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Genetics and Neuropsychiatric Disorders: Untangling the Complexities

Dive into the genetics behind neuropsychiatric disorders and their intricate connections.

Qiuman Liang, Yi Jiang, Annie W. Shieh, Dan Zhou, Rui Chen, Feiran Wang, Meng Xu, Mingming Niu, Xusheng Wang, Dalila Pinto, Yue Wang, Lijun Cheng, Ramu Vadukapuram, Chunling Zhang, Kay Grennan, Gina Giase, Kevin P White, Junmin Peng, Bingshan Li, Chunyu Liu, Chao Chen, Sidney H. Wang

― 7 min read


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Table of Contents

Neuropsychiatric Disorders are a group of complex diseases that involve both the brain and behavior. These can include conditions such as schizophrenia, bipolar disorder, and autism spectrum disorder. Understanding what causes these disorders is tricky since many factors, including Genetics, environment, and social factors, play a part. If we picture it, it’s like trying to find out why a stew tastes a certain way when it could be the mix of ingredients that makes it special.

The Role of Genetics

One major piece of the puzzle is genetics. Scientists have long known that genetics can influence the risk of developing neuropsychiatric disorders. In fact, many studies show that if someone in your family has a condition, you're more likely to develop it too. It’s like having a family recipe that seems to run in the family and tastes great. Genetic studies have identified many specific bits of DNA, known as loci, associated with different disorders. Recently, these studies have blossomed into a big field of research thanks to advances in technology.

Genome-Wide Association Studies (GWAS)

Genome-Wide Association Studies, or GWAS for short, are like scavenger hunts where researchers look through the entire human genome to find genetic variants linked to diseases. Thousands of these genetic variants have been identified that seem to increase the risk of various neuropsychiatric disorders. However, this doesn't mean that having these variants guarantees someone will develop a disorder. Think of it like having a lottery ticket; just because you have one doesn't mean you're going to win the jackpot.

The Mystery of Non-Coding Regions

As researchers dove deeper into the results from GWAS, they found that many of the genetic variants linked to disorders are located in non-coding regions of the DNA. Non-coding regions are the parts of DNA that do not directly tell cells how to make proteins, which is the job of coding DNA. This has left researchers scratching their heads, as the way these regions affect disease isn't straightforward.

The Importance of Regulatory Variants

Regulatory variants in these non-coding areas are now seen as strong candidates for influencing disease risk. These variants can affect how genes are turned on or off, similar to how a dimmer switch controls the brightness of a light. This is where Gene Expression comes into play. By integrating gene expression information with genetic data, researchers can begin to pinpoint the causal variants or identify which genes may be involved in the risk for neuropsychiatric disorders.

Multi-Omics Approaches

In recent years, scientists have started to squeeze more juice from their genetic studies by using multi-omics approaches. Imagine trying to understand a movie by only watching it without ever reading the book or talking to the director. Multi-omics merges different types of biological data: genetics, gene expression, protein levels, and more, to create a fuller picture.

With brain-related disorders, integrating data such as RNA sequencing (which tells us about gene expression), ribosome profiling (which gives clues about how proteins are made), and proteomics (which measures the amount of proteins) can enhance our understanding of how these genetic variants influence disease risk. This combination of data offers a more detailed view, like having multiple cameras capturing various angles of the same event.

The Challenge of Transcription and Translation

In the process of understanding gene regulation, researchers have discovered that just because a gene is expressed doesn't mean that the corresponding protein is produced in the expected amounts. It’s a bit like baking a cake; even if you follow the recipe, sometimes the cake doesn’t rise as much as you thought it would. This is where the idea of translational and post-translational regulation comes into play.

Translational regulation controls the efficiency of converting RNA into protein, while post-translational regulation affects how proteins behave after they are made. These layers of control mean that variants influencing gene expression can get lost in translation, quite literally!

Studying the Brain

When studying the brain, scientists look at brain tissues to understand how genetic variants affect gene expression, translation, and ultimately the levels of proteins. In recent studies done on postmortem brain samples, researchers collected vast amounts of data to understand how genetic variants affect protein synthesis in the prefrontal cortex, the area of the brain responsible for complex behaviors.

With ribosome profiling, they can see how efficiently ribosomes (the machines that produce proteins) are working. Using more than 200 brain samples, researchers were able to capture about 62 billion data points. That’s a lot of information!

Finding Genetic Signals

In their quest to find which genetic variants really matter, researchers used something called cis-QTL mapping. This technique helps identify variants that influence gene expression. They found thousands of these variants, leading them to conclude that many genetic variants have different strengths and can affect gene expression in various ways.

The researchers also noted that as they moved downstream from gene expression to proteins, the number of significant signals reduced drastically. It’s much harder to find the variants that affect protein synthesis than it is to find those that affect gene expression. This suggests that the further they go from the gene to the protein, the less clear the connection becomes, much like a game of telephone where the original message gets distorted.

The Role of Specific Variants

Different types of QTLs were identified in this study, including eQTLs (expression QTLs), rQTLs (ribosome occupancy QTLs), and pQTLs (protein QTLs). Each type represents a different layer of regulation, and researchers observed that protein QTLs tended to have more coding variants compared to expression and ribosome occupancy QTLs.

They also found that many of these QTLs shared similarities with the genes known to be associated with neuropsychiatric disorders. This illustrates how certain genetic variants may lead to increased risks for these conditions.

Colocalization with Brain Disorders

A crucial part of this research involved looking for colocalization between QTL signals and known genetic signals associated with brain disorders like schizophrenia. In fact, many QTL signals were found to overlap with signals from these brain disorders, suggesting that they might be involved in the risk for developing these conditions.

Finding New Risk Genes

Researchers also identified new risk genes that hadn’t been reported before. This was possible due to the combination of their multi-omics data approach and the significance of certain genetic variants. Imagine finding hidden treasures that others missed because they weren’t using the right map!

Among the new gene discoveries, some were linked to important functions in the brain, hinting that they might help explain why someone may be more vulnerable to developing specific neuropsychiatric disorders.

Translational Effects in Action

The researchers observed that while many genetic variants significantly affected gene expression, their impact on protein levels was not as pronounced. This raised interesting questions about how these variants might influence protein synthesis without affecting protein levels.

By comparing independent datasets from different studies, researchers were able to strengthen their conclusions. They found that translational regulation seemed to account for a more considerable reduction of effect size.

Implications for Future Research

By piecing together these complex datasets, researchers are getting a clearer picture of how genetics, protein synthesis, and neuropsychiatric disorders intersect. Their findings open new avenues for research, suggesting that understanding molecular mechanisms may lead to better treatments and interventions for these disorders.

Additionally, they emphasize the potential of translating genetic signals into real-world impacts, underscoring the importance of understanding how genes can influence behavior and risk for mental health issues.

Conclusion

In summary, the genetics behind neuropsychiatric disorders is a complicated web of interactions among various factors. There is still much to uncover, and the journey continues. As they probe deeper and utilize innovative methods, researchers hope to shed more light on understanding these conditions.

Who knew genetics could be so tangled, like spaghetti? Yet, with determination and the right tools, researchers are unraveling this pasta of science, one strand at a time.

Original Source

Title: The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk

Abstract: BackgroundThe impact of genetic variants on gene expression has been intensely studied at the transcription level, yielding invaluable insights into the association between genes and the risk of complex disorders, such as schizophrenia (SCZ). However, the downstream impact of these variants and the molecular mechanisms connecting transcription variation to disease risk are not well understood. ResultsWe quantitated ribosome occupancy in prefrontal cortex samples of the BrainGVEX cohort. Together with transcriptomics and proteomics data from the same cohort, we performed cis- Quantitative Trait Locus (QTL) mapping and identified 3,253 expression QTLs (eQTLs), 1,344 ribosome occupancy QTLs (rQTLs), and 657 protein QTLs (pQTLs) out of 7,458 genes from 185 samples. Of the eQTLs identified, only 34% have their effects propagated to the protein level. Further analysis on the effect size of prefrontal cortex eQTLs identified from an independent dataset clearly replicated the post-transcriptional attenuation of eQTL effects. We identified omics-specific QTLs and investigated their potential in driving disease risks. Using a variant based approach, we found expression-specific QTLs (esQTLs) for 1,553 genes, ribosome- occupancy-specific QTLs (rsQTLs) for 155 genes, and protein-specific QTLs (psQTLs) for 161 genes. Among these omics-specific QTL, 38 showed strong colocalization with brain associated disorder GWAS signals, 29 of them are esQTLs. Because a gene could contain multiple QTL signals, each could either be shared across omics or omics-specific, we aggregated QTL signals from each omics for each gene and found 11 brain associated disorder risk genes that are driven predominantly by omics-specific QTL, all of them are driven by variants impacting transcriptional regulation. This gene-based approach also enabled us to categorize risk genes containing both omics-specific and shared QTL signals. The limited number of GWAS colocalization discoveries from gene-based omics-specific mapping, however, prompted us to take a complementary approach to investigate the functional relevance of genes driven predominantly by attenuated eQTL signals. Using S-PrediXcan we identified 74 SCZ risk genes across the three omics, 30% of which were novel, and 67% of these risk genes were confirmed to be causal in a MR-Egger test using data from the corresponding omics. Notably, 52 out of the 74 risk genes were identified using eQTL data and 68% of these SCZ-risk-gene-driving eQTLs show little to no evidence of driving corresponding variations at the protein level. ConclusionThe effect of eQTLs on gene expression in the prefrontal cortex is commonly attenuated post- transcriptionally. Many of the attenuated eQTLs still correlate with GWAS signals of brain associated complex disorders, indicating the possibility that these eQTL variants drive disease risk through mechanisms other than regulating protein expression level. Further investigation is needed to elucidate the mechanistic link between attenuated eQTLs and brain associated complex disorders.

Authors: Qiuman Liang, Yi Jiang, Annie W. Shieh, Dan Zhou, Rui Chen, Feiran Wang, Meng Xu, Mingming Niu, Xusheng Wang, Dalila Pinto, Yue Wang, Lijun Cheng, Ramu Vadukapuram, Chunling Zhang, Kay Grennan, Gina Giase, Kevin P White, Junmin Peng, Bingshan Li, Chunyu Liu, Chao Chen, Sidney H. Wang

Last Update: Dec 24, 2024

Language: English

Source URL: https://www.biorxiv.org/content/10.1101/2023.06.04.543603

Source PDF: https://www.biorxiv.org/content/10.1101/2023.06.04.543603.full.pdf

Licence: https://creativecommons.org/licenses/by/4.0/

Changes: This summary was created with assistance from AI and may have inaccuracies. For accurate information, please refer to the original source documents linked here.

Thank you to biorxiv for use of its open access interoperability.

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