Kalinowski, A. | Search bioRxiv

bioRxiv2025

Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes

The lack of disease-modifying treatments for schizophrenia necessitates the exploration of novel aspects of its pathophysiology, including innate immune mechanisms in the periphery. C4 protein activation, associated with the complement cascade of innate immunity, associates with symptoms and predicts outcomes. However, C4 protein activation does not coincide with expected changes to other proteins in the complement cascade, suggesting another source of C4 protein activation. Using a combination of fresh whole blood from ten anonymous donors and a large set of publicly available microarray data, we show, for the first time, that C4 protein is found and expressed primarily in neutrophils and monocytes. Then, we compared the correlation between C4 protein in neutrophils, classical monocytes, plasma and the number of C4A gene copies. We determined the number of C4A genes using digital droplet PCR, C4 protein in neutrophils (15 patients/21 controls) and plasma (30 patients/38 controls) using western blotting, and classical monocytes (30 patients/38 controls) using flow cytometry. We found a moderate positive correlation between the number of C4A gene copies and the amount of C4 protein only in neutrophils and only in the schizophrenia group (Spearmans rho, r = 0.64, p = 0.01, Cohens d [~]1.67). Our results indicate a convergence of innate immunity mechanisms associated with schizophrenia. This novel mechanism of innate immunity in schizophrenia deserves further study to determine whether it could be a useful drug target.

immunology↗

bioRxiv2019

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

Active retrotransposons in the human genome (L1, Alu and SVA elements) can create genomic mobile element insertions (MEIs) in both germline and somatic tissue1. Specific somatic MEIs have been detected at high levels in human cancers2, and at lower to medium levels in human brains3. Dysregulation of somatic retrotransposition in the human brain has been hypothesized to contribute to neuropsychiatric diseases4, 5. However, individual somatic MEIs are present in small proportions of cells at a given anatomical location, and thus standard whole-genome sequencing (WGS) presents a difficult signal-to-noise problem, while single-cell approaches suffer from limited scalability and experimental artifacts introduced by enzymatic whole-genome amplification6. Previous studies produced widely differing estimates for the somatic retrotransposition rates in human brain3, 6-8. Here, we present a highly precise machine learning method (RetroSom) to directly identify somatic L1 and Alu insertions in <1% cells from 200x deep WGS, which allows circumventing the restrictions of whole-genome amplification. Using RetroSom we confirmed a lower rate of retrotransposition for individual somatic L1 insertions in human neurons. We discovered that anatomical distribution of somatic L1 insertion is as widespread in glia as in neurons, and across both hemispheres of the brain, indicating retrotransposition occurs during early embryogenesis. We characterized two of the detected brain-specific L1 insertions in great detail in neurons and glia from a donor with schizophrenia. Both insertions are within introns of genes active in brain (CNNM2, FRMD4A) in regions with multiple genetic associations with neuropsychiatric disorders9-11. Gene expression was significantly reduced by both somatic insertions in a reporter assay. Our results provide novel insights into the potential for pathological effects of somatic retrotransposition in the human brain, now including the large glial fraction. RetroSom has broad applicability in all disease states where somatic retrotransposition is expected to play a role, such as autoimmune disorders and cancer.

bioinformatics↗