Thread by @Joni_Coleman

Day 2 of #WCPG2022 kicks off as @BFranke_lab introduces another awesome speaker: @kristenbrennand who is going to talk about using stem cells to study the genetics of brain disease.

KB starts by nicking @dr_appie's visualisation of the polygenicity of common complex psychiatric disorders #WCPG2022

Animal models have been useful, but are not good for studying non coding variants - lack of conservation, takes time to insert gene effects. Stem cells offer an alternative #WCPG2022

Modeling brains with hiPSCs. Skin cells reprogrammed to stem cells, genetically engineered, derived to other cell types including neurons, neural progenitors etc. #WCPG2022

hiPSCs best approximate prenatal cells, so they model risk in a dish, rather than disease state in a dish #WCPG2022

SCZ neurons do not differ from controls on a low magnification level, but show more subtle differences on a group level e.g. in cell migration #wcpg2022

See reduced levels of miR-9 in SCZ cases than controls, but not separable (i.e. levels across cases overlap levels across controls) #WCPG2022

Initial studies on 14 cases, 16 controls. Effects are subtle - need larger cohorts to identify genetic findings. GWAS type analysis discover genetic effects more efficiently than functional experiments: more useful to functionally validate and explain findings instead #WCPG2022

E.g. NRXN1, highly alternatively spliced. Hard to study in mice. Examined NRXN1 isoform space in cells and brain extracts - over 100 isoforms found in brain, and most present in iPSCs, so can study isoforms in cells #WCPG2022

NRXN1 +/- have decreased neurites and activity - neurons don't mature in the expected way, branch less. How does this relate to isoforms? #WCPG2022

50% of isoforms decreased in cases. 31 isoforms are unique to cases. Control neurons are impaired by overexpressing these case specific isoforms, and are not rescued by OE of wildtype. Mutant isoforms may explain ~20% of NRXN1 cases in ASD #WCPG2022

[Non-tweetable things happen. They are exciting - keep monitoring @kristenbrennand's publications!] #WCPG2022

How do risk variant effects from SCZ GWAS vary by context in iPSCs? Hey look, it's rs4702 again [it's the most interesting variant in psychiatric genetics, Pamela Sklar said it years ago and fine-mapping bears it out] #WCPG2022

Impact of genotype on proximal gene expression and neuronal phenotype. AA --> GG at rs4702 in edited isogenic cells (editing took years), FURIN expression lower but only in presence of miR338. Also see reductions in neurites. #WCPG2022

Impact of SARS-COV-2 on genotype and phenotypes. SARS-COV-2 effects FURIN cleavage. Examined effects of rs4702 cells on alveolar cells - dramatically reduced infection in GG cells (where FURIN expression is reduced) #WCPG2022

Impact of genotype on distal target gene expression. DNA is not a 1D string, so genetic effects happen across chromatin loops, not just proximal to variants. E.g. deletion of loops affects protocadherin cluster #WCPG2022

[More untweetable stuff happens] #WCPG2022

Psychiatric genetic risk doesn't act in isolation - how do risk variants sum? Manipulation of SNAP91 effects pre and post synaptic activity. Manipulated with TSNARE1 --> some interaction effects (departure from additivity), some downstream genes more or less expressed #WCPG2022

That was 4 genes - what happens if you add more genes? What happens if you carry pathway-saturating versus pathway-crossing genetic variants? #WCPG2022

[More untweetable things - VERY. COOL. UNTWEETABLE. THINGS.] #WCPG2022

[This is biology. This is GWAS actually meaningfully informing our understanding of neuropsychiatric biology. Obviously much more to be understood from this, context, environment, development etc. to be integrated. But GWAS can actually inform biology] #WCPG2022

Research approach worked at the scale used as an arrayed approach. To get above this scale, need to switch to pooling, putting the guides in together and then deconvolute later. This allows more genes to be studied. #WCPG2022

See talk from Kayla Townsey tomorrow. No more tweets on this today... #WCPG2022

Fantastic talk! #WCPG2022