Omics Technology facility

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

According to our goals and objectives, the Genetics Branch (GB) Omics Technology Facility team supported numerous projects of GB PIs and their collaborators with a wide repertoire of cutting-edge genomic, proteomic and cytogenetic technologies, adding unique data and developing tailored novel approaches to help answer complex research questions. In particular, the Omics Technology Facility Wet Lab team provided pertinent experiments and data to the following projects: Comprehensive Spectral Karyotyping (SKY) analysis served as important cytogenetic baseline for copy number changes in a study of "Genome reorganization and its functional impact during breast cancer progression." (Collaborators: Drs. Tom Misteli and Kathleen Reed, Preprint PMID 40463073, currently in revision in eLife). Karyotype, ploidy and gene copy number data (SKY and multiplex miFISH) in a Medullary Thyroid Cancer study revealed differences in chromosome numbers and increased oncogene (RET) copy numbers as a mechanism of drug resistance. (Collaborators: Drs. Javed Khan, David Milewski and Arwa Fallatah, "Selpercatinib plus trametinib overcomes resistance to single-agent RET inhibitors in RET-mutant medullary thyroid carcinoma", manuscript in preparation). Characterization of isogenic neuroblastoma cell lines using Spectral Karyotyping and tailored FISH gene probe panels (multiplex miFISH) to understand the role of MYCN amplification in adrenergic and mesenchymal neuroblastoma cells. (Collaborators: Drs. Carol Thiele, Stefano Di Giulio, Javed Khan. "MYCN Amplification shapes heterogeneity and cellular state dynamics in Neuroblastoma", Oral presentation at the Advances in Neuroblastoma Research Meeting 2025). Defining the role of MYCN in the MEKi-resistant, RAS pathway-altered, MYCN overexpressed neuroblastoma cell line, NB-Eb-C1. The GB OMICS team characterized the karyotype, ploidy and structural variants using Spectral karyotyping and analyzed copy numbers of important neuroblastoma genes, specifically MYCN, with tailored miFISH panels. FISH revealed a clonal low level MYCN gain which could be pinpointed to a translocation between chromosome 2 (harboring MYCN) and chromosome 5 applying a SKY and miFISH approach. The Omics Facility furthermore determined the exact translocation breakpoints by Oxford Nanopore Technologies (ONT) long-read sequencing, and we are currently applying Hi-C analysis to understand whether promoter/enhancer hijacking could be an explanation for the relatively high MYCN overexpression. (Collaborators: Drs. Marielle Yohe, Subhra Dash, Javed Khan. "Investigating mechanisms responsible for MAP kinase pathway resistance in RAS-altered Neuroblastoma cells." Poster presentation at the Advances in Neuroblastoma Research Meeting 2025). Development of a high-throughput capture based NGS assay to detect mitochondrial DNA mutations with the goal to screen mouse and human leukemias and cell lines for the acquisition of mitochondrial DNA variants that may affect treatment response. The Omics Wet Lab and Bioinformatics team delivered mitochondrial mutation data for over 100 samples to the collaborators, Drs. Peter Aplan and Dengchao Cao, who are currently reviewing the results. ONT long-read RNA sequencing using a direct cDNA approach to detect and quantify novel transcripts of the LincRNA 02582 in colorectal cell lines. The Omics Facility also helped to compare the ONT data to PacBio data generated for the same LincRNA and cell line. Drs. Ashish Lal and Ragini Singh are currently preparing a manuscript including the ONT and PacBio data. Single cell RNA-Seq using the Illumina PIP-Seq assay to understand transcriptome changes caused by transcription factor ETS1 activation in Ewing sarcomas on a single cell level. Similar to previous bulk RNA-Seq results, the single cell assay showed clear-cut upregulation of downstream targets like Vimentin, S100A11, TIMP1, RAMP1, CST3 and CCK compared to the control cells (empty vector). CRISPR activated cell lines clustered together, clearly distinct from the clusters of unmodified parental cells and the empty-vector control cell lines. Unfortunately, ETS1 expression was low in the individual cells which prohibited single cell correlations of ETS1 expression with downstream target expression. This project was a collaboration with Drs. Natasha Caplen and Soumya Sundara Rajan. Meso Scale Diagnostics (MSD) test development which allowed successful assessment of the pharmacokinetics of FGFR4-targeted antibody-drug-conjugates (ADCs) that demonstrated unprecedented efficacy in human cancers expressing FGFR4 including aggressive rhabdomyosarcoma and breast cancers. This MSD test was developed in collaboration with Drs. Javed Khan and Meijie Tian. Their manuscript "Development of potent FGFR4-targeted antibody-drug conjugate therapies for rhabdomyosarcoma and FGFR4-high cancers" was favorably reviewed and is currently in revision. The GB Omics Bioinformatics team provided experimental design, analysis, and data management support for all GB Omics Wet Lab and numerous other Genetics Branch projects including: bulk RNA-Seq (i.e., differential expression, alternative splicing, immune infiltration); scRNA-Seq, multimodal single cell analysis, and spatial transcriptomics; CutandRun; long read transcriptomics; miFISH; and whole exome and custom panel sequencing. They validated protocols for the Wet Lab (e.g., PIPseq and CutandRun) and performed large-scale integrative analyses using public data. They established bioinformatics resources supporting GB projects, including pipelines for PacBio IsoSeq data, spatial transcriptomics, and detection of low VAF mitochondrial variants. They also established comprehensive data management tools, including an HPC DME archive for raw and processed data generated by the facility, as well as disseminating developed tools via Github.