View source for HyeongJin Yun Scientific Essay


<span style="font-size:10pt"><span style="line-height:107%"><span style="font-family:">'''<span lang="EN-US" style="font-size:14.0pt"><span style="line-height:107%"><span style="font-family:">Necessity of RNA Sequencing in Human BBB Models</span></span></span>'''</span></span></span><br/> <span style="font-size:10pt"><span style="line-height:107%"><span style="font-family:">'''<span lang="EN-US" style="font-size:14.0pt"><span style="line-height:107%"><span style="font-family:">&nbsp;and Drug Delivery Research</span></span></span>'''</span></span></span><br/> <span style="font-size:10pt"><span style="line-height:107%"><span style="font-family:"><span lang="EN-US" style="font-family:">20191193 HyeongJin Yun</span></span></span></span><br/> <br/> <span style="font-size:14px;"><span style="line-height:107%">'''<span lang="EN-US">Introduction</span>'''</span></span>

<span style="font-size:14px;">I have always been deeply interested in diseases caused by brain dysfunction, such as brain cancer, depression, and dementia. This interest led me to pursue research and development in the field of drug delivery to the brain, particularly through the blood-brain barrier (BBB). I am currently developing a human blood-brain barrier (BBB) model and conducting extensive research to understand how carriers penetrate the BBB for drug delivery. My work primarily involves building basic cell culture techniques and creating an in vitro BBB model. The carrier samples used in this experiment are provided by our collaborative research partner. We plan and execute further experimental procedures by determining the permeability of these carriers across the BBB.</span>

<span style="font-size:14px;">Currently, I have completed the process of determining whether lipid nanoparticles (LNPs) can pass through the BBB. Now, I have shifted my focus to exploring the mechanisms by which these nanoparticles pass through the barrier. I became particularly interested in this area because I believe RNA-sequencing, which was mentioned in the Genomics course, would help me explore these mechanisms further.&nbsp;RNA-sequencing can provide detailed insights into the gene expression changes and molecular pathways activated during nanoparticle transport across the BBB, thereby elucidating the specific biological processes and interactions involved.</span>

<br/> <br/> <span style="font-size:14px;"><span style="line-height:107%">'''<span lang="EN-US">Blood-Brain Barrier and Lipid Nanoparticles</span>'''</span><br/> <span style="line-height:107%"><span lang="EN-US">The human blood-brain barrier (BBB) is a unique and selective barrier that regulates the transport of substances from Blood to the brain. It plays an important role in maintaining the neurons and glia function. BBB is composed of Brain microvascular endothermic cells (BMVECs), Astrocytes, Pericytes, and ECM (<span style="color:#0070c0">1,2</span>). BMVECs have a much lower degree of endocytosis/transcytosis activity than peripheral endothelium contributing to the characteristics of BBB as a barrier (<span style="color:#0070c0">3</span>).</span></span><br/> <span style="line-height:107%"><span lang="EN-US">&nbsp;Lipid nanoparticles (LNPs) are widely used in the field of drug delivery. LNPs are primarily composed of cholesterol and lipids and can encapsulate DNA, RNA, or drugs. Additionally, ligands or antibodies can be attached to the surface to aid in targeting (<span style="color:#0070c0">4</span>).</span></span><br/> <span style="line-height:107%"><span lang="EN-US">My research is conducting a study on whether LNPs using a new fabrication method called Liposome Under Cryo-Assembly (Luca) can pass through the human BBB model. The identification of LNP samples that penetrate well is finished and the mechanism study process is in the process.</span></span></span><br/> <br/> <img style="width: 700px; height: 509px;" src=http://Biolecture.org/upload/20240611155233_image.png><br/> <span style="font-size:14px;">'''Figure1.'''<br/> The Timeline and Structure of Human BBB Transwell model.<br/> <br/> <span style="line-height:107%">'''<span lang="EN-US">Overview of RNA sequencing technology</span>'''</span><br/> <span style="line-height:107%"><span lang="EN-US">Principles of RNA Sequencing</span></span><br/> <span style="line-height:107%"><span lang="EN-US">RNA sequencing (RNA-seq) is a high-throughput sequencing technology used to determine the nucleotide sequence of RNA molecules and quantify specific RNA species within a population. The process of RNA sequencing includes the following steps (<span style="color:#0070c0">5</span>):</span></span></span>

#<span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">RNA Extraction: Extracting RNA from biological samples such as cells or tissues.</span></span></span> 

&nbsp;
<ol start="2">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">cDNA Synthesis: Converting the extracted RNA into complementary DNA (cDNA) using reverse transcriptase.</span></span></span></li>
</ol>

&nbsp;
<ol start="3">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Library Preparation: Fragmenting the cDNA, attaching adapters, and amplifying the cDNA fragments through PCR.</span></span></span></li>
</ol>

&nbsp;
<ol start="4">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Sequencing: Sequencing the prepared library using platforms such as Illumina or Nanopore.</span></span></span></li>
</ol>

&nbsp;
<ol start="5">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Data Analysis: Aligning the generated sequences to a reference genome and quantifying gene expression levels.</span></span></span></li>
</ol>

<br/> <span style="font-size:14px;"><span style="line-height:107%">'''<span lang="EN-US">Methods for Gene Expression Analysis Using RNA Sequencing</span>'''</span><br/> <span style="line-height:107%"><span lang="EN-US">The analysis of gene expression using RNA sequencing involves several steps:</span></span></span><br/> &nbsp;

#<span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Data Quality Control: Assessing the quality of sequencing data and removing low-quality reads.</span></span></span> 

&nbsp;
<ol start="2">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Data Alignment: Aligning the reads to a reference genome to determine the location of each read.</span></span></span></li>
</ol>

&nbsp;
<ol start="3">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Gene Expression Quantification: Calculating the expression levels of genes, typically represented as RPKM, FPKM, or TPM values.</span></span></span></li>
</ol>

&nbsp;
<ol start="4">
<li><span style="font-size:14px;"><span style="line-height:107%"><span lang="EN-US">Differential Expression Analysis: Identifying differentially expressed genes between specific conditions to understand changes in gene expression due to factors such as inflammation, stress, or drug treatment</span></span></span></li>
</ol>

<br/> <br/> <span style="font-size:14px;"><span style="line-height:107%">'''<span lang="EN-US">Necessity of RNA Sequencing in BBB Models</span>'''</span><br/> <span style="line-height:107%"><span lang="EN-US">Through fluorescence image analysis, I found out that LNPs migrate to the transcytosis pathway. In addition, I checked the difference in transmittance by performing several transcytosis inhibitor treatments.</span></span><br/> <span style="line-height:107%"><span lang="EN-US">Through RNA sequencing, I would like to check whether the permeability has changed due to changes in the genetic level of the cells that actually make up BBB.</span></span><br/> <br/> <span style="line-height:107%">'''<span lang="EN-US">Future Plan</span>'''</span><br/> Taking the Genomics course, I realized that conducting research at various gene levels is essential to achieving high-level research outcomes. My goal is to proceed with the RNA sequencing mentioned above to uncover the detailed mechanisms of nanoparticle transport that have not yet been identified. To facilitate this, I am eager to collaborate actively with the bioinformatics labs at UNIST for detailed RNA sequencing analysis. After discovering the mechanisms, I plan to treat the surface of the nanoparticles with Aptamers to observe changes in permeability and ultimately encapsulate actual drugs for targeted delivery.</span><br/> <br/> <br/> <span style="font-size:14px;"><span style="line-height:107%">'''<span lang="EN-US">References</span>'''</span><br/> <span style="line-height:107%"><span lang="EN-US" style="line-height:107%">(1) Cecchelli, Romeo, et al., Modelling of the blood–brain barrier in drug discovery and development., '''2007''', ''Nature Reviews Drug Discovery''. vol. 6, no. 8, pp. 650–661,.</span></span><br/> <br/> <span style="line-height:107%"><span lang="EN-US" style="line-height:107%">(2) Park, Tae-Eun, et al., Hypoxia-enhanced blood-brain barrier chip recapitulates human barrier function and shuttling of drugs and antibodies., '''2019''', ''Nature Communications'', vol. 10, no. 1, 13</span></span><br/> <br/> <span style="line-height:107%"><span lang="EN-US" style="line-height:107%">(3) Abbott, N. Joan, Lars Rönnbäck, and Elisabeth Hansson., Astrocyte–Endothelial Interactions at the Blood–Brain Barrier., '''2006''', ''Nature Reviews Neuroscience 7'', no. 1: 41–53.</span></span><br/> <br/> <span style="line-height:107%"><span lang="EN-US" style="line-height:107%">(4) Mehta, M., Bui, T. A., Yang, X., Aksoy, Y., Goldys, E. M., & Deng, W., Lipid-based nanoparticles for drug/gene delivery: An overview of the production techniques and difficulties encountered in their industrial development., '''2023''', ''ACS Materials Au'', 3(6), 600–619.</span></span><br/> <br/> <span style="line-height:107%"><span lang="EN-US">(5)</span> <span lang="EN-US">Deshpande, Dhrithi, et al., RNA-seq data science: From RAW data to effective interpretation.,'''2023''', ''Frontiers in Genetics'', vol. 14,</span></span></span>