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Long‑Range Gene Networks Uncover 641 New Schizophrenia‑Associated Genes

Long‑Range Gene Networks Uncover 641 New Schizophrenia‑Associated Genes

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Schizophrenia’s genetic landscape just expanded dramatically. A new study in Nature Genetics identifies 641 previously unrecognized genes associated with schizophrenia, thanks to a modeling framework that captures how distant genetic variants regulate gene expression through co‑expression networks. The work reframes schizophrenia not as a collection of isolated genetic hits, but as a disorder shaped by long‑range regulatory relationships across the brain. The study is titled, “Co‑expression‑based models improve eQTL predictions for transcriptome‑wide association studies and highlight new schizophrenia‑associated genes.”

The research team, led by Giulio Pergola, PhD, at the Lieber Institute for Brain Development (LIBD), developed two trans‑aware predictive models—INGENE and MODULE—that quantify how variants far from a gene influence its expression through co‑regulated partners. Traditional transcriptome‑wide association studies (TWAS) focus almost exclusively on cis‑expression quantitative trait loci (ciseQTLs), variants within ±1 Mb of a gene. But as the paper noted, “Most transcriptome‑wide association approaches primarily model local (cis) genetic effects, leaving much of gene regulation unexplained.” By contrast, the new models incorporate distal (trans) regulatory effects, capturing regulatory relationships that behave more like social networks than neighborhood blocks.

Using RNA‑seq data from six human post‑mortem brain regions and genetic data from more than 102,000 individuals, the team integrated cis‑based predictors (CIS, EpiXcan) with their new trans‑based frameworks. The combined approach improved gene‑expression prediction for 18,744 genes, and when applied to Psychiatric Genomics Consortium (PGC3) datasets, it identified 766 schizophrenia‑associated genes, including 641 not previously detected by TWAS.

Pergola said the field has been “looking for the light under the lamppost, focusing only on genes close to disease‑associated DNA variants.” By illuminating long‑range interactions, he explained, “we’ve essentially turned on lights across the entire neighborhood, revealing how distant genetic variants coordinate to build the genetic basis of schizophrenia.”

The findings converge on pathways involved in glutamate signaling, neuronal communication, immune processes, and neurodevelopment—biological systems repeatedly implicated in psychiatric risk. MODULE‑derived trans‑single nucleotide polymorphisms (SNPs) showed particularly strong enrichment for schizophrenia‑associated variants, and many overlapped with cis‑eQTLs for transcription factors such as GATAD2A, RERE, IRF3, and SP4, all previously prioritized in schizophrenia GWAS.

Daniel Weinberger, MD, CEO and director of LIBD, emphasized the shift in perspective: “Schizophrenia risk isn’t just about individual genes acting one after another—it’s about how networks of genes work together. Understanding these coordinated genetic programs brings us closer to precision psychiatry.”

By demonstrating that trans‑regulatory architecture is both detectable and biologically meaningful, the study provides a roadmap for expanding TWAS beyond local effects. It also underscores the importance of integrating multi‑region brain transcriptomics with large‑scale genetic cohorts to reveal disease‑relevant regulatory relationships.

The post Long‑Range Gene Networks Uncover 641 New Schizophrenia‑Associated Genes appeared first on GEN – Genetic Engineering and Biotechnology News.

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Labs see rising demand for nitrosamine, topical performance and microbiome testing

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Recent BioSpace industry conference conversations point to sponsors pushing earlier on safety, quality and performance data, leading to demand for nitrosamine analysis, IVRT/IVPT and microbiome database capabilities.

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10 companies hiring in San Francisco, South San Francisco (plus a few in Brisbane, San Rafael)

10 companies hiring in San Francisco, South San Francisco (plus a few in Brisbane, San Rafael)

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Looking for a new role in and around San Francisco? Check out these companies hiring across all disciplines.​ ​Read More

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Drug Targets LDL Receptor Pathway to Control Cholesterol

Drug Targets LDL Receptor Pathway to Control Cholesterol

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Cholesterol-related heart disease remains the leading cause of death worldwide, and while doctors have more tools than ever to treat it, many patients still can’t achieve safe cholesterol levels or can’t tolerate the side effects of available medications. Researchers at the University of California (UC), San Diego, School of Medicine have now uncovered a hidden biological pathway, dependent on a protein known as Ral, which explains why high-cholesterol diets steadily chip away at our body’s ability to clear harmful low-density lipoprotein (LDL) cholesterol from the blood. The team‘s preclinical study, including tests in mice, also identified a drug candidate already proven safe in humans that could potentially target the pathway.

“We’ve known for a long time that a high-cholesterol diet reduces the liver’s ability to clear cholesterol from the blood, but we didn’t fully understand why,” said Alan Saltiel, PhD, professor of medicine at UC San Diego School of Medicine and director of the UC San Diego/UCLA Diabetes Research Center. “This new discovery explains a critical piece of that puzzle.” Saltiel is senior author of the researchers’ published paper in Nature, titled “Dietary cholesterol activates a Ral-dependent pathway driving LDLR turnover,” in which they concluded, “Together, our findings reveal a Ral-dependent signalling pathway as a key regulator of LDLR turnover and cholesterol homeostasis.”

Disruptions in cholesterol homeostasis are closely linked to an increased risk of atherosclerosis and cardiovascular disease (CVD), the authors wrote. “Elevated low-density lipoprotein cholesterol (LDL-C) significantly contributes to CVD by promoting the formation of atherosclerotic plaques in arteries.”

The liver is the main organ involved in removing cholesterol from the blood so it can be broken down and used elsewhere. This is done through LDL receptors (LDLRs), which sit on the surface of liver cells and act like docking stations, grabbing LDL cholesterol from the bloodstream and pulling it inside the cell for processing. “LDLRs have a crucial role in the uptake of LDL-C from the circulation by hepatocytes,” the investigators continued. The more LDL receptors on liver cells, the more cholesterol gets cleared from the blood, which is why most cholesterol-lowering drugs, such as statins or PCSK9 inhibitors, work by preserving or increasing the number of these receptors. However, the team noted, such treatments have their limitations. “The molecular switches that coordinate LDLR trafficking and turnover in response to nutritional cues, including high dietary cholesterol, remain poorly defined.”

The new research, carried out in mice and in human cells, reveals a previously unknown mechanism that quietly works against the cholesterol removal process, slowly reducing the number of LDL receptors and contributing to high blood cholesterol. The team found that this process begins when a protein called Ral—which Saltiel has previously studied in fat cells—is activated by high dietary cholesterol. “We describe here a previously unrecognized role for Ral signaling in orchestrating LDLR cellular trafficking and lysosomal routing in hepatocytes under chronic cholesterol stress,” the team stated.

Their studies showed that the more Ral is activated, the fewer LDL receptors remain available to clear cholesterol from the blood. This depletion process ultimately relies on a lysosomal protease enzyme called cathepsin A (CTSA). They further explained, “Ral engages the endocytic RalBP1–REPS1 complex to promote LDLR internalization and lysosomal routing, where LDLR is degraded by the lysosomal protease cathepsin A (CTSA).”

The researchers also found that blocking CTSA with a selective small molecule inhibitor (SAR164653) was enough to stabilize LDL receptors and dramatically lower circulating LDL cholesterol in mice. “Pharmacological inhibition of CTSA activity increases hepatic LDLR function and improves cholesterol clearance, offering a potential new therapeutic strategy for hypercholesterolaemia and cardiovascular disease,” they stated.

“There’s still a real need for new cholesterol-lowering options, since some people can’t get to safe levels even with the drugs we have now,” said Saltiel. “This new pathway we discovered is completely separate from anything that existing drugs target, so it gives us a new opportunity to fill that gap.”

After a fundamental biological breakthrough, it typically takes significant additional research to find drugs that target it. However, in this case, a CTSA inhibitor has already been through the early stages of drug development, with the initial goal of treating heart failure. While it was eventually shelved for strategic reasons, the drug had previously advanced to a Phase I clinical trial, where it was successfully tested for safety.

This discovery suggests that the investigational drug is already ready for testing in a Phase II trial for high cholesterol. “Luckily, there’s an experimental drug sitting on the shelf that’s already been shown to be safe in humans,” said Saltiel. “We hope to test whether this might be effective by conducting a clinical trial, which could potentially bring a new treatment option to patients much sooner than would have been expected.”

The post Drug Targets LDL Receptor Pathway to Control Cholesterol appeared first on GEN – Genetic Engineering and Biotechnology News.

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