Six readers
| reader | found | score |
|---|---|---|
| genetics Open Targets | no genetic evidence; overall 0.29 from other evidence | 0.00 |
| cell type Human Protein Atlas | expressed broadly, no clear home in brain cells | 0.40 |
| chemistry Open Targets | a small-molecule pocket | 0.60 |
| 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 | 3 pathways; mostly dopamine synapse | 1.00 |
Knock down and overexpress PTPRF in a dopamine neuron, astrocyte and microglia tri-culture; measure evoked dopamine release and dopamine transporter uptake and dopamine neuron survival after α-synuclein fibril challenge.
- Cell type
- a dopamine neuron, astrocyte and microglia tri-culture
- Direction
- Both arms: public data does not say which way helps.
- Molecular readout
- evoked dopamine release and dopamine transporter uptake
- Functional readout
- dopamine neuron survival after α-synuclein fibril challenge
- Rule-out
- If neither arm moves evoked dopamine release 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 PTPRF in a tri-culture of iPSC dopamine neurons, astrocytes and microglia; n = 3 differentiations; readouts: evoked dopamine release and dopamine transporter uptake; dopamine neuron survival after α-synuclein fibril challenge. Controls: non-targeting guide, empty vector. About 8 to 10 weeks, most of it differentiation.
Sealed predictions
- PTPRF in dopamine neurons, braak+0.41 (p 0.273) → -0.38 (p 0.318)receipt 1367
Swarm cases
receipt 1367: PTPRF in dopamine neurons, braak
- power
- full sample -0.18 (p 0.465, n 18), 95% CI -0.60 to +0.31. the interval is wide: not enough donors to tell.
- confounder
- adjusted for sex: -0.23 (p 0.369, n 18). does not hold up.
- composition
- dopamine neurons share of nuclei vs axis +0.05 (p 0.854); controlling for it: -0.42 (p 0.084, n 18). could be the mix.
- skeptic
- leave-one-out range -0.27 to -0.08, sign flips 0; without severely affected donors -0.18 (p 0.465, n 18). fragile.
- cell type
- strongest in oligodendrocytes: -0.64 (p 0.0045, n 18) vs -0.18 in dopamine neurons. proposing oligodendrocytes.
- axis
- no measure beats "tracks Braak Lewy-body stage" for PTPRF in dopamine neurons.
follow-up registered; not confirmed in substantia nigra, an independent cohort.
follow-up PTPRF · oligodendrocytes · braak: substantia nigra, an independent cohort (Parkinson's or LBD vs controls) -0.82 p 0.0034 (needs p < 0.0010)
Receipts
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