Biology subjects

Dion, C.

Publications and source records attributed to Dion, C..

6 recordsLinked to original sources

bioRxiv2025

Global re-organisation of genome architecture at the transition to gametogenesis

Global epigenetic resetting in the gonadal primordial germ cells (PGCs) enables transition from early PGCs to gametogenesis and eventual restoring of totipotency after fertilisation. This reprogramming process involves global DNA demethylation, changes in nuclear morphology as well as remodeling of repressive histone modifications. Here, using combined cytological and Hi-C based methods, we reveal that following the epigenetic reprogramming and concomitant with their commitment to gametogenesis, pre-meiotic gonadal germ cells are characterised by a unique chromosome and genome architecture. This involves separation of individual chromosomes and anchoring of centromeres at the nuclear periphery, reduction of inter-chromosome interactions and disentangling of chromosome ends. Furthermore, genome-wide contact mapping documents striking remodeling of 3D genome architecture across all observable levels including disruption of topological associating domains (TADs), loss of detectable loops and reduced active-active compartment interactions. We further show that the diminished TADs correlate with the reduced levels of CTCF thus providing a unique in vivo physiological model to understand genome folding principles. Finally, we show that primordial germ cell like cells (PGCLCs), derived from embryonic stem cells, do not exhibit the same chromatin organisation as embryonic germ cells suggesting that the 3D genome remodeling accompanies acquisition of meiotic competency. Collectively, our findings uncover the existence of a unique chromatin architecture in premeiotic male and female gonadal germ cells and document that alongside global DNA demethylation, the germline epigenetic reprogramming involves erasure of memory at the genome architectural level through a complete re-organisation of the 3D genome.

cell biology↗

bioRxiv2025

High resolution multi-scale profiling of embryonic germ cell-like cells derivation reveals pluripotent state transitions in humans

Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which can be expanded and maintained in standard human pluripotent stem cell medium. hEGCLCs are transcriptionally similar to human pluripotent stem cells (hPSCs) and can differentiate into all three germ layers, as well as giving rise to PGCLCs once more - demonstrating the interconvertibility of pluripotent states. This is also evident at the epigenetic level, as the initial DNA demethylation that occurs in hPGCLCs is largely reversed in hEGCLCs, restoring DNA methylation to the level observed in hPSCs. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/632914v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@14572bcorg.highwire.dtl.DTLVardef@6fa7c1org.highwire.dtl.DTLVardef@6eaa99org.highwire.dtl.DTLVardef@1822307_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefWe report the first fully defined system to efficiently convert hPGCLCs to a pluripotent stem cell (PSC) state. We tracked pluripotent state transitions by multi-omic analysis and provided a high-resolution map of the transcriptional and epigenomic transitions upon entry to and exit from the human germline. HighlightsO_LIEfficient derivation of hEGCLC in fully defined feeder-free conditions C_LIO_LISingle-cell transcriptomic profiling of transitions from the hPSC state to hPGCLCs and back. C_LIO_LILongitudinal DNA methylation profiling highlights the overall reversibility of epigenetic states C_LIO_LIMulti-omic gene regulatory network analysis identifies key regulators of pluripotent transitions C_LI

developmental biology↗

bioRxiv2024

Human melanoma cell lines that possess wild-type BRAF alleles but are dependent on ERBB4 and ERBB2

Metastatic skin cutaneous melanomas that contain wild-type BRAF alleles typically possess an activating mutation in a RAS allele or a loss-of-function mutation in an NF1 allele ("BRAF-WT&RAS/NF1-mutant melanomas"). Nonetheless, these tumors remain a significant clinical challenge; they are resistant to MEK and BRAF inhibitors, their response to immune checkpoint inhibitors is less robust than the response of BRAF mutant melanomas to these agents, and additional validated targets for therapeutic intervention have yet to be identified. Previous work from our laboratory has demonstrated that ERBB4 is required for the proliferation of the IPC-298, MEL-JUSO, MeWo, and SK-MEL-2 BRAF-WT&RAS/NF1-mutant melanoma cell lines. Surprisingly, the synthetic constitutively dimerized and active Q646C ERBB4 mutant allele appears to strongly inhibits the proliferation of BRAF-WT&RAS/NF1- mutant melanoma cell lines. Given that we have also previously demonstrated that ERBB4-ERBB2 and ERBB4-EGFR heterodimers are more potent drivers of proliferation than are ERBB4 homodimers, here we begin to test the hypothesis that ERBB4 heterodimers drive the proliferation of BRAF-WT&RAS/NF1-mutant melanoma cell lines. Here we demonstrate that the kinase-deficient (dominant-negative) ERBB2 K753A mutant allele inhibits the clonogenic proliferation of the IPC-298, MEL-JUSO, and MeWo ERBB4-dependent, BRAF-WT&RAS/NF1-mutant melanoma cell lines. Moreover, the kinase-deficient (dominant-negative) EGFR K721A mutant allele inhibits the clonogenic proliferation of the MeWo cell line, but not the IPC-298 or MEL-JUSO cell lines. Finally, the clonogenic proliferation of the SK-MEL-2 ERBB4-dependent, BRAF-WT&RAS/NF1-mutant melanoma cell line is unaffected by the ERBB2 K753A or EGFR K721A dominant-negative mutant alleles. We discuss these findings in the context of our hypothesis that ERBB4 heterodimers drive the proliferation of BRAF-WT&RAS/NF1-mutant melanoma cell lines.

cancer biology↗

bioRxiv2023

Primordial germ cell DNA demethylation and development require DNA translesion synthesis.

Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. It remains unclear if the role of DDR is solely in meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for pre-meiotic germ cell development in the embryo. Loss of the central TLS component, REV1, significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/- or PcnaK164R/K164R) or extension (Rev7-/-) result in a >150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both activation of the germ cell transcriptional program and in DNA demethylation, a critical step in germline epigenetic reprogramming. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for progression through the earliest stages of germ cell development in mammals.

developmental biology↗

bioRxiv2021

SMCHD1 variants may induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome

An expanding number of genetic syndromes are linked to mutations in genes encoding factors that guide chromatin organization. Recently, distinct genetic syndromes have been linked to mutations in the SMCHD1 gene. However, the function of this non-canonical SMC protein remains partly defined in Human tissues. To address this question, we determined its epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS) linked to heterozygous mutations in this gene. By combining RNA-Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers. Our results emphasize dual functions for SMCHD1, in chromatin compaction, chromatin insulation and gene regulation with variable outcomes and targets depending on tissues. We propose that altered DNA methylation and long-range chromatin organization at a number of loci required for development and tissue differentiation, trigger variegated gene expression in rare genetic diseases linked to heterozygous SMCHD1 mutations.

genetics↗

bioRxiv2018

Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy.

Facio-Scapulo Humeral dystrophy (FSHD) is the third most common myopathy, affecting 1 amongst 10,000 individuals (FSHD1, OMIM #158900). This autosomal dominant pathology is associated in 95% of cases with genetic and epigenetic alterations in the subtelomeric region at the extremity of the long arm of chromosome 4 (q arm). A large proportion of the remaining 5% of cases carry a mutation in the SMCHD1 gene (FSHD2, OMIM #158901). Here, we explored the 3D organization of the 4q35 locus by three-dimensions DNA in situ fluorescent hybridization (3D-FISH) in primary cells isolated from patients. We found that D4Z4 contractions and/or SMCHD1 mutations impact the spatial organization of the 4q35 region and trigger changes in the expression of different genes. Changes in gene expression was corroborated in muscle biopsies suggesting that long distance interaction modulate expression of a number of genes at the 4q35 locus in FSHD. Using induced pluripotent stem cells (hIPSC), we examined if chromatin organization is inherited or acquired during differentiation. Our data suggest that folding of the 4q35 region is modified upon differentiation. These results together with previous findings highlight the role of the D4Z4 repeat in the organization of chromatin and further indicate that the D4Z4-dependent 3D structure induces transcriptional changes of 4q35 genes expression.

cell biology↗