Translational questions
| Arthur's comments | Jaewon's questions |
|---|---|
|
There are some concerns in terms of the rationale for PD. NLRP3 is not genetically associated with PD risk or progression rate. Although NLRP3 is a major regulator of IL1β, IL1β mRNA is only very slightly upregulated in the PD brain (based on an analyses done by Takeda Computational Biology.) |
Can you share Takeda Comp Bio data that shows this? I know (Mogi., 1994 #1659) reported considerably elevated IL1b in postmortem PD brains. A very old paper though. Do you have other evidence whether IL1b is significantly increased in PD brains? |
| . In addition, IL1β mRNA is not correlated with progression rate. Both findings are based on an analyses done by Takeda Computational Biology. |
Can you share Takeda Comp Bio data that showed this? This is strange since I heard that Takeda Comp Bio analysis showed correlation of IL-1β serum levels with motor severity & progression in PPMI (p=6.02 e-6) & PDBP (p=0.0034). But I haven't seen this data. |
|
A meta-analysis of CSF studies {Chen, 2018 #1635} (https://www.frontiersin.org/articles/10.3389/fimmu.2018.02122/full) found a PD patient versus control standardized difference of g=0.37 which is consistent with the mRNA analysis and suggests that there is a slight elevation but with a lot of overlap between groups. If IL1β levels were markedly higher in patients with PD then we could use a reduction in IL1β as a biomarker readout in early clinical trials but the group difference is not large enough to allow for this in a small study. Along the same lines, TSPO PET imaging could be considered as a biomarker but does not seem to show an abnormal signal in PD based on this paper: https://jneuroinflammation.biomedcentral.com/articles/10.1186/s12974-016-0778-1. | In a separate email, Paul McQuade recommended TSPO or CSF1R imaging as means to monitor mechanism modulation. From biology/mechanistic perspective do you consider these PETs as biomarkers for NLRP3? NLRP3 is a special type of neuroinflammation, not having general features of neuroinflammation. Is there any evidence or rationale that TSPO or CSF1R is upregulated in the patients with overactivated pyroptosis pathway? |
| Overall, we do not seem to have a good handle on how to measure neuroinflammation that is downstream of NLRP3 in patients with PD, which will greatly complicate early clinical development. This is a really important issue since we cannot push risk into late phase development. | |
| Overall the case that neuroinflammation is important in PD is not that strong. | |
RBD+PD
| Hypothesis | HOT to verify? | Tissue | Current evidence | Plan? | |
|---|---|---|---|---|---|
| ↑NLRP3 in RBD+PD (vs HC) | Human-derived data | Postmortem | In brain: ↑NLRP3 in RBD+PD (vs HC) | ||
| CSF | {Hu, 2015 #1794} IL-1b, PRBD (n=51)>control (n=31), Effect size PRBD vs control is ~0.7 |
NCNP, Dr. Yuji Takahashi Molecular BM discovery using CSF and PBMC from PD and RBD patients [Embedded slide content:] Summary: REM sleep behavior disorder (RBD) is thought to be a reliable prodromal stage of Parkinson's disease. In order to discover novel biomarkers for early therapeutic intervention, clinical CSF and PBMC samples from RBD and PD patients have been collected and multiple omics analysis will be performed. Deliverable: Biomarker for early therapeutic intervention and patient segmentation Impact on portfolio: Biomarker for PD Milestone: 1. Sample collection from RBD, PD and HC. 2. Multiple omics analysis using cells in CSF and PBMC. 3. Identification of biomarkers Period: Feb 2019-Feb 2021 (48 month) Funding: 0.12 OKY at Sep 2019 (IMM, immunology unit), 0.12 OKY at Sep 2020 (NS DDU) | |||
| IL-1b, PRBD (N=16) >> NPRBD | {Hu, 2015 #1794} IL-1b, PRBD (n=51)>control (n=31), Effect size PRBD vs control is ~0.7 | ||||
| Serum | {Hu, 2015 #1794} IL-1b, PRBD (n=102)>control (n=31) | {Hu, 2015 #1794} IL-1b, PRBD (N=40) >> NPRBD | 22 | ||
| Genetic | |||||
| Cellular | |||||
| In vitro / in vivo pharmacological validation | In vitro | ||||
| In vivo | (Shen, 2020 #1800) aSyn PFF based mouse model. We injected preformed α-syn fibrils into the sublaterodorsal tegmental nucleus and performed regular polysomnographic recordings and parkinsonian behavioural and histopathological studies in these mice. As a result, we recapitulated RBD-like behaviours in the mice and further showed that the α-synopathy and neuron degeneration identified within the sublaterodorsal tegmental nucleus acted as the neuropathological substrates. |
NCNP CSF sample
20211126 Kamiguchi:
- NCNP: Hattori Kotaro, Takeda: Yugami (but Kamiguchi san himself)
- 2nd y: RBD 25, HC 10, (Spd was only in y1)
- $20K (kamiguchi san group 돈 없다고 내가 내겠다고 했음)
- ERB 는 불필요 할 듯
- If we use O-link, turnaround time is 1 m, so all can be finished by Mar 22.
Email: RE: RBDの研究・期間延長させていただけますでしょうか_263-5 — Kamiguchi, Hidenori
CC: Yugami, Masato; Ootake, Kentarou; D.Araio, Shinsuke; Oid, Akiko; Kamiguchi, Hidenori
1st year は下記の通りのvolume（提供希望量の値）でそれぞれ分注された状態で送付いただい
2nd year も同様のformatを希望します。
| 検体 | 使用量 (提供量) | 濃縮想定量 (~a) |
|---|---|---|
| CSF |
Lipidomics: 0.2 mL Exosome-lipidomics: 0.05 mL Proteomics: 0.2 mL MultiPlex: (0.05 mL) | 0.95 mL / 1.11 mL |
| Plasma |
Lipidomics: 0.025 mL Exosome-lipidomics: 0.24 mL Proteomics: 0.01 mL (0.05 mL) | 0.25 / 0.06 / 0.025 / 0.405 mL |
| Blood | PBMC-transcriptome: 2 mL | 2 mL |
こちら分注するとなるとそれなりに時間がかかるので、できれば前回同様にNCNP様のほうで かと思いますが、
一方、前回volume不足のサンプルもあったので、その点はご意見いただければと思います。
なお、multiplex用の60 uLは余剰というか、multiplex目的で保存してあります（現状どんな multiplex 想定か決まってないので、そのまま取っておいてあります）
- Amount Available for nlrp3: 0.06 mL (multiplex) → will ask for more
- In general: singleplex (reliable/stable) is better than multiplex, and needs 50-100 uL per readout.
- Timeline: ERB required
- Flow
- Negotiation with NCNP for additional readout, & amount (current 1.1 mL → 1.5 mL) → sebastian to define readout, assay, and amount → ask Laura for budget → ERB → analysis (AXClead)
from Toshiya
| Available at academia | |
|---|---|
| NLRP3 | Matt's lab has already developed an MSD ELISA for NLRP3 ({Anderson, 2021 #1560} (table1 plasma)) That should be better than a ... |
Uncertain Spans
| location | transcription | uncertainty |
|---|---|---|
| Q&A row 4 cell | row label 22 in plan column | A solitary 22 appears in the Plan? column for the Serum row; reading is consistent with the visible cell. |
| Email subject line | RBDの研究・期間延長させていただけますでしょうか_263-5 | Subject string is partly stylized in the Outlook screenshot; reading preserved. |
| Email volume table | numeric values such as 0.95 mL / 1.11 mL, 0.405 mL | Numbers are rendered in a small Outlook window screenshot; readings are best-effort and may differ in last digit. |
| RBD+PD Postmortem in-brain cell | Slide screenshot | The In-brain plan cell contains an embedded slide image; text is transcribed in a paragraph, but the layout (six-row colored panel with images) is not fully reproduced. |