Biology subjects

Kemkem, Y.

Publications and source records attributed to Kemkem, Y..

6 recordsLinked to original sources

bioRxiv2025

Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery and analyses in pituitary gland research

Previous single-cell profiling studies of the pituitary gland have yielded minimally reproducible insights largely due to their low statistical power and methodological inconsistencies. To address this problem, we generated a uniformly pre-processed Consensus Pituitary Atlas (CPA) using all existing mouse pituitary single-cell datasets (267 biological replicates, >1.1 million high-quality cells). The CPA revealed novel cell typing and lineage markers, including low-expression transcripts that previous analyses could not detect. The scale of the CPA enabled the development of machine learning models to automate and standardize cell type annotation and doublet identification for future studies. Leveraging the curated metadata, we identified sex-biased and age-dependent gene expression patterns at cell type resolution. To identify drivers of cell fates, first we determined consensus cell communication patterns. Secondly, we used RNA-sequencing and chromatin accessibility data to identify transcription factors associated with cell fates across modalities. The epitome platform acts as an interface with the CPA, allowing streamlined user-friendly analyses. HighlightsO_LIUniform processing of 267 mouse pituitary single-cell datasets (>1.1M cells) C_LIO_LIThe statistical power enabled cell type, sex- and age-specific marker discovery C_LIO_LIMachine learning models facilitate doublet detection and cell typing in new datasets C_LIO_LIepitome platform provides programming-free data access and visualizations C_LI

bioinformatics↗

bioRxiv2025

Phaeochromocytomas and paragangliomas harbour tumour-initiating SOX2+ stem cells

Phaeochromocytomas (PCCs) and paragangliomas (PGLs), are rare neuroendocrine tumours that arise in the neural crest (NC)-derived adrenal medulla and the paraganglia, respectively. Approximately 10%-15% of patients with PCCs and 35%-40% with PGLs go on to develop metastatic disease, leading to a reported median overall survival of 7 years. The development of prognostic markers and subsequent personal therapeutic strategies are hindered by a lack of understanding of tumourigenesis. In other organs, cells with stem-like properties are at the root of tumour initiation and maintenance, due to their ability to self- renew and give rise to differentiated cells. We have recently shown that, in the human adrenal, a subset of sustentacular cells, endowed with a support role, are in fact SOX2+ postnatal adrenomedullary stem cells, that are specified along the neural crest migratory route. In this study, we intended to determine if SOX2+ cells in PCCs and PGLs can behave as tumour-initiating stem cells. Using expression and transcriptomic studies, we demonstrate the presence of SOX2/SOX2-expressing cells across a broad range of PCCs and PGLs, irrespective of tumour aggressiveness, location, and causative mutation. In silico analyses reveal the co-expression of SOX2 and chromaffin cell markers in the tumour, and the active proliferation of these double-positive cells. Isolation of these cells in vitro in stem cell-promoting media, and their xenotransplantation on chicken chorioallantoic membranes, demonstrates that they have the potential to expand and metastasise in ovo, supporting their potential as tumour-initiating cells.

cancer biology↗

bioRxiv2024

Chromatin folding motifs define the basic grammar of TAD architecture in single alleles

Chromatin folding exhibits extensive cell-to-cell variability, yet whether this variability is dominated by continuously varying conformations or by recurrent organizational patterns remains unclear. Here, we combined high-resolution chromatin tracing with a novel machine learning algorithm to show that chromatin organization can be compactly represented by a limited repertoire of recurrent folding motifs. Using polymer simulations and cohesin depletion experiments, we further show that these motifs arise primarily from loop extrusion. Analysis of distinct tissues reveals that a shared motif repertoire is sufficient to describe diverse structural ensembles, with biological differences arising primarily through changes in motif occupancy and combinatorial usage. More generally, rather than generating entirely new conformations, transcriptional and disease-associated changes, including those occurring during disease onset, act primarily by redistributing motif occupancy within this common repertoire. In particular, gene activation is associated with a shift toward decompacted states and reduced contact frequencies, revealing a quantitative link between transcription and chromatin organization at the single-allele level. Together, these findings reveal that single-allele chromatin variability is structured by a constrained repertoire of recurrent folding motifs whose usage is modulated by regulatory context, providing a new framework to interpret how chromatin organization relates to gene activity.

genomics↗

bioRxiv2023

SOX2+ sustentacular cells are stem cells of the postnatal adrenal medulla

Renewal of the catecholamine-secreting chromaffin cell population of the adrenal medulla is necessary for physiological homeostasis throughout life. Definitive evidence for the presence or absence of an adrenomedullary stem cell has been enigmatic. In this work, we demonstrate that a subset of sustentacular cells endowed with a support role, are in fact adrenomedullary stem cells. Through genetic tracing and comprehensive transcriptomic data of the mouse adrenal medulla, we show that cells expressing Sox2/SOX2 specialise as a unique postnatal population from embryonic Schwann Cell Precursors and are also present in the normal adult human adrenal medulla. Postnatal SOX2+ cells give rise to chromaffin cells of both the adrenaline and noradrenaline lineages in vivo and in vitro. We reveal that SOX2+ stem cells have a second, paracrine role in maintaining adrenal chromaffin cell homeostasis, where they promote proliferation through paracrine secretion of WNT6. This work identifies SOX2+ cells as a true stem cell for catecholamine-secreting chromaffin cells.

developmental biology↗

bioRxiv2020

Pituitary stem cells produce paracrine WNT signals to control the expansion of their descendant progenitor cells

In response to physiological demand, the pituitary gland generates new hormone-secreting cells from committed progenitor cells throughout life. It remains unclear to what extent pituitary stem cells (PSCs), which uniquely express SOX2, contribute to pituitary growth and renewal. Moreover, neither the signals that drive proliferation nor their sources have been elucidated. We have used genetic approaches in the mouse, showing that the WNT pathway is essential for proliferation of all lineages in the gland. We reveal that SOX2+ stem cells are a key source of WNT ligands. By blocking secretion of WNTs from SOX2+ PSCs in vivo, we demonstrate that proliferation of neighbouring committed progenitor cells declines, demonstrating that progenitor multiplication depends on the paracrine WNT secretion from SOX2+ PSCs. Our results indicate that stem cells can hold additional roles in tissue expansion and homeostasis, acting as paracrine signalling centres to coordinate the proliferation of neighbouring cells.

developmental biology↗

bioRxiv2019

Maternal hypothyroidism in mice influences glucose metabolism in adult offspring

During pregnancy, maternal metabolic diseases and hormonal imbalance may alter fetal beta cell development and/or proliferation, thus leading to an increased risk for developing type 2 diabetes in adulthood. Although thyroid hormones play an important role in fetal endocrine pancreas development, the impact of maternal hypothyroidism on glucose homeostasis in adult offsprings remains poorly understood. Here, we show that when fed normal chow, adult mice born to hypothyroid mothers were more glucose-tolerant due to beta cell hyperproliferation and increased insulin sensitivity. However, following high fat feeding, these offsprings became profoundly hyperinsulinemic, insulin-resistant and glucose-intolerant compared to controls from euthyroid mothers. Suggesting presence of epigenetic changes, altered glucose metabolism was maintained in a second generation of animals. As such, gestational hypothyroidism induces long-term and persistent alterations in endocrine pancreas function, which may have important implications for type 2 diabetes prevention in affected individuals.\n\nSIGNIFICANCEDiabetes and hypothyroidism are two major public health issues, affecting [~] 9 and 2 % of the population worldwide, respectively. As master metabolic gatekeepers, the thyroid hormones play an essential role in metabolism and fetal development. However, gestation increases demand on the thyroid axis in the mother, leading to hypothyroidism in 0.5 % of pregnancies. Maternal hypothyroidism is associated with deficits in fetal growth that may lead to long-term alterations in metabolism in the offspring. We therefore sought to investigate the effects of gestational hypothyroidism on glucose metabolism in adult offspring and their descendants, and how this may predispose to diabetes development.

physiology↗