Comment[GEAAccession]	E-GEAD-429
MAGE-TAB Version	1.1
Investigation Title	Skin liquid biopsy method for assessing the immune environment of cutaneous T-cell lymphoma lesions
Experiment Description	Detailed analysis of cells infiltrating lesional skin cannot be performed in skin biopsy specimens by immunohistochemistry or cell separation techniques because small amounts of protein and minor cell populations in the biopsy specimen might be destroyed by enzyme treatment in the isolation step. Here, we describe a skin liquid biopsy method that enables T cell isolation in small amounts of lesional whole blood from patients with cutaneous T-cell lymphoma. Lesional blood, assumed to contain lesional resident cells, cells from capillary vessels, and blood overflowing from capillary vessels in the lesion area, was obtained during regular skin biopsy. The lesional blood showed substantial increases in distinct cell populations, chemokines, and expression of various genes. CD8+CD45RO+ T cells in the lesional blood negatively correlated with the modified severity-weighted assessment tool scores. CD4+CD45RO+ T cells in the lesional blood expressed genes associated with the development of cancer and progression of cutaneous T-cell lymphoma. The skin liquid biopsy technique might provide new insight into the pathogenesis of mycosis fungoides and facilitate evaluation of the treatment efficacy for other skin inflammatory diseases.
Experimental Design	cell type comparison design
Experimental Factor Name	tissue
Experimental Factor Type	tissue
Person Last Name	Torii
Person First Name	Kan
Person Affiliation	Dermatology, Nagoya City University Graduate School of Medicine
Person Roles	submitter
Public Release Date	2021-08-07
Protocol Name	P-GEAD-820	P-GEAD-821	P-GEAD-822	P-GEAD-823	P-GEAD-824
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	CD4+CD45RO+ and CD8+CD45RO+ T cells from lesional blood and peripheral blood were sorted using the BD FACSMelody Cell Sorter.	The RNA was extracted with chloroform/isopropanol and recovered from the supernatants using RNA Clean and Concentrator-5 columns.	The RNA was subjected to library preparation with the TaKaRa SmartSeq Stranded Kit (Takara Bio) and used for next experiment.	The RNA was sequenced with Illumina Hiseq (Illumina). Sequences were mapped to grch38 with HISAT2 (version 2.0.1).	In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
SDRF File	E-GEAD-429.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB11504
Comment[Last Update Date]	2021-08-07