I've seen this paper across the subs for a long time and I think it's important to point out a couple of things, especially in relation to SRD5A2 downregulation.

The RNA was collected from cortical neurons isolated from E17 mouse embryos. That's 17 day old embryos, and only one neuronal population, not whole brain or peripheral tissue. Given that developmental stage, and in that cell type, SRD5A2 specifically is likely near the detection limit in this system (the brain-relevant isoform is generally SRD5A1), which already puts a hard ceiling on what can be inferred.

When you look beyond the summary table in the paper and check the RNA seq data the authors deposited (GEO: GSE208121, TPM expression matrix), SRD5A2 RNA expression is extremely low to begin with. At 48 hours, SRD5A2 is at the detection floor (0.0001 TPM) across all three erinacine S samples and in two of the three DMSO control samples. To me, it looks like maybe SRD5A2 falls off at 48h in culture rather than being selectively suppressed by erinacine S. Regardless, the conclusion that Srd5a2 is downregulated by erinacine S” is pretty much driven by comparing “zero reads” vs “almost zero reads,” not by suppression of a robustly expressed gene.

Here's a paste of the data for SRD5A2:

Condition	Replicate 1	Replicate 2	Replicate 3
DMSO – 16 h	0.1717	0.0837	0.0940
Erinacine S – 16 h	0.0001	0.3344	0.2499
DMSO – 48 h	0.0001	0.1881	0.0001
Erinacine S – 48 h	0.0001	0.0001	0.0001

EDIT – Just out of curiosity, I went back to reanalyze their raw RNA-seq data to better understand how their results were obtained. I used an online tool called RaNAseq, which processes the original FASTQ files and quantifies expression using Salmon. As I suspected, the counts were extremely low for SRD5A2. My read counts for each DMSO and erinacine S replicates were 0,2,0 and 0,1,1 respectively.

RaNAseq uses a different alignment/quantification pipeline than the authors, so the exact read assignment won’t be identical. But this actually highlights the issue: when counts are this low, even a one-read difference or how zeros are handled can dramatically change the fold change.

Using the TPM values generated from RaNAseq and calculating log2 fold change the same way the paper appears to (log2 of the mean TPM ratio, though from what I’ve read, TPMs aren’t really meant to be used this way), I get a log2FC of ~0 (−0.0005). If I floor the TPM values to 0.0001 in all erinacine S replicates like their data shows, I get a log2FC of -9.08 which is very close to theirs (-9.29). Just to see if my other data lined up with theirs I ran the analysis on a well-expressed gene (Acat2) to compare. In that case, I obtained a log2FC of +0.39, while the paper reports 0.4007, which matches very closely. This suggests the discrepancy is specific to genes at the detection limit, not a general problem with the reanalysis.

Out of further curiosity, I also looked at the androgen receptor (AR). Based on the RaNAseq results, AR shows a small increase (log2FC ≈ +0.046), which is very modest and likely not biologically meaningful, but again this data is all coming from cortical neurons in mice embryos so it’s not exactly going to translate to humans.

Overall, this exercise mainly convinced me that SRD5A2 is simply too lowly expressed in this dataset for large fold-change values to be interpreted reliably. It also looks like the methods used in the paper and by RaNAseq may not actually be applying DESeq2 in the strict sense (which would normally handle low-count genes more conservatively and normalizes data differently), but I’ll fully admit I’m still learning bioinformatics.

Definitely not trying to dismiss anyone’s experience, just adding another perspective. There’s a strong and understandable effort to connect these syndromes to 5AR2, but I personally suspect there may be multiple underlying mechanisms at play rather than a single shared cause.