Six readers
| reader | found | score |
|---|---|---|
| genetics Open Targets | genetic association 0.38 (overall 0.23) | 0.38 |
| cell type Human Protein Atlas | cell type enhanced in oligodendrocyte progenitor cells (4092 nCPM) | 1.00 |
| chemistry Open Targets | reachable by antibody | 0.36 |
| trials ClinicalTrials.gov | no Parkinson's trials on record: an open field | 1.00 |
| literature PubMed | no papers tie it to Parkinson's yet | 1.00 |
| pathways Reactome | 1 pathway; mostly other | 0.30 |
Knock down and overexpress LRRTM4 in oligodendrocytes; measure a transcriptome-wide state shift (bulk RNA-seq) and α-synuclein uptake and myelin basic protein output under oxidative stress.
- Cell type
- oligodendrocytes
- Direction
- Both arms: public data does not say which way helps.
- Molecular readout
- a transcriptome-wide state shift (bulk RNA-seq)
- Functional readout
- α-synuclein uptake and myelin basic protein output under oxidative stress
- Rule-out
- If neither arm moves a transcriptome-wide state shift (bulk RNA-seq) by 20% or more against non-targeting and empty-vector controls, across three independent differentiations, the hypothesis is wrong.
- Lab request
- CRISPRi knockdown and lentiviral overexpression of LRRTM4 in iPSC-derived oligodendrocytes; n = 3 differentiations; readouts: a transcriptome-wide state shift (bulk RNA-seq); α-synuclein uptake and myelin basic protein output under oxidative stress. Controls: non-targeting guide, empty vector. About 8 to 10 weeks, most of it differentiation.
Sealed predictions
- LRRTM4 in dopamine neurons, braak+0.13 (p 0.733) → +0.33 (p 0.386)receipt 1831
- LRRTM4 in oligodendrocytes, braak-0.31 (p 0.414) → +0.89 (p 0.001)receipt 1830
Swarm cases
receipt 1831: LRRTM4 in dopamine neurons, braak
- power
- full sample +0.28 (p 0.265, n 18), 95% CI -0.22 to +0.66. the interval is wide: not enough donors to tell.
- confounder
- adjusted for sex: +0.24 (p 0.337, n 18). does not hold up.
- composition
- dopamine neurons share of nuclei vs axis +0.05 (p 0.854); controlling for it: +0.18 (p 0.487, n 18). could be the mix.
- skeptic
- leave-one-out range +0.18 to +0.46, sign flips 0; without severely affected donors +0.28 (p 0.265, n 18). fragile.
- cell type
- no other cell group does better.
- axis
- no measure beats "tracks Braak Lewy-body stage" for LRRTM4 in dopamine neurons.
case closed: nothing better to follow up.
receipt 1830: LRRTM4 in oligodendrocytes, braak
- power
- full sample +0.21 (p 0.403, n 18), 95% CI -0.28 to +0.62. the interval is wide: not enough donors to tell.
- confounder
- adjusted for sex: +0.22 (p 0.384, n 18). does not hold up.
- composition
- oligodendrocytes share of nuclei vs axis +0.03 (p 0.915); controlling for it: +0.25 (p 0.315, n 18). could be the mix.
- skeptic
- leave-one-out range +0.14 to +0.39, sign flips 0; without severely affected donors +0.21 (p 0.403, n 18). fragile.
- cell type
- no other cell group does better.
- axis
- no measure beats "tracks Braak Lewy-body stage" for LRRTM4 in oligodendrocytes.
case closed: nothing better to follow up.
Receipts
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