NBDC Research ID: hum0130.v2

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SUMMARY

Aims: To compare genetic features of plasma cells from polyneuropathy, organomegaly, endocrinopathy, M-Protein, and skin changes (POEMS) syndrome, multiple myeloma (MM), and monoclonal gammopathy of undetermined significance (MGUS). We herein performed single-cell RNA sequencing (scRNA-Seq) and bulk RNA sequencing of bone marrow (BM) plasma cells from patients with POEMS syndrome. These data unveil unique features of POEMS clones among plasma cell neoplasms and enhance our understanding of the pathogenesis of POEMS syndrome.

Methods: Genomic analysis of POEMS syndrome, and gene expression analysis of 3 dieases. For scRNA-Seq, CD138+ plasma cells were purified by FACS after MACS CD138 positive selection from BM aspiration samples. Single cell isolation and library preparation were performed by Fluidigm C1, and then the samples were read by single-end sequencing with Illumina HiSeq 3000. For bulk RNA-Seq, library preparation were performed by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and NEBNext Ultra DNALibrary Prep Kit, and then the samples were read by paired-end sequencing with Illumina HiSeq 2000.

Participants/Materials: Plasma cells from POEMS syndrome, MM, MGUS, and Normal control (lymphoma without BM invasion)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000150 NGS (Exome, Target Capture, RNA-seq) Controlled-access (Type I) 2019/01/18
JGAS000289 NGS (scRNA-seq, bulk RNA-seq) Controlled-access (Type I) 2022/09/27

*Release Note

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MOLECULAR DATA

Exome

Participants/Materials POEMS syndrome (ICD10: C90.2): 15 cases
Targets Exome
Target Loci for Capture Methods Coding exons
Platform Illumina [HiSeq 2500]
Library Source DNA purified from Plasma cells or buccal cell of POEMS syndrome, MM, MGUS
Cell Lines -
Library Construction (kit name) SureSelect Human ALL Exon V5
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end or Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 121 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000226
Total Data Volume 171 GB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials POEMS syndrome (ICD10: C90.2): 20 cases
Targets Target Capture
Target Loci for Capture Methods Coding exons
Platform Illumina [MiSeq]
Library Source DNA purified from Plasma cells or buccal cell of POEMS syndrome, MM, MGUS
Cell Lines -
Library Construction (kit name) custom designed SureSelect XT2 Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 273 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000226
Total Data Volume 171 GB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

POEMS syndrome (ICD10: C90.2): 5 cases

MM (ICD10: C90.0): 4 cases

MGUS (ICD10: D47.2): 5 cases

Targets RNA-seq
Target Loci for Capture Methods
Platform Illumina [HiSeq 1500]
Library Source RNA purified from Plasma cells or buccal cell of POEMS syndrome, MM and MGUS
Cell Lines -
Library Construction (kit name) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, NEBNext Ultra DNALibrary Prep Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 60 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000226
Total Data Volume 171 GB (fastq)
Comments (Policies) NBDC policy

 

bulk RNA-seq

Participants/Materials

POEMS syndrome (ICD10: C90.2): 4 cases

MM (ICD10: C90.0): 3 cases

Normal control (lymphoma without BM invasion): 2 cases

Targets RNA-seq
Target Loci for Capture Methods
Platform Illumina [HiSeq 2000]
Library Source RNA purified from Plasma cells or buccal cell of POEMS syndrome and normal controls
Cell Lines -
Library Construction (kit name) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, NEBNext Ultra DNALibrary Prep Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 60 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000395
Total Data Volume 12.6 GB (fastq)
Comments (Policies) NBDC policy

 

scRNA-seq

Participants/Materials

POEMS syndrome (ICD10: C90.2): 11 cases (1 case is also used for JGAD000226)

MM (ICD10: C90.0): 2 cases

MGUS (ICD10: D47.2): 2 cases

lymphoma without BM invasion (Control): 2 cases

Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 3000]
Library Source RNA purified from CD138+ plasma cells of POEMS syndrome, MM, MGUS and lymphoma
Cell Lines -
Library Construction (kit name) Fluidigm C1
Fragmentation Methods Tagmentation using Nextera XT DNA Sample Preparation kit (Illumina)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000395
Total Data Volume 350.5 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Emiko Sakaida

Affiliation: Chiba University Graduate school of Medicine, Clinical Cell Bilogy and Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Genetic and transcriptional landscape of plasma cells in POEMS syndrome 26461397
KAKENHI Grant-in-Aid for Scientific Research (C) Clonal immunoglobulin lamda light-chain gene rearrangements detected by NGS in POEMS syndrome 15K09494
KAKENHI Grant-in-Aid for Scientific Research (C) Elucidation of the molecular mechanism of POEMS syndrome by single cell analysis of bone marrow plasma cells 18K08338
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas - Platforms for Advanced Technologies and Research Resources Platform for Advanced Genome Science 16H06279
KAKENHI Grant-in-Aid for Scientific Research (C) Deciphering of the epigenetic machinery that determines the hallmarks of hematopoietic stem cell aging 19H05653
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) Characterization of chromatin replication associated with stem cell fate decision 19H05746
KAKENHI Grant-in-Aid for Scientific Research (S) Establishment of diagnostic and therapeutic strategies by identification of small clones in POEMS syndrome 22K08471

 

PUBLICATIONS

TitleDOIDataset ID
1 Genetic and transcriptional landscape of plasma cells in POEMS syndrome. doi: 10.1038/s41375-018-0348-x JGAD000226
2 Unraveling unique features of plasma cell clones in POEMS syndrome by single-cell analysis doi: 10.1172/jci.insight.151482 JGAD000395

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000226 2022/12/26-2025/03/31