NBDC Research ID: hum0130.v3
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 WES, target sequencing, bulk RNA-seq, single-cell RNA Seq of bone marrow (BM) plasma cells from patients with POEMS syndrome and compared them with other diseases and normal controls. 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 diseases. 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 was performed by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and NEBNext Ultra DNA Library Prep Kit. Then the samples were read by paired-end sequencing with Illumina HiSeq 2000. RAN-seq was performed on bone marrow plasma cells purified by fluorescence-activated cell sorting (FACS) after CD138-positive magnetic cell separation. RNA samples were obtained from 3 early-stage lymphoma patients without BM invasion as normal controls.
Participants/Materials: Plasma cells from POEMS syndrome, MM, MGUS, and Normal control (lymphoma without BM invasion)
| Dataset ID | Type of Data | Criteria | Release 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 |
| JGAS000150 (data addition) | NGS (RNA-seq) | Controlled-access (Type I) | 2024/06/17 |
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MOLECULAR DATA
| 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 |
| 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 |
| 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 |
| Participants/Materials |
POEMS syndrome (ICD10: C90.2): 5 cases MM (ICD10: C90.0): 4 cases MGUS (ICD10: D47.2): 5 cases Normal control (lymphoma without BM invasion): 3 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, MGUS 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 | JGAD000226 |
| Total Data Volume | 171 + 2.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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 |
| 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 Normal control (lymphoma without BM invasion): 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 with single-cell analysis | doi: 10.1172/jci.insight.151482 | JGAD000395 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data 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 |
| Tatsusada Okuno | Department of Neurology, Osaka University Graduate School of Medicine | Japan | Pathophysiological Understanding of Neuromuscular Diseases | JGAD000226, JGAD000395 | 2024/11/26-2030/03/31 |
