Comparison of the modulation of FGFR signalling by thalidomide and its analogs lenalidomide and pomalidomide

Thalidomide, a powerful teratogen, re-emerged as a wonder drug for its teratogenic, anti-angiogenic and anti-tumor properties. Being FDA approved for Multiple Myeloma along with the analogs lenalidomide and pomalidomide is currently being tested in more than 2000 clinical trials for a range of conditions including solid tumors and inflammatory disorders. Fibroblast growth factor receptors (FGFRs) play key roles in embryonic development and cancer. There are indications that thalidomide might be linked to FGFR biology, however no experimental evidence is available till now. To understand the effects of thalidomide and its analogs, lenalidomide and pomalidomide, we utilized in silico predictive tools, kinome profiling, transcriptome and phophoproteome tools to study the modulation of FGFR signalling in endothelium. Genecodis and Enrichr with the differentially expressed genes were used to obtain the Gene Ontology, Transcription factor, Pathway and miRNA enrichments. The association of the drug with FGFR signalling was investigated at various levels. Protein-chemical network tool, STITCH and Pocketome predicted strong association of thalidomide with FGFR2. At gene expression level, FGFR1 and FGFR2 were found to be affected under the three drug treatments in in vitro and in vivo models. Kinomescan results suggest the binding of thalidomide with high affinity to a mutant FGFR3 (G697C) and FGFR2. To validate this, we checked the activity of FGFR2 kinase under the three drug treatments and found that they affected the kinase activity in a dose-dependent manner with pomalidomide having lowest IC50 value. Blind docking using Autodock revealed the possible binding sites and interestingly all the three analogs were predicted to bind to Lys517 of FGFR2. Lys517 is one of the ATP binding sites, suggesting that possibly analogs interfere with the ATP binding. Taken together, FGFRs could be potential targets of thalidomide and its analogs and the modulation of FGFRs by thalidomide partially explain the teratogenic and anti-tumor properties of the drug. Thus through different platforms, the mechanisms of drugs could be understood in a better way. This in turn will aid in modifying the drug structures resulting in the development of new analogs with more efficacy and reduced undesired effects

Transcriptomic Analysis of Thalidomide Challenged Chick Embryo Suggests Possible Link between Impaired Vasculogenesis and Defective Organogenesis

Since the conception of thalidomide as a teratogen, approximately 30 hypotheses have been put forward to explain the developmental toxicity of the molecule. However, no systems biology approach has been taken to understand the phenomena yet. The proposed work was aimed to explore the mechanism of thalidomide toxicity in developing chick embryo in the context of transcriptomics by using genome wide RNA sequencing data. In this study, we challenged the developing embryo at the stage of blood island formations (HH8), which is the most vulnerable stage for thalidomide-induced deformities. We observed that thalidomide affected the early vasculogenesis through interfering with the blood island formation extending the effect to organogenesis. The transcriptome analyses of the embryos collected on sixth day of incubation showed that liver, eye, and blood tissue associated genes were down regulated due to thalidomide treatment. The conserved gene coexpression module also indicated that the genes involved in lens development were heavily affected. Further, the Gene Ontology analysis explored that the pathways of eye development, retinol metabolism, and cartilage development were dampened, consistent with the observed deformities of various organs. The study concludes that thalidomide exerts its toxic teratogenic effects through interfering with early extra-embryonic vasculogenesis and ultimately gives an erroneous transcriptomic pattern to organogenesis

An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate

International audienceOTX2 is a potent oncogene that promotes tumor growth in Group 3 medulloblastoma. However, the mechanisms by which OTX2 represses neural differentiation are not well characterized. Here, we perform extensive multiomic analyses to identify an OTX2 regulatory network that controls Group 3 medulloblastoma cell fate. OTX2 silencing modulates the repressive chromatin landscape, decreases levels of PRC2 complex genes and increases the expression of neurodevelopmental transcription factors including PAX3 and PAX6. Expression of PAX3 and PAX6 is significantly lower in Group 3 medulloblastoma patients and is correlated with reduced survival, yet only PAX3 inhibits self-renewal in vitro and increases survival in vivo. Single cell RNA sequencing of Group 3 medulloblastoma tumorspheres demonstrates expression of an undifferentiated progenitor program observed in primary tumors and characterized by translation/elongation factor genes. Identification of mTORC1 signaling as a downstream effector of OTX2-PAX3 reveals roles for protein synthesis pathways in regulating Group 3 medulloblastoma pathogenesis

Subgroup and subtype-specific outcomes in adult medulloblastoma

Medulloblastoma, a common pediatric malignant central nervous system tumour, represent a small proportion of brain tumours in adults. Previously it has been shown that in adults, Sonic Hedgehog (SHH)-activated tumours predominate, with Wingless-type (WNT) and Group 4 being less common, but molecular risk stratification remains a challenge. We performed an integrated analysis consisting of genome-wide methylation profiling, copy number profiling, somatic nucleotide variants and correlation of clinical variables across a cohort of 191 adult medulloblastoma cases identified through the Medulloblastoma Advanced Genomics International Consortium. We identified 30 WNT, 112 SHH, 6 Group 3, and 41 Group 4 tumours. Patients with SHH tumours were significantly older at diagnosis compared to other subgroups (p < 0.0001). Five-year progression-free survival (PFS) for WNT, SHH, Group 3, and Group 4 tumours was 64.4 (48.0–86.5), 61.9% (51.6–74.2), 80.0% (95% CI 51.6–100.0), and 44.9% (95% CI 28.6–70.7), respectively (p = 0.06). None of the clinical variables (age, sex, metastatic status, extent of resection, chemotherapy, radiotherapy) were associated with subgroup-specific PFS. Survival among patients with SHH tumours was significantly worse for cases with chromosome 3p loss (HR 2.9, 95% CI 1.1–7.6; p = 0.02), chromosome 10q loss (HR 4.6, 95% CI 2.3–9.4; p < 0.0001), chromosome 17p loss (HR 2.3, 95% CI 1.1–4.8; p = 0.02), and PTCH1 mutations (HR 2.6, 95% CI 1.1–6.2; p = 0.04). The prognostic significance of 3p loss and 10q loss persisted in multivariable regression models. For Group 4 tumours, chromosome 8 loss was strongly associated with improved survival, which was validated in a non-overlapping cohort (combined cohort HR 0.2, 95% CI 0.1–0.7; p = 0.007). Unlike in pediatric medulloblastoma, whole chromosome 11 loss in Group 4 and chromosome 14q loss in SHH was not associated with improved survival, where MYCN, GLI2 and MYC amplification were rare. In sum, we report unique subgroup-specific cytogenetic features of adult medulloblastoma, which are distinct from those in younger patients, and correlate with survival disparities. Our findings suggest that clinical trials that incorporate new strategies tailored to high-risk adult medulloblastoma patients are urgently needed