Understanding how genes can be activated or suppressed in different cells under physiological or pathological conditions of the brain is crucial to studying brain diseases and brain function. A team led by a team from the University of Arizona School of Medicine-Bonnick University and the University of Washington School of Medicine, led by Xiaokuang MA, PhD, Zhiyu Dai, and Dr. Shenfeng Qiu, has developed a new approach to improve the way scientists study genetic activity, which refers to high-resolution mapping in specific cell types in the brain. Their work was published in Star Agreementa refined approach is proposed in fixed frozen brain samples that improve the accuracy and efficiency of spatial transcriptomics – mapping the location and manner in which genes are expressed in the brain at the cellular level.
Dr. MA, Dr. Dai and Professor Qiu have developed a step-by-step method for preparing fixed frozen brain tissue on Xenium slides, a specialized tool for studying gene activity at precise locations. The process involves preserving the brain in a typical way most neuroscientists use for immunofluorescence, frozen slices it into thin slices (10 μm thickness), and carefully image them on slides, meaning high-resolution pictures of tissues to analyze gene richness. “Fixed floating cross-sections with floating mounting allow for better preparation of samples and imaging areas” said Dr. MA, meaning their approaches can maintain mRNA integrity while making full use of available imaging space. Unlike the conventional method of fixing paraffin-wrapped (FFPE) tissue with freshly frozen or formalin, this new technology helps maintain mRNA integrity, which has an indication of human function while improving imaging quality.
Using this optimized approach, the researchers obtained highly detailed images that accurately showed gene expression in different brain regions. By utilizing precise slices and free-floating installation techniques, the team achieved explicit and reliable images of gene activity, i.e., the basic building blocks of the body, at the single cell level. This improvement is especially useful for brain research, because understanding where genes are active can help scientists study brain diseases and how the brain develops. The ability to analyze gene activity in specific brain regions can provide key insights into neurodevelopmental diseases, neurodegenerative diseases, and brain injury mechanisms.
Dr. MA, Dr. Dai and Professor Qiu also pointed out several advantages of their technology compared to older methods. Their approach reduces problems such as tissue folding, which distort images, prevent damage to genetic material and make imaging more effective. Professor Qiu explained: “This approach ensures optimal data collection while reducing costs and improving repeatability.” Repeatability means that results can be consistently repeated by other researchers, making the discovery more reliable. By enhancing spatial transcriptomics, their work may lead to more reliable research on gene activity in different regions of the brain, helping scientists make new discoveries about neurological diseases that affect the brain and nervous system.
This improved approach is an important step forward for researchers studying gene expression in the brain. By maintaining mRNA integrity and improving imaging makes it a valuable tool in neuroscience, neurological research, and other areas of biomedical research. As scientists continue to refine these technologies, such approaches are crucial to promoting our understanding of the complex functions of the brain.
Journal Reference
MA X., Chen P., Wei J., Zhang J., Chen C., Zhao H., Ferguson D., McGee AW, Dai Z., Qiu S. “Xenium Space Transcriptomics Research Protocol using Fixed Frozen Mouse Brain Sections.” Star Protocol, 2024. doi: https://doi.org/10.1016/j.xpro.2024.103420
About the Author
Dr. MAis a researcher/scientist III from the University of Arizona School of Medicine-Shawnicks University. He received his PhD in pharmacology in 2020 from a joint doctoral degree training program between Shantou University School of Medicine and the University of Arizona Medicine-Phoenix. His goal is to understand how MET signals affect the development of synaptic connectivity and plasticity, an important function of the forebrain circuit and have an impact on brain pathophysiology associated with autism. His future research involves how brain development and brain circumcision affect neurodevelopmental disorders and neuropsychiatric disorders, such as autism spectrum disorder and Alzheimer’s disease.
Dr. Zhiyu Daiis an associate professor of medicine at Washington University School of Medicine in St. Louis. He received a bachelor’s degree from Shandong University and his Ph.D. In 2013, he received his PhD in Biochemistry and Molecular Biology from Zhongshan Medical College at Sunsen University in China. Dr. Dai completed his training in pulmonary vascular biology after training in pulmonary vascular biology at the University of Illinois in Chicago. DAI’s lab aims to understand the pathogenesis of pulmonary vascular homeostasis and lung disease using novel animal models, integrated pharmacological approaches, genome editing and single-cell RNA sequencing, and spatial transcriptomics. In addition, he also studied the molecular and cellular mechanisms of correct heart failure in patients with pulmonary hypertension and determined the therapeutic targets for treating patients with pulmonary vascular diseases.
Dr. Shenfeng Qiu, MDis a working professor at the University of Arizona School of Medicine – Shawnicks University. He received his PhD degree from Nanjing Medical University in 1994 and received his PhD. In 2004, the University of California has been involved in the fields of environmental toxicology and neuroscience. The overall interest of Dr. ShenfengQiu’s laboratory is to understand the origins of neurodevelopmental and neuropsychiatric diseases, especially autism spectrum disorders. An ongoing project focuses on the role of MET tyrosine kinase, a major risk factor for ASD in human genetic studies. His laboratory aims to determine the mechanisms by which MET signaling affects neuronal growth, maturation, and brain circuit function. His lab is also interested in the role of UBE3A protein in Angelman syndrome and the different brain circuit mechanisms mediating anxiety and depression.
