Biology subjects

Craciun, L.

Publications and source records attributed to Craciun, L..

7 recordsLinked to original sources

bioRxiv2025

Sox9-dependent plasticity of esophageal progenitors is fine-tuned by cues from the microenvironment

Cell plasticity governs tissue regeneration but can also drive metaplasia, the replacement of one cell type with another. This process increases the risk of cancer development in several tissues, including esophagus. Esophageal metaplasia development partly depends on keratinocyte plasticity, making regulation of esophageal progenitor fate critical. We previously identified Sox9 as instrumental in regulating esophageal cell plasticity following Hedgehog pathway activation. Our current study reveals that Hedgehog indirectly regulates Sox9 by modifying epithelial-stromal communication. This activates TGF-{beta} and BMP pathways in epithelial cells, which synergistically regulate Sox9 and stimulate a transcriptomic program resembling squamo-columnar junction progenitors, which are prone to initiate metaplasia. Importantly, we demonstrate pharmacological modulation of this plasticity in vivo. Indeed, Ibuprofen inhibits Hedgehog-induced Sox9 expression by directly targeting epithelial cells, providing proof of concept for pharmacological intervention in cell plasticity with implications for regenerative medicine and metaplasia treatment.

cell biology↗

bioRxiv2024

Tcf4 Deficiency Causes Recurrent Seizures in Mice

Transcription factor 4 (TCF4) is a transcription factor that is critical for the normal development and function of the central nervous system. Haploinsufficiency of TCF4 causes Pitt-Hopkins Syndrome (PTHS), a lifelong neurodevelopmental disorder characterized by seizures and intellectual disability. To expand our currently limited understanding of TCF4 function and PTHS pathophysiology, we created a mouse model of PTHS with largely astrocyte-specific heterozygous knockout of Tcf4. These mice developed severe recurrent seizures and had decreased lifespans. In addition, we found that these mice had astrogliosis as well as increased neuronal activity in the cortex, hippocampus, amygdala, and hypothalamus. Furthermore, single nucleus RNA sequencing analysis revealed global changes in the gene expression profiles of excitatory neurons, inhibitory neurons, astrocytes, and oligodendrocytes of PTHS compared to wild-type mice. Overall, this is the first report of a PTHS mouse model with seizures, providing the field with a tool to investigate the mechanisms of PTHS development and progression and develop therapeutics for PTHS and its associated epilepsy. HIGHLIGHTSO_LINovel PTHS mouse model that targets astrocytes develops epilepsy C_LIO_LIPTHS mice exhibit astrogliosis and increased neuron activity C_LIO_LIChanges in gene expression profile observed in PTHS mice across neurons and glial cells C_LI

neuroscience↗

bioRxiv2024

Role of copper during microglial inflammation

Copper plays crucial roles in various physiological functions of the nervous and immune systems. Dysregulation of copper homeostasis is linked to several diseases, including neurodegenerative diseases. Since dysfunctional microglial immunity can contribute to such diseases, we investigated the role of copper in microglial immunity. We found that both increased and decreased copper levels induced by chemical treatments suppresses lipopolysaccharide (LPS)-mediated inflammation in microglial cells, as determined by RT-qPCR analysis. RNA sequencing (RNA-seq) analysis confirmed that increased copper level reduces the inflammatory response to LPS; however, it also showed that decreased copper level affects genes involved in cell proliferation, transcription, and autophagosome regulation. These findings suggest that copper is vital for maintaining normal immune function in microglia, and both copper excess and deficiency can disrupt microglial immunity.

neuroscience↗

bioRxiv2024

Single nuclei and spatial transcriptomes suggest a stratification of papillary and anaplastic thyroid cancer cells

Sixty percent of papillary thyroid cancers (PTCs) are driven by BRAFV600E, a mutation associated with high inter- and intra-tumoral heterogeneity. PTCs may become highly aggressive anaplastic thyroid cancers (ATC). While single cell transcriptomics may resolve this heterogeneity, it is potentially confounded by technical effects whose correction may dampen inter-tumor variations. Here we profiled ATCs and BRAFV600E PTCs with single nuclei RNA-seq and spatial transcriptomics, and an experimental design disentangling biological and technical variations. It reveals that much transcriptional variation in cancer cells and several immune cell types is idiosyncratic, i.e. tumor-specific, a phenomenon obscured by batch integration in a number of single cell studies. Idiosyncrasies are associated in some cases with genomic aberrations and global tissue states like hypoxia. Beyond idiosyncrasies, differentiation markers SLC5A5 (NIS), TPO, TG and TSHR are lost in a sequence mirrored by their gain during human thyroid organoids maturation, suggesting a new classification of cancer cell states. PTC cells retain TSHR expression and show features of partial EMT with a massive expression of FN1, which promotes proliferation via an autocrine loop. In contrast, ATCs undergo full blown EMT, with expression of mesenchymal extracellular components and loss of TSHR. Finally, we show that the microenvironment of cancer cells is driven by inflammation. These findings may help future stratifications of BRAFV600E PTCs.

cancer biology↗

bioRxiv2023

CDK4 phosphorylation status and rational use for combining CDK4/6 and BRAF/MEK inhibition in advanced thyroid carcinomas

Despite overall good prognosis associated to thyroid cancer (TC), poorly differentiated carcinomas (PDTC) and anaplastic carcinomas (ATC, one of the most lethal human malignancies) represent major clinical challenges. We have shown that the presence of active T172-phosphorylated CDK4 predicts sensitivity to CDK4/6 inhibitory drugs (CDK4/6i) including palbociclib. Here, CDK4 phosphorylation was detected in all well-differentiated TC (n=29), 19/20 PDTC, 16/23 ATC, and 18/21 TC cell lines including 11 ATC-derived ones. The cell lines lacking CDK4 phosphorylation were insensitive to CDK4/6i. RNA-sequencing and immunohistochemistry revealed that tumors and cell lines without phosphorylated CDK4 presented very high p16CDKN2A levels that were associated with proliferative activity. No RB1 mutations were found in 5 of these 7 tumors. p16/KI67 immunohistochemistry and a previously developed 11-gene signature identified the likely insensitive tumors lacking CDK4 phosphorylation. In cell lines, palbociclib synergized with dabrafenib/trametinib, completely and irreversibly arresting proliferation. The combined drugs prevented resistance mechanisms induced by palbociclib, most notably Cyclin E1-CDK2 activation and a paradoxical stabilization of phosphorylated CDK4 complexes. Our study supports the evaluation of CDK4/6i for ATC/PDTC treatment, including in combination with MEK/BRAF inhibitors.

cancer biology↗

bioRxiv2018

Transcriptional output, cell types densities and normalization in spatial transcriptomics

Spatial transcriptomics measures mRNA at hundreds of 100 micrometer-diameter spots evenly spread across 6.5x6.9 mm2 histological slices. Gene expression within each spot is commonly normalized by total read counts. However we show that the transcriptional output of individual spots reflects the number of cells they contain, hence total read counts per spot reflect relevant biology. Although per-spot read-count normalization reveals important enrichment trends, it may heavily distort cell-type-related absolute local expression and conceal important biological information.

genomics↗

bioRxiv2017

Distinctive desmoplastic 3D morphology associated with BRAFV600E in papillary thyroid cancers

Textbooks suggest that cancers are compact balls with an inner core and an invasive front in contact with non-cancerous cells, and that tumor growth is driven by tumor cell proliferation subsequent to oncogenic genome mutations. We reconstructed at histological scale the 3D volume occupied by tumor cells in two regions of a BRAFV600E-mutated papillary thyroid carcinoma (PTC) with low tumor purity, as determined by sequencing, but initially considered high purity during pathology review. In contrast with a compact ball, tumor cells formed a sparse mesh deeply embedded within the stroma. The concepts of inner core and invasive front broke down in this morphology: all tumor cells were within short distance from the stroma. The fibrous stroma was highly cellular and proliferative, a result confirmed in an independent series. This case was not unique: 3.5% of The Cancer Genome Atlas PTCs had purities <25%, 27% were below the 60% purity inclusion criterion. Moreover, the presence of BRAFV600E was associated with extensive fibrosis, high stromal activation, and dedifferentiation. Thus, non-tumor cells make most of the tumor mass and contribute to its expansion in a significant fraction of BRAFV600E PTCs. Therapeutics targeting the tumor-stroma crosstalk could be beneficial in this context.

cancer biology↗