GSE128794 Single cell RNA sequencing of KPC1199 cell line mouse scRNA-seq
In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).
Conditions: Pancreatic Cancer; Metastatic Pancreatic Cancer Interventions: Drug: Niraparib; Drug: Dostarlimab; Radiation: Radiation Sponsors: Massachusetts General Hospital; Tesaro, Inc. Not yet recruiting
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In this study, we applied Drop-seq, a high throughput single cell RNA-seq platform, to characterize the different cell types present in pancreatic cancer organoids. We sequenced the transcriptomes of 7675 single cells from organoids derived from a patient undergoing a Whipple procedure for pancreatic ductal adenocarcinoma (PDAC). We then developed a novel clustering approach based on a class of probabilistic generative models called topic models, leading to the identification of subpopulations of cells.
Nature Reviews Gastroenterology &Hepatology, Published online: 01 June 2020; doi:10.1038/s41575-020-0324-6Obesity is a known risk factor for pancreatic cancer. Now, a new study reports that obesity accelerates early pancreatic cancer development and growth in mice through local perturbations in the pancreatic microenvironment and implicates pancreatic islet-derived cholecystokinin as a driving factor.
This study sought to develop diagnostic algorithms using multiple biomarker panels and to validate their performance in the diagnosis of pancreatic ductal adenocarcinoma (PDAC). We used blood samples from 180 PDAC patients and 573 healthy controls. Candidate markers consisted of 11 markers that are commonly expressed in various cancers and which have previously demonstrated increased expression in pancreatic cancer. Samples were divided into training and validation sets. Five linear or non-linear classification methods were used to determine the optimal model. Differences were identified in 10 out of the 11 markers tested....
Uwe A. Wittel Pancreatic ductal adenocarcinoma (PDAC) is associated with high mortality and will become the second most common cause of cancer-associated mortality by 2030. The poor prognosis arises from a lack of sensitive biomarkers, limited therapeutic options, and the astonishingly high recurrence rate after surgery of 60–80%. The factors driving this recurrence, however, remain enigmatic. Therefore, we generated patient-derived organoids (PDOs) from early- and late-recurrent PDAC patients. Cellular identity of PDOs was confirmed by qPCR, ddPCR, and IHC analyses. This is the first study investigating the ...
ConclusionsFrom our data we conclude that JAG1 may be a promising therapeutic target in pancreatic cancer.
Nature Reviews Gastroenterology &Hepatology, Published online: 01 June 2020; doi:10.1038/s41575-020-0321-9Most patients who undergo curative intent surgery for pancreatic cancer will still die of recurrent disease. A new study shows that pancreatic tumours that pass through the genetic bottlenecks of surgery and additional chemoradiotherapy have altered mutational signatures, driver genes and subclonal architecture.