of both oculocutaneous albinism and congenital melanocytic naevi, and have a possible effect on birthweight.\n\nMethods and ResultsBy in situ hybridization, RT-PCR and immunohistochemistry, we show that MC1R is widely expressed during human, chick and mouse embryonic and fetal stages in many somatic tissues, particularly in the musculoskeletal and nervous systems, and conserved across evolution in these three amniotes. Its dynamic pattern differs from that of TUBB3, a gene overlapping the same locus in humans and encoding class III {beta}-tubulin. The MSH peptide and the transcript for its precursor, pro-opiomelanocortin (POMC), are similarly present in numerous extra-cutaneous tissues. MC1R genotyping of variants p.(V60M) and p.(R151C) was undertaken for 867 healthy children from the Avon Longitudinal Study of Parent and Children (ALSPAC) cohort, and birthweight modelled using multiple logistic regression analysis. A significant positive association initially found between R151C and birth weight, independent of known birth weight modifiers, was not reproduced when combined with data from an independent genome-wide association study of 6,459 additional members of the same cohort.\n\nConclusionsThese data clearly show a new and hitherto unsuspected role for MC1R in non-cutaneous solid tissues before birth.

developmental biology↗

bioRxiv2017

Pericyte ontogeny: the use of chimeras to track a cell lineage of diverse germ line origins

The goal of lineage tracing is to understand body formation over time by discovering which cells are the progeny of a specific, identified, ancestral progenitor. Subsidiary questions include unequivocal identification of what they have become, how many descendants develop, whether they live or die, and where they are located in the tissue or body at the end of the window examined. A classical approach in experimental embryology, lineage tracing continues to be used in developmental biology, stem cell and cancer research, wherever cellular potential and behavior need to be studied in multiple dimensions, of which one is time. Each technical approach has its advantages and drawbacks. This chapter, with some previously unpublished data, will concentrate non-exclusively on the use of interspecies chimeras to explore the origins of perivascular (or mural) cells, of which those adjacent to the vascular endothelium are termed pericytes for this purpose. These studies laid the groundwork for our understanding that pericytes derive from progenitor mesenchymal pools of multiple origins in the vertebrate embryo, some of which persist into adulthood. The results obtained through xenografting, like in the methodology described here, complement those obtained through genetic lineage tracing techniques within a given species.

developmental biology↗