Effects of sSLAMF7 on NK cells in multiple myeloma patients

2020 Fiscal Year Research-status Report

• Project/Area Number: 19K08874
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: ARNER ERIK 国立研究開発法人理化学研究所, 生命医科学研究センター, チームリーダー (20571839)
• Co-Investigator(Kenkyū-buntansha): 萩原 將太郎 東京女子医科大学, 医学部, 講師 (50306635)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Keywords: Transcriptome analysis

Outline of Annual Research Achievements

We collected samples of NK cells from the active multiple myeloma patients and inactive patients. We collected 12 of the active myeloma patient samples, and 14 of the inactive myeloma. Out of the 12 active multiple samples, 4 were from fresh multiple myeloma cases and 8 were from relapsed cases. Samples from 12 healthy donors were also collected.

Transcriptome analysis was carried out by performing CAGE library preparation, sequencing and initial analysis. 8 samples failed quality control due to having too few mapped CAGE reads (a minimum of 1 million reads was required) and were discarded from further analysis. CAGE transcriptome data was then subjected to several initial analyses: hierachical clustering, variable genes analysis, principal component analysis, and motif activity response analysis. the principal component analysis showed considerable individual variation between the samples, but also that there were differences between samples from multimple myeloma patients and healthy controls. Results from motif activity response analysis were inconclusive and it was decided that further analysis is needed to understand better the transcriptional regulation behind the difference in gene expression between multiple myeloma cases and healthy controls.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

Once all samples had been collected, transcriptome analysis proceeded as expected. We will proceed with deeper analysis and follow-up experiments in FY2021.

Strategy for Future Research Activity

Using the CAGE data, we will attempt to reconstruct the NK cell transcriptional regulatory network (TRN) that governs multiple myeloma and is modulated by sSLAMF7.

For identifying the TRN, promoters of differentially expressed genes will be examined for the occurrence of transcription factor binding sites(TFBSs), which makes it possible to infer regulatory edges in the regulatory network. Candidate regulatory interactions will be overlaid with complementary data where possible, for example publicly available ChIP-seq data.

For validation, transcription factors will be chosen and their predicted targets will be investigated. Interactions will be assessed using siRNA knock-down of TFs followed by qRT-PCR of their putative targets.

Causes of Carryover

The remaining budget will be used for follow-up experiments and validation experiments in FY2021.