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- Postdoctoral Scholar - Neurodevelopment and Brain Tumors, Tsankova lab:
Job Description: Looking for an enthusiastic, motivated postdoctoral fellow with both computational and experimental background and interest in neurodevelopment and neuro-oncology to join the laboratory of Dr. Nadejda Tsankova, MD/PhD, in the Departments of Pathology and Neuroscience, at the Icahn School of Medicine at Mount Sinai, Manhattan, NYC.
The lab’s main research question is to understand how brain tumor (glioma) cells highjack normal neurodevelopmental molecular programs to maintain their malignant cancer stem cell-like phenotype, focusing on the role of epigenetics and transcriptional regulation, with the ultimate goal of uncovering better strategies for reversing malignant tumor growth and spread.
There are two parallel, recently NIH-funded, ongoing computational projects, in which the applicant is expected to be involved. The first is the integrated analysis of bulk and single cell transcriptome (RNA-seq) and epigenome (ATAC-seq, HI-C, ChiP-seq) datasets, generated across five stages of normal human neural development, with a strong focus on uncovering the transcriptional footprints driving normal human gliogenesis. Single cell sequencing analysis will be performed in collaboration with the bioinformatics lab of Dr. Alexander Tsankov, who will co-mentor the applicant. The second project builds on our lab’s recent finding for the role of TEAD1 in glioma migration (Tome-Garcia et al, Nature Communications 2018), and will involve further dissection of the transcriptional regulatory network driving tumor stem cell migration and progression in glioblastoma, using a large dataset of bulk and single cell RNA-seq, chromatin accessibility (ATAC-seq) and TEAD1-ChIP-seq datasets in various glioblastoma subtypes derived from primary and recurrent tumor samples. Integrated analysis of the above datasets is focused on defining transcriptionally active chromatin cis regulatory elements and trans TF footprint occupancy in the context of tumor migration and progression. For both projects, experimental validation in organoid models is expected.
Some of the commonly used techniques in the Tsankova lab include FACS isolation of neural / glioma stem cell populations from fresh tissues, CRISPR/Cas9 gene editing (knockout), bulk and single cell RNA-seq using the 10X chromium droplet-based technology, chromatin accessibility studies (ATAC-seq), chromatin immunoprecipitation (ChIP), in vitro migration and proliferation assays, in vivo migration analyses in orthotopic xenografts, live cell imaging, and drug screening for new inhibitors of glioma cell migration. Our model systems include primary patient-derived cells / spheroids and orthotopic xenograft mouse models.
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