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| Status |
Public on May 15, 2024 |
| Title |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Spatial transcriptomics on de-identified human ONB samples] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The olfactory epithelium relies on active neuron regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare, aggressive tumor of unclear origins. Here, we establish a new, highly-penetrant, genetically-engineered mouse model of ONB with alterations in Rb1/Trp53/Myc that exhibit a NEUROD1+ immature neuronal state. ASCL1 loss leads to emergence of non-neuronal histopathologies, including a POU2F3+ microvillar-like state. We find ONB tumor heterogeneity to recapitulate developmental states of multipotent globose basal cells (GBCs), which our data demonstrate is a cell of origin for ONB. Similar to small cell lung cancer (SCLC), mouse and human ONB exhibit: mutually exclusive ASCL1, NEUROD1, and POU2F3- like states, an immune-cold tumor microenvironment, intratumoral subtype heterogeneity comprising neuronal and non-neuronal lineages, and subtype plasticity—as evidenced by barcode-based lineage tracing and single-cell transcriptomics. Collectively, our findings highlight conserved developmental trajectories between ONB and SCLC subtypes with significant implications for ONB classification and treatment.
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| Overall design |
We performed multiplexed and spatially resolved transcriptomic profiling using the NanoString GeoMx digital spatial profiling (DSP) platform, with mostly default parameters. 5 µm sections from high quality archival ONB tissue blocks was mounted on glass slides for profiling. In total, we included 12 seperate ONB specimens, and 1 normal control OE. Two adjacent sections were cut and positioned on separate slides to allow for side-by-side H&E comparison. Following deparaffinization, antigen retrieval was performed with Tris-EDTA buffer (pH 9.0) in a steamer for 20 min. Slides were then incubated for 15 min at 37°C in PBS buffer with 0.1 µg/mL proteinase K for RNA target exposure. In situ hybridization was conducted by incubating slides with GeoMx Human Whole Transcriptome Atlas Probe Mix (NanoString) overnight at 37°C. Slides were then stained with fluorescence-conjugated morphology markers for two hr at RT with the following labels: Syto 83 nuclear dye (NanoString) 250nM, CD45-532 (NovusBio cat# NBP2-34528AF532) 7.50µg/mL, TUBB3-594 (Biolegend, cat# 657408) 1:50, KI67-647 (CST cat# 12075) 1:100. Slides were then loaded on the NanoString GeoMx DSP instrument, and 2-3 representative ROIs in spatially distinct locations were selected based on tumor morphology and antibody staining markers. In general, ROIs were 200-600µm in diameter, and contained 100-300 nuclei. Note, some tumor specimens also contained normal overlying OE, which was captured for controls. ROIs were then segmented based on morphology markers, and RNA probe oligos were photocleaved and collected in the following order: CD45, KI-67, TUBB3, negative. Oligos were then processed for library preparation according to the standard Nanostring protocol, with the exception that beads were dried for 1 min instead of 5. DNA libraries were sequenced on an Illumina NovaSeq 6000 S-Prime flow cell with a read length of 2x27bp and a 5% PhiX spike-in by volume. Output .fastq files from sequencing runs were converted to .dcc using the GeoMx NGS Pipeline with default parameters.
*** FASTQ raw data files have been requested. ***
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| Contributor(s) |
Finlay J, Goldstein B |
| Citation(s) |
38788720 |
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| Submission date |
Sep 26, 2023 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Trudy Oliver |
| E-mail(s) |
tgo@duke.edu, trudy.oliver@duke.edu
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| Phone |
6174607487
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| Organization name |
Duke University
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| Department |
Pharmacology & Cancer Biology
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| Lab |
theoliverlab
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| Street address |
Duke University, Box 3813, LSRC Room C138B, 308 Research Drive
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL30991 |
NanoString GeoMx Human Whole Transcriptome Atlas [do not use this platform, see NOTE below] |
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| Samples (96)
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| This SubSeries is part of SuperSeries: |
| GSE244123 |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer |
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| Relations |
| BioProject |
PRJNA1021255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE244117_RAW.tar |
4.1 Mb |
(http)(custom) |
TAR (of DCC) |
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