Biology subjects

Sinnett, D.

Publications and source records attributed to Sinnett, D..

8 recordsLinked to original sources

bioRxiv2025

Therapeutic Inducers of NK cell Killing (ThINKK)-induced NK cell cytotoxicity against childhood acute lymphoblastic leukemia: unraveling the dual role of TRAIL leads to the establishment of an efficacy biomarker

BackgroundTherapeutic Inducers of Natural Killer cell Killing (ThINKK) represent a novel class of immunotherapy designed to enhance the graft-versus-leukemia effect of hematopoietic stem cell transplantation in pediatric patients with high-risk or relapse leukemia. Our previous work identified high expression of TRAIL as a key signature of Natural Killer (NK) cell stimulation by ThINKK. In this study, we aim to elucidate the mechanisms underlying acute lymphoblastic leukemia (ALL) killing by ThINNK-stimulated NK cells and to identify predictive sensitivity markers of this innovative approach. MethodsWe performed NK cell cytotoxic assays using a panel of genetically diverse ALL cell lines and patients samples. Gene deletion and gene enforced expression in sensitive or resistant cell lines were performed to demonstrate the role of TRAIL-receptors expression and death receptor signaling pathway in ALL cell death induced by ThINKK-stimulated NK cells. These findings were further validated through the analysis of primary patients samples and transcriptomic profiling of a cohort of 320 ALL patients from the CHU Sainte-Justine. ResultsWe found that ALL sensitivity to ThINKK-stimulated NK cell killing was independent of their genetic background or their HLA expression. In addition, our data revealed the dual role of TRAIL: first, a strong NK cell activating receptor that induced rapid killing of ALL expressing TRAIL-R2, and second, a death-receptor ligand inducing ALL apoptosis following sustained engagement with its receptors. The transcriptomic analysis of ALL patients samples indicated that TRAIL-R2 and TRAIL-R1 are widely expressed across ALL subtypes and are not downregulated at relapse. ConclusionThese findings support the use of TRAIL receptor expression as a biomarker of sensitivity to ThINKK immunotherapy and establish a mechanistic framework to guide patient stratification and therapeutic optimization.

immunology↗

bioRxiv2025

Unveiling the temporal impact: Exploring dynamic changes in the paediatric solid tumour immune microenvironment through time

The composition of the tumour immune microenvironment (TIME) influences tumour evolution and responsiveness to immunotherapy. While longitudinal changes in TIME have been well-characterized in adult cancers, its dynamics in childhood cancers remain poorly documented, limiting our ability to predict treatment responses and tailor immunotherapeutic strategies. This study aimed to evaluate the plasticity of TIME in paediatric solid tumours, investigate its longitudinal evolution, and identify time-dependent immune alterations. Transcriptomic data from longitudinal samples of 27 paediatric patients (<21 years old) with relapsed or refractory solid tumours were analysed, encompassing 70 timepoints: 16 diagnoses and 54 successive relapses. TIME plasticity was assessed using gene expression clustering and immune cell infiltration enumeration. Patient-adjusted longitudinal analyses were performed using generalised linear mixed models (glmmSeq), adjusted for age and sex. Temporal associations of immune changes were further explored using dynamic regression models. Thirteen patients exhibited significant changes in their TIME profile, indicating high TIME plasticity. Over time, the TIME shifted toward a tolerogenic and immunosuppressive state, characterised by decreased activity in immune pathways (e.g., T cell receptor signalling) and enrichment of tolerogenic (e.g., macrophage differentiation) and oncogenic pathways (e.g., IL6-JAK-STAT3). The core enrichment of upregulated pathways contained key immunosuppressive factors: immune checkpoints (CTLA-4), tumour-associated macrophage activators (CSF1/CSF1R), T-regulatory cell activators (TGFB1), and immunosuppressive genes (IL10RA). This study provides evidence that the TIME in paediatric solid tumours is plastic and remodels towards immune depletion and tolerogenicity. This evolution may underlie treatment resistance and disease progression, underscoring the need for TIME-informed therapeutic approaches in paediatric oncology. Significance StatementThis article demonstrates the plasticity of the tumour immune micro-environment (TIME) of paediatric solid tumours throughout disease evolution. Longitudinal transcriptomic analyses of 70 tumour samples from 27 patients showed a progressive remodelling towards tolerogenicity and immune depletion. Key immunosuppressive factors, including immune checkpoints and tumour-associated macrophages, were identified as potential contributors to immune escape. These findings support the relevance of longitudinal immune monitoring in paediatric oncology and may inform future strategies for immunotherapeutic interventions.

cancer biology↗

bioRxiv2025

Time-dependent chromatin maturation during 3D spheroid culture improves preclinical modeling of non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is the deadliest cancer worldwide. Therapeutic progress stagnate, highlighting the complexity to replicate NSCLC in preclinical models. Drug discovery studies rely mostly on cancer cells in two-dimension (2D), which poorly predict drug efficacy in patients. There is a growing interest in three-dimensional (3D) preclinical models, such as 3D spheroids, to better model tumor phenotype and improve therapeutic prediction. However, a comprehensive view of 3D culture methods impact on transcriptomes, epigenomes and pharmacological responses and their correlations to NSCLC tumors is still missing. Here, we demonstrate that NSCLC spheroids undergo time-dependent transcriptomic and epigenomic changes, which peak after 3 weeks of culture. While DNA methylome remained stable, chromatin methylation and acetylation marks gained features of advanced NSCLC in a time-dependent manner. Single-cell transcriptomic profiling of spheroids demonstrated that time of 3D culture improved the correlation to NSCLC tumors. Moreover, long-term culture of 3D spheroids increased drug screening predictability, by showing resistance to drugs that failed in NSCLC patients (such as HDAC inhibitors) while demonstrating novel pharmacological vulnerabilities and synergistic interactions (such as combination of PRMT and HDAC inhibitors). Strikingly, reverting 3D spheroids back to 2D culture rapidly reversed transcriptomic, epigenetic and pharmacological signatures acquired after 3 weeks of 3D culture, highlighting the critical impact of cell culture conditions on NSCLC phenotype. Collectively, our findings demonstrate that implementing a time-dependent maturation process into 3D spheroid culture induces chromatin and transcriptomic changes that enhance NSCLC preclinical modeling.

cancer biology↗

bioRxiv2024

Mouse embryonic stem cells require sustained DNMT1-mediated DNA methylation maintenance for epigenomic, genomic and functional integrity

Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. However, only partial reversal could be achieved. Extensive changes in DNA methylation, histone modifications and gene expression were detected, along with transposable element de-repression and genomic instability. Reduction of cellular size, complexity and proliferation rate were observed, as well as lasting effects in germ layer lineages and embryoid bodies. Interestingly, by analyzing the impact on imprinted regions, we uncovered 20 regions exhibiting imprinted-like signatures. Notably, while many permanent effects persisted throughout Dnmt1 inactivation and rescue, others arose from the rescue intervention. Lastly, rescuing DNMT1 after differentiation initiation worsened outcomes, reinforcing the need for early intervention. Our findings highlight the far-reaching functions of DNMT1 and provide valuable perspectives on the repercussions of epigenetic perturbations during early development and the challenges of rescue interventions. HIGHLIGHTS- Extensive changes to epigenomic landscapes and gene expression following transient loss of DNMT1 activity - Dysregulation of known imprinted regions and identification of 20 regions with imprinted-like signatures - De-repression of MERVL and MT2 LTRs with evidence of chimeric gene transcript generation - Shorter telomeres, DNA damage accumulation and reduction of cell size, internal complexity and proliferation rate - Lasting effects upon differentiation toward germ layer lineages and embryoid bodies - Worsened molecular and cellular outcomes when delaying Dnmt1 rescue until after differentiation initiation O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/592204v3_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@d88ea7org.highwire.dtl.DTLVardef@17d7c87org.highwire.dtl.DTLVardef@17ab304org.highwire.dtl.DTLVardef@7ef981_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG

cell biology↗

bioRxiv2020

Pre-Implantation Alcohol Exposure Induces Lasting Sex-Specific DNA Methylation Programming Errors in the Developing Forebrain

BackgroundPrenatal alcohol exposure is recognized for altering DNA methylation profiles of brain cells during development, and to be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol exposure during pre-implantation, the early embryonic window marked with dynamic DNA methylation reprogramming, and on how this may rewire the brain developmental program. ResultsUsing a pre-clinical in vivo mouse model, we show that a binge-like alcohol exposure during pre-implantation at the 8-cell stage leads to surge in morphological brain defects and adverse developmental outcomes during fetal life. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinting control regions, and abnormal de novo DNA methylation profiles in various biological pathways (e.g., neural/brain development). ConclusionThese findings support that alcohol-induced DNA methylation programming deviations during pre-implantation could contribute to the manifestation of neurodevelopmental phenotypes associated with FASD.

developmental biology↗

bioRxiv2019

Developmental Genome-Wide DNA Methylation Asymmetry Between Mouse Placenta and Embryo

In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.

developmental biology↗

bioRxiv2019

Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

Childhood acute lymphoblastic leukemia (cALL) is the most common pediatric cancer. It is characterized by bone marrow lymphoid precursors that acquire genetic alterations, resulting in disrupted maturation and uncontrollable proliferation. More than a dozen molecular subtypes of variable severity can be used to classify cALL cases. Modern therapy protocols currently cure 85-90% of cases, but other patients are refractory or will relapse and eventually succumb to their disease. To better understand these difficult cases, we investigated the nature and extent of intra-individual transcriptional heterogeneity of cALL at the cellular level by sequencing the transcriptomes of 39,375 individual cells in eight patients (six pre-B and two pre-T) and three healthy pediatric controls. We observed intra-individual transcriptional clusters in five out of the eight patients. Using pseudotime maturation trajectories of healthy B and T cells, we obtained the predicted developmental state of each leukemia cell and observed distribution shifts within patients. We showed that the predicted developmental states of these cancer cells are inversely correlated with ribosomal protein expression levels, which could be a common contributor to intra-individual heterogeneity in cALL patients.

cancer biology↗

bioRxiv2018

Targeting MYC Overexpressing Leukemia with Cardiac Glycoside Proscillaridin Through Downregulation of Histone Acetyltransferases

Targeting MYC oncogene remains a major therapeutic goal in cancer chemotherapy. Here, we demonstrate that proscillaridin, a cardiac glycoside approved for heart failure treatment exhibit anticancer selectivity towards high MYC expressing leukemic cell lines and leukemia stem cells. At a clinically relevant concentration, proscillaridin induced a rapid downregulation of MYC protein level, due to a significant decrease in MYC protein half-life. Proscillaridin treatment induced a downregulation of gene sets involved in MYC pathway, and a concomitant upregulation of genes involved in hematopoietic differentiation. Proscillaridin induced a significant loss of lysine acetylation in histone H3 (K9, K14, K18 and K27) and in non-histone proteins such as MYC, MYC target proteins, and a series of histone acetylation regulators. Loss of lysine acetylation correlated with a rapid downregulation of histone acetyltransferase protein levels, involved in histone and MYC acetylation (CBP, P300, GCN5, TIP60, and MOZ), preferentially in MYC overexpressing leukemia as compared to other cancer cells. These results support the repurposing of proscillaridin in MYC overexpressing leukemia and propose a novel strategy to target MYC in cancer.

pharmacology and toxicology↗