Biology subjects

Maenhaut, C.

Publications and source records attributed to Maenhaut, C..

5 recordsLinked to original sources

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↗

bioRxiv2019

Vps34/PIK3C3 deletion in thyroid impairs thyroid hormonogenesis and autophagic flux

BACKGROUNDThe production of thyroid hormones (T3, T4) depends on thyroid organization in follicles, lined by a monolayer of thyrocytes with strict apico-basal polarity. Polarization supports vectorial transport of thyroglobulin for storage into, and recapture from, the colloid. It also allows selective addressing of channels, transporters, pumps and enzymes to their appropriate basolateral (NIS and Na+/K+-ATPase) or apical membrane domain (pendrin, anoctamin, DUOX2, DUOXA2 and TPO). How these actors of T3/T4 synthesis reach their final destination remains poorly understood. Vps34/PIK3C3 is now recognized as a main component in the general control of vesicular trafficking and of cell homeostasis via autophagy. We recently reported that conditional Vps34 inactivation in kidney proximal tubular cells by Pax8-driven excision prevents normal addressing of apical membrane proteins and causes abortive macroautophagy. METHODSVps34 was inactivated using a Pax8-driven Cre recombinase system. The impact of Vps34 inactivation in thyrocytes was analyzed by histological, immunolocalization and mRNA expression profiling. Thyroid hormone synthesis was assayed by 125I injection and by serum plasma analysis. RESULTSVps34cKO mice were born at the expected Mendelian ratio and showed normal growth until postnatal day 14, then stopped growing and died at around 1 month of age. We therefore analyzed thyroid Vps34cKO before postnatal day 14. We found that loss of Vps34 in thyrocytes causes: (i) disorganization of thyroid parenchyma with abnormal thyrocyte and follicular shape and reduced PAS+ colloidal spaces; (ii) impaired 125I organification at comparable uptake and frequent occurrence of follicles with luminal thyroglobulin but non-detectable T4-bearing thyroglobulin; (iii) severe non-compensated hypothyroidism with extremely low T4 levels (<0.25 {+/-} 1.5 g/dL) and huge TSH plasma levels (19,300 {+/-} 10,500 mU/L); (iv) intense signal in thyrocytes for the lysosomal membrane marker, LAMP-1, as well as thyroglobulin and the autophagy marker, p62, indicating defective proteolysis. CONCLUSIONSWe conclude that Vps34 is crucial for thyroid hormonogenesis, at least by controlling delivery of apical actors responsible for biogenesis of thyroid hormones on Tg as well as defective proteolytic T3/T4 excision in lysosomes.

cell 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↗