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Pancreatic intraepithelial neoplasia (PanIN) is a pre-pancreatic ductal adenocarcinoma (PDAC) malignancy diagnosed from formalin-fixed and paraffin-embedded (FFPE) specimens, limiting single-cell-based research
。 On July 16, 2022, an article published on bioRxiv titled "Spatial transcriptomics of FFPE pancreatic intraepithelial neoplasias reveals cellular and molecular alterations of progression to pancreatic ductal.
" Carcinoma"'s preprint article, which develops a new spatial transcriptome analysis protocol for FFPE samples by combining single-cell transcriptome data with 10x Visium FFPE spatial transcriptome data, complemented by two new transfer learning methods
.
The first is to assign cell types to ST sites and integrate transcriptional signatures, indicating that PanINs are surrounded by PDAC cancer-associated fibroblasts (CAFs) subtypes, including rare antigen-presenting CAFs
.
The second is the integration of ST PanIN data with PDAC scRNA-seq data, which identifies the transfer
between inflammatory and proliferative signals as PanINs progress to PDAC.
This study is the first to identify similar CAF populations and associated molecular changes in PanINs that may be early mediators
of precancerous conversion to PDAC.
This integrated experimental and computational approach provides a way to develop models of PDAC development and progress by integrating imaging, ST, and SCRNA-SEQ datasets
.
。 On July 16, 2022, an article published on bioRxiv titled "Spatial transcriptomics of FFPE pancreatic intraepithelial neoplasias reveals cellular and molecular alterations of progression to pancreatic ductal.
" Carcinoma"'s preprint article, which develops a new spatial transcriptome analysis protocol for FFPE samples by combining single-cell transcriptome data with 10x Visium FFPE spatial transcriptome data, complemented by two new transfer learning methods
.
The first is to assign cell types to ST sites and integrate transcriptional signatures, indicating that PanINs are surrounded by PDAC cancer-associated fibroblasts (CAFs) subtypes, including rare antigen-presenting CAFs
.
The second is the integration of ST PanIN data with PDAC scRNA-seq data, which identifies the transfer
between inflammatory and proliferative signals as PanINs progress to PDAC.
This study is the first to identify similar CAF populations and associated molecular changes in PanINs that may be early mediators
of precancerous conversion to PDAC.
This integrated experimental and computational approach provides a way to develop models of PDAC development and progress by integrating imaging, ST, and SCRNA-SEQ datasets
.
The researchers in the preprint article above mentioned that due to the requirements of the scRNA-seq method on cell viability, the technique is currently not compatible with FFPE samples, making it impossible for them to directly perform PanINs analysis
.
Here Xiaobian reveals a good news to everyone, FFPE samples can also be single cells! 10x Genomics recently launched a solution for single-cell transcriptome sequencing of FFPE samples, and here's a look at the preliminary data
from the 10x test.
A piece of invasive ductal cancer tissue was cleaved and isolated by a combination of manual dissociation and enzymatic digestion, and then sample fixation using the 10x single-cell fixed RNA analysis kit launched this year was fixed for single-cell transcriptome sequencing, and through the processing of the data, multiple cell types were obtained, and we can see from the figure that many immune cells
can be detected from this FFPE sample.
Breast cancer is a highly heterogeneous disease, in order to guide the prognosis, often use TNM staging, clinical pathological indicators, and later due to the generation of high-throughput data, polygenic prediction became a new approach
.
Traditional methods, which are typically based on the bulg level to classify cancer based on signature, are now applied to every cell population in this dataset, associating each cluster with the PAM50 gene signature, and the results show that in fact only one cell population17 shows a strong correlation with cancer subtypes, while other cell populations are associated
with normal features.
There has been literature on fresh samples that have previously performed such analyses, but finding this on the data of FFPE samples could allow researchers to apply it to a large number of biobank FFPE samples, unlocking more archived samples
.
The FFPE method is the standard method for the collection and preservation of surgical pathological specimens, which are used by pathologists to determine the visual characteristics of the disease on FFPE slices, and these samples can often be linked to valuable metadata, such as patient information records, drugs used, and even clinical outcomes
。 The ability to observe transcriptome gene expression at single-cell resolution on these longitudinal samples will add a whole new axis of information to the study of disease processes, and it is believed that this single-cell solution for FFPE samples launched by 10x can unlock more clinical archived samples and bring more new research discoveries! For more details, please feel free to contact us! Tel: 010-84409661, E-mail: marketing@emtd.
com.
cn
.
。 The ability to observe transcriptome gene expression at single-cell resolution on these longitudinal samples will add a whole new axis of information to the study of disease processes, and it is believed that this single-cell solution for FFPE samples launched by 10x can unlock more clinical archived samples and bring more new research discoveries! For more details, please feel free to contact us! Tel: 010-84409661, E-mail: marketing@emtd.
com.
cn
.
