U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX24360402: GSM8229207: DSP-1012340055901-B-A09; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 26.6M spots, 1.4G bases, 451.2Mb downloads

External Id: GSM8229207_r1
Submitted by: Department of Surgery, Klinikum rechts der Isar
Study: Phenotype screens of murine pancreatic cancer identify a Tgfa-Ccl2-paxillin axis driving human-like neural invasion
show Abstracthide Abstract
Solid cancers like pancreatic cancer (PDAC) frequently exploit nerves for rapid dissemination. This neural invasion (NI) is an independent prognostic factor in PDAC, but insufficiently modelled in genetically-engineered mouse models (GEMM) of PDAC.Here, we systematically screened for human-like NI in Europe's largest repository of GEMM of PDAC comprising 295 different genotypes. This phenotype screen uncovered two GEMM of PDAC with human-like NI, which are both characterized by pancreas-specific overexpression of transforming-growth-factor-alpha (TGFa) and conditional depletion of p53. Mechanistically, cancer-cell-derived TGFa upregulated CCL2 secretion from sensory neurons, which induced hyperphosphorylation of the cytoskeletal protein paxillin via CCR4 on cancer cells. This activated the cancer migration machinery and filopodia formation toward neurons. Disrupting CCR4 or paxillin activity limited NI, and dampened tumor size and tumor innervation. In human PDAC, phospho-paxillin and TGFa-expression constituted strong prognostic factors. Therefore, TGFa-CCL2-CCR4-p-paxillin axis is a clinically actionable target for constraining NI and tumor progression in PDAC. Overall design: In the spatial transcriptome analyses with murine DRG, DRGs T8 to T12 were extracted bilaterally from TPAC (Ela-TGFa; Ptf1a-Cre; Trp53fl/fl;RelAfl/fl , n=6, 47-54 weeks old), KPC (Ptf1a-Cre; LSL-Kras+/G12D; Trp53+/fl , n=3, 20-21 weeks old) and age-similar tumor-free control mice (Ela-TGFa; Trp53fl/fl;RelAfl/fl , n=3, 48-50 weeks old for TPAC and LSL-Kras+/G12D; Trp53+/fl , n=1, 20 weeks old; Trp53+/fl , n=1, 21 weeks old and LSL-Kras+/G12D; n=1, 22 weeks old for KPC). Following the extraction, DRGs were briefly washed in ice-cold, fresh PBS (D5262, Sigma-Aldrich) and fixated in freshly prepared 4% PFA (15710, Electron Microscopy Sciences; diluted with PBS) for 24 hours at room temperature. The samples were consecutively dehydrated, paraffine embedded and sectioned. A whole transcriptome analysis was performed on NeuN rich regions within the DRG sections using the NanoString GeoMx® digital spatial profiler. 5µm thick unstained sections on slides were subjected to incubation for 35 minutes at 60°C. Afterwards, the slides were moved into Leica BOND Rx. Proteinase K (1ug/ml, for 5 minutes) and HIER2 (20 minutes) were used for RNA antigen retrieval. NanoString GeoMx Mouse Whole Transcriptome Atlas RNA probes were added for hybridization for 16 hours at 37°C. Following the stringent washes per manufacturer's instructions, slides were blocked with W buffer for 1 hour. The slides were then stained with AF647 anti-NeuN (1:100, ab190565, Abcam), AF594 anti-Cd68 (1:200, sc-20060, Santa Cruz) AF532 Syto83 (1:10, ThermoFisher) and AF488 anti-GFAP (1:200, NBP2-3318AF488, Novus) antibodies. After washing the slides twice with SSC buffer, slides were loaded to the DSP and scanned for the regions of interest (ROI) selection. Two NeuN rich region per mouse were selected as ROIs.For the human spatial transcriptome studies, two patients with pancreatic ductal adenocarcinoma were selected for transcriptome spatial analysis using the NanoString GeoMx Digital Spatial Profiler (DSP)/Human NGS Whole Transcriptome Atlas. Cases were selected based on the presence of perineural invasion in tissue sections. Each slide was stained with fluorescence-labeled antibodies to allow identification of tissue: pan-cytokeratin for epithelial cells and PGP9.5 for nerves. Tumor and Nerve areas of interest (AOI) were selected as follows: (i) NI Tumor: nerve-invading pancreatic (N=6); (ii) no NI Tumor: non-invading tumor cells (n=7); (iii) NI Nerve: tumor-invaded nerve (n=5); (iv) no NI Nerve: non-invaded nerve (n=4). AOIs were drawn manually around nerves and tumor cells. Following the ROI selection, UV-photocleaved oligonucleotide barcodes from each ROI were collected and prepared by the NanoString GeoMx protocol. Sequencing was performed on the NextSeq 2000. Raw basecell files were demultiplexed into fastsq files. NanoString's GeoMx NGS Pipeline v.2.0.0 was used to convert the fastsq files to Digital Count Conversion files. None of the 45 AOIs were below the warning sequencing saturation of 50%. Data was then normalized, and the downstream gene expression analyses were performed using the R package DESeq2.
Sample: DSP-1012340055901-B-A09
SAMN41074265 • SRS21117723 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM8229207
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: DNA oligonucleotide probes were designed to bind mRNA targets. From 5′ to 3′, each probe is comprised of a 35- to 50-nucleotide target complementary sequence, an ultraviolet (UV) photo cleavable linker and a 66-nucleotide indexing oligonucleotide sequence containing a unique molecular identifier (UMI), RNA ID sequence and primer binding sites. Oligomers from ROIs were disintegrated by UV irradiation, passed through capillaries, pooled into collection plates, and resealed with DAPI fluoromount G mounting medium. Entire slides were imaged at ×20 magnification and morphologic markers were used to select Region Of Interest (ROI) either using circle or organic shapes. Automatic segmentation of ROI based on NeuN marker was used to defined Area of Illumination (AOIs). This allowed to separate Neurons (NeuN+) and cells around. A total of AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited in a 96-well plate for subsequent processing. The indexing oligonucleotides were dried down overnight and resuspended in 10 μl of DEPC-treated water. Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer's protocol. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow on an Illumina NovaSeq S4 instrument. FastQ files were converted into DCC files according to manufacturer's pipeline. Digital Count Conversion files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.4.2.2 (Nanostring).
Runs: 1 run, 26.6M spots, 1.4G bases, 451.2Mb
Run# of Spots# of BasesSizePublished
SRR2879613726,581,2161.4G451.2Mb2024-04-25

ID:
32675058

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...