diff --git a/src/contents/description.tsx b/src/contents/description.tsx index 39ddfbe2ee0977199c7eb5e151d2246c46da90c2..e9ccfa369cac57129dd05a5c2bc677c121067dcd 100644 --- a/src/contents/description.tsx +++ b/src/contents/description.tsx @@ -71,8 +71,8 @@ export function Description() { <Collapsible id="classes-mutations-collapsible" title="Different classes of mutations"> <p>The mutations can be divided into <u>six classes</u> <SupScrollLink label="15"/> :</p> <p><b>Class I</b> mutations prevent the synthesis of CFTR proteins altogether, meaning no channels are produced.</p> - <p><b>Class I</b> mutations, which include the common F508del mutation (responsible for about 85% of cases <SupScrollLink label="16"/> , disrupt the maturation process of the protein. As a result, the defective channels are quickly degraded by the cell.</p> - <p><b>Class I</b> mutations, known as “gating†mutations, reduce the likelihood that the CFTR channel will open correctly, impairing its function.</p> + <p><b>Class II</b> mutations, which include the common F508del mutation (responsible for about 85% of cases <SupScrollLink label="16"/> , disrupt the maturation process of the protein. As a result, the defective channels are quickly degraded by the cell.</p> + <p><b>Class III</b> mutations, known as “gating†mutations, reduce the likelihood that the CFTR channel will open correctly, impairing its function.</p> <p><b>Class IV, V</b> and <b>VI</b> mutations are rare. These mutations result in the production of unstable or inefficient CFTR proteins, which do not function adequately and are produced in insufficient numbers.</p> </Collapsible> <p>The prevalence of CF varies globally, with higher concentrations of cases in Europe, North America, and parts of Oceania. This geographic variation underscores the need for regionally tailored healthcare solutions. </p> @@ -245,7 +245,7 @@ export function Description() { <p>Additionally, this reversed architecture alters the positioning of the reverse transcription template (RTT) and primer binding site (PBS) on the pegRNA. In Cas9-based systems, the RTT is located at the 3' end of the pegRNA, which leaves it more exposed and increases the risk of reverse transcription continuing past the intended stop point. This "scaffold read-through" effect can result in the synthesis of unintended DNA sequences, leading to undesired mutations or genomic alterations at the target site<SupScrollLink label="95"/> , potentially compromising the safety of the Prime Editing process. In CasX and Fanzor systems, however, the RTT is positioned at the 5' end of the pegRNA, while the spacer is located near the 3' end and is closely bound to the protein. This reversed layout helps ensure that reverse transcription stops precisely at the end of the RTT sequence, significantly reducing the risk of unintended extensions and improving the precision and reliability of the editing process.</p> <p>By incorporating these smaller, more stable nickases into the Prime Editing complex, we aim to reduce its overall size while maintaining or even enhancing its functionality and reliability. </p> </Collapsible> - <p>In terms of the pegRNA, we opted for a pegRNA, including a 16-base primer binding site (PBS) and a 30-base reverse transcription template (RTT), with no silent edits and a structural motif, the tevopreQ1. After extensive screening using a reporter system, this pegRNA demonstrated the highest performance, leading us to select it as the best candidate for further development. While other pegRNAs also showed promise, pegRNA_PEAR_05 was ultimately chosen for its superior results in our testing.</p> + <p>In terms of the pegRNA, we opted for a pegRNA, including a 16-base primer binding site (PBS) and a 30-base reverse transcription template (RTT), with no silent edits and a structural motif, the tevopreQ1. After extensive screening using a reporter system, this pegRNA demonstrated the highest performance, leading us to select it as the best candidate for further development. While other pegRNAs also showed promise, pegRNA_PEAR_04 was ultimately chosen for its superior results in our testing.</p> <Collapsible id="pegRNA-genau-collapsible" title="Optimization of the pegRNA"> <p><b>Stability improvement: tevopreQ1 extension</b></p> <p>The pegRNA was specifically optimized to enhance its stability in the cellular environment. To achieve this, a structural motif known as tevopreQ1 was added to the basic pegRNA structure. This motif was selected based on its known ability to improve RNA stability by preventing degradation. By integrating tevopreQ1, the goal was to extend the half-life of the pegRNA, allowing it to remain functional in cells for a longer duration, thus improving the likelihood of successful gene edits. This stabilizing addition was particularly valuable in the context of CFTR gene editing, where higher RNA stability could lead to better editing outcomes.</p> @@ -348,7 +348,7 @@ export function Description() { <p>Central to our <b>delivery system</b> is <b>AirBuddy</b>, a lung-specific lipid nanoparticle designed to stabilize and protect the prime editing complex during transport to lung epithelial cells. <b>AirBuddy</b> ensures that the protein complex is delivered specifically to lung cells, enhancing the efficiency of the gene-editing process. By modifying the lipid nanoparticle with protective features, we achieved increased stability, ensuring effective delivery to the target cells. </p> <p>We further optimized the prime editing fusion protein, <b>PrimeGuide</b>, to streamline its components, resulting in a smaller and more efficient prime editing complex. This improvement significantly enhances the precision of the gene editing process, reducing off-target effects and increasing the overall success of mutation correction. </p> <p>In subsequent experiments, <b>HEK and lung (CFBE41o-)cells</b> carrying the CFTR <i>F508del</i> mutation were successfully <b>transfected</b> with the optimized prime editing complex. Our results indicated successful correction of the mutation, confirming the potential of our approach for treating Cystic Fibrosis. </p> - <p>Additionally, we explored <b>downstream applications</b>. Primary cell cultures were treated with lipid nanoparticles to introduce a reporter RNA. We also established 2D cultures transfected with YFP, a sodium-sensitive reporter protein, to assess ion channel functionality. Finally, in CFTR-deficient organoids, our system facilitated repair of the CFTR channel, evidenced by an increase in organoid volume upon treatment. This suggests successful functional restoration of CFTR activity. </p> + <p>Additionally, we explored <b>downstream applications</b>. Primary cell cultures were treated with lipid nanoparticles to introduce a reporter RNA. </p> </Section> <Section title="Our Vision" id="Our Vision"> <p>At <b>PreCyse</b>, we envision a future where gene therapy for Cystic Fibrosis (CF) is as simple and user-friendly as using an inhaler. Our goal is to develop a fully integrated Prime Editing system, <b>PrimeGuide</b>, delivered via a cutting-edge lipid nanoparticle (LNP) platform, <b>AirBuddy</b>. The therapy would allow patients to inhale the therapeutic complex, targeting the underlying genetic mutation that causes CF—specifically, the F508del mutation in the CFTR gene. </p> diff --git a/src/contents/results.tsx b/src/contents/results.tsx index 796fd52aed4f99831e1ebe2de869e3255a9c280c..ae822f9d6169361c20fc6fe0dce8b1daadab4d2d 100644 --- a/src/contents/results.tsx +++ b/src/contents/results.tsx @@ -19,7 +19,7 @@ export function Results() { return ( <><Section title="Abstract" id="Abstract"> <p>For the prime editing of <strong>Cystic Fibrosis</strong> (CF), we on the one hand optimized a prime editing complex and on the other hand developed an efficient delivery system. For testing, we set up cell culture with model cell lines as well as primary cells taken from team members and a patient.</p> -<p>For editing, we first compared different existing prime editors <strong>(pCMV-PE2, pLV-PE_CO-Mini, pCMV-PE6c)</strong> and constructed a reporter plasmid simulating the <strong>CFTR context</strong>. In addition and to further enhance the editing process, we designed various pegRNAs tailored to our construct incorporating features such as <strong>silent edits</strong>, for a lower mismatch repair, and a 3′ stabilizing stem loop <strong>(tevropQ1)</strong>. The aim was to identify the most effective pegRNA for our specific target, which is why pegRNA especially for CFTR F508del mutation were designed.</p> +<p>For editing, we first compared different existing prime editors <strong>(pCMV-PE2, pMLV-PE_CO-Mini, pCMV-PE6c)</strong> and constructed a reporter plasmid simulating the <strong>CFTR context</strong>. In addition and to further enhance the editing process, we designed various pegRNAs tailored to our construct incorporating features such as <strong>silent edits</strong>, for a lower mismatch repair, and a 3′ stabilizing stem loop <strong>(tevopreQ1)</strong>. The aim was to identify the most effective pegRNA for our specific target, which is why pegRNA especially for CFTR F508del mutation were designed.</p> <p>As proof of concept, we transfected these constructs in <strong>HEK293 and CFB41o- cells</strong> and observed significant prime editing of our reporter via fluorescence microscopy. We identified the PE6c editor and our pegRNA variant 4 as optimal. This resulted in our <strong>Best New Basic Part</strong>, <strong>PEAR_CFTR</strong>. Furthermore, we extended our approach to primary human nasal epithelial cells generated from our own nasal epithelial cells through nasal swabs. By cultivating them in Air Liquid Culture (ALI) and Apical-Our Organoids, we successfully tested our technologies <i>in vitro</i>, mimicking the <i>in vivo</i> situation.</p> @@ -38,7 +38,7 @@ export function Results() { <H5 text="Conclusion"/> <p>The microscopy data validates our proof of concept. Compared to our internal positive control, pDAS12124-preedited (see Figure 1), less cells co-transfected with pDAS12489 and pCMV-PE2 (see Figure 1) showed fluorescence. Contrary to our expectations, the technical transfection control with pZMB938 showed lower transfection efficiency. All negative controls showed no fluorescence.</p> <ThreeVertical - description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals." + description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals. BF = Brightfield" num={1} pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild1-1.png" alt1="pZMB" @@ -52,7 +52,7 @@ export function Results() { <H5 text="Conclusion"/> <p>All 4 different transfection conditions were done with pZMB938 and showed good results, but best result were done when lipofectamine 2000 was diluted 1:10 and 1000 ng DNA was transfected.</p> <TwoVertical - description="Microscopy of HEK293 72h post transfection with lipofectamin 2000. Transfection with 1:10 or 1:25 diluted lipofectamine and 800 ng or 1000 ng of out technical positive control pZMB938." + description="Microscopy of HEK293 72h post transfection with lipofectamin 2000. Transfection with 1:10 or 1:25 diluted lipofectamine and 800 ng or 1000 ng of out technical positive control pZMB938. BF = Brightfield" num={2} bg="white" alt1="1000ng DNA with 1:10 and 1:25 Lipofectamine 2000" @@ -64,7 +64,7 @@ export function Results() { <H5 text="Conclusion"/> <p>Internal control and technical control showed higher transfection efficiency then in previous experiments, therefore transfection with lipofectamine 3000 seems to be more efficient than transfection with lipofectamine 2000. The fluorescence of pDAS12189+pCMV-PE2 was still quite low. All negative controls are showed no fluorescence.</p> <ThreeVertical - description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals." + description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals. BF = Brightfield" num={3} bg="white" alt1="pZMB and pDAS12124" @@ -77,7 +77,7 @@ export function Results() { <H5 text="Conclusion"/> <p>The results of the test were not as good as expected. Nearly no transfection efficiency was visible. This could be due to too old HEK293 cells</p> <TwoVertical - description="Microscopy of HEK293 72h post transfection with lipofectaine 3000. Transfection of 500 ng or 1000 ng of our technical positive control pZMB938 with 1 µl or 1.5 µl of lipofectamine 3000." + description="Microscopy of HEK293 72h post transfection with lipofectaine 3000. Transfection of 500 ng or 1000 ng of our technical positive control pZMB938 with 1 µl or 1.5 µl of lipofectamine 3000. BF = Brightfield" num={4} bg="white" alt1="500ng DNA 1 µl or 1.5 µl of lipofectamine 3000" @@ -93,11 +93,11 @@ export function Results() { num={5} bg="white" alt1="Microscopy of HEK293 72h post transfection with lipofectamine 3000 with 1000 ng or 1500 ng technical positive control pZMB938. Both transfections show fluorescence signals" - description="Microscopy of HEK293 72h post transfection with lipofectamine 3000 with 1000 ng or 1500 ng technical positive control pZMB938. Both transfections show fluorescence signals" + description="Microscopy of HEK293 72h post transfection with lipofectamine 3000 with 1000 ng or 1500 ng technical positive control pZMB938. Both transfections show fluorescence signals. BF = Brightfield" /> <TwoVertical - description="Microscopy of HEK293 72h post transfection with CaCl2 with 500 ng, 1000 ng or 1500 ng pZMB938. All transfections show fluorescence signals." + description="Microscopy of HEK293 72h post transfection with CaCl2 with 500 ng, 1000 ng or 1500 ng pZMB938. All transfections show fluorescence signals. BF = Brightfield" num={6} bg="white" alt1="" @@ -110,7 +110,7 @@ export function Results() { <p>The transfection efficiency was much better. Our proof-of-concept was working correctly. The reporter system pDAS12189 only led to production of a fluorescent signal when co transfected with a prime editing complex as pCMV-PE2.</p> <TwoVertical alt1="" - description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals." + description="Microscopy of HEK293 72h post transfection with lipofectamine 2000. Transfection with technical positive control pZMB938, internal positive control pDAS12124-preedited, co-transfection of pDAS12489 with pCMV-PE2, NTC, PE2 as control and pDAS12489 as control. All controls are negative and both positve controls as well as pDAS12489+pCMV-PE2 show fluorescence signals. BF = Brightfield" num={7} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild7-1.png" @@ -124,7 +124,7 @@ export function Results() { <H5 text="Conclusion"/> <p>The Flow Cytometry analysis shows that pegRNA without silent edits (pegRNA1) had a 2.05 times higher transfection efficiency than pegRNA with silent edits (pegRNA2).</p> <TwoHorizontal - description="Flow Cytometry analysis of pegRNAs with and without silent edits." + description="Flow cytometry analysis of pegRNAs with and without silent edits. Histograms of cell count applied against fluorescence intensity of healthy HEK293 cells (left) with untransfected cells as negative control, pDAS12124 pre-edited as internal positive control and pegRNAs with (pegRNA1) and without (pegRNA2) silent edits 72 h after transfection. The portion of fluorescent cells is normalized to the internal positive control (right)." num={8} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/se-nose.png" @@ -143,7 +143,7 @@ export function Results() { pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild9.png" num={9} alt1="Flow Cytometry results of all screened pegRNAs" - description="Flow Cytometry results of all screened pegRNAs" + description="Percentage of fluorescent HEK293 cells 72 h after transfection with various pegRNAs (pegRNA1-14) normalized to pDAS12124 pre-edited as internal positive control as result of flow cytometry analysis." /> </div> </div> @@ -154,7 +154,7 @@ export function Results() { <p>Transfection of CFBE41o- with pDAS12124-preedited was successful (see Figure 10). After 24 hours a successful co transfection of pPEAR_CFTR with PE6c and pegRNA4 was visible, although the transfection efficiency was really bad (see Figure 10).</p> <TwoVertical alt1="" - description="Microscopy results after 24h or 48h. Transfection of pDAS12124-preedited with lipofectamine 3000 was successfully done in CFBE41o- cell line and visible after 48h. CFBE41o- cell line was transfected with pDAS-IDT with Lipofectamine 3000 and afterwards with LNPs including PE6c and pegRNA4 and was after 24h fluorescence visible." + description="Microscopy results after 24h or 48h. Transfection of pDAS12124-preedited with lipofectamine 3000 was successfully done in CFBE41o- cell line and visible after 48h. CFBE41o- cell line was transfected with pDAS-IDT with Lipofectamine 3000 and afterwards with LNPs including PE6c and pegRNA4 and was after 24h fluorescence visible. BF = Brightfield" num={10} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild10-1.png" @@ -163,7 +163,7 @@ export function Results() { <p>Moreover transfection was conducted in human nasal epithelial cells (hNECs) in Air-liquid interface cultures as well as apical-out airway organoids (see Figure 11). No fluorescence was visible. </p> <TwoVertical alt1="" - description="Microscopy of HEK 72h post transfection with lipofectamine 3000. Co-transfection of pPEAR_CFTR with PE6c and pegRNA4. Both show no fluorescence signals." + description="Microscopy of HEK 72h post transfection with lipofectamine 3000. Co-transfection of pPEAR_CFTR with PE6c and pegRNA4. Both show no fluorescence signals. BF = Brightfield" num={11} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/ali-tr.png" @@ -178,7 +178,7 @@ export function Results() { <div className="col"> <TwoVertical alt1="" - description="Microscopy of HEK 72h post transfection with lipofectamine 3000. Co-transfection of pDAS12489 with pCMV-PE2 or pDAS12489 with LV-PE_CO-Mini. Both show fluorescence signals." + description="Microscopy of HEK 72h post transfection with lipofectamine 3000. Co-transfection of pDAS12489 with pCMV-PE2 or pDAS12489 with LV-PE_CO-Mini. Both show fluorescence signals. BF = Brightfield" num={12} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild11-1.png" @@ -192,7 +192,7 @@ export function Results() { pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/pe2-pe-co.png" num={13} bg="white" - description="Flow Cytometry analysis to compare prime editing complexes PE2 and PE_CO-Mini" + description="Flow Cytometry analysis to compare prime editing complexes PE2 and PE_CO-Mini. Histograms of cell count applied against fluorescence intensity of healthy HEK293 cells (left) with untransfected cells as negative control, pDAS12124 pre-edited as internal positive control 72 h after transfection." /> </div> </div> @@ -206,13 +206,13 @@ export function Results() { pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/bild13.png" num={14} bg="white" - description="Microscopy of HEK293 72h post transfection with lipofectamine 3000 and co transfection with pCMV-PE6c and pDAS12489." + description="Microscopy of HEK293 72h post transfection with lipofectamine 3000 and co transfection with pCMV-PE6c and pDAS12489. BF = Brightfield" alt1="Microscopy of HEK293 72h post transfection with lipofectamine 3000 and co transfection with pCMV-PE6c and pDAS12489." /> <TwoHorizontal alt1="" - description="Flow Cytometry results for evaluation of PE6c performance." + description="Flow cytometry analysis for evaluation of performance of prime editor variants. Histograms of cell count applied against fluorescence intensity of healthy HEK293 cells (left) with untransfected cells as negative control, pDAS12124 pre-edited as internal positive control and PE6c, PE2 and PE2_Co-Mini 72 h after transfection. The portion of fluorescent cells is normalized to the internal positive control (right)." num={15} bg="white" pic1="https://static.igem.wiki/teams/5247/photos/facs-results-mechanism/pe2-pe-co-pe6c.png" diff --git a/src/data/hptimelinedata.tsx b/src/data/hptimelinedata.tsx index 140d425d9a2f26b0de426f56bbfa1f6a6bbac47d..2f366bfd40c5d6482cf3dcd5777a5fe4d275d812 100644 --- a/src/data/hptimelinedata.tsx +++ b/src/data/hptimelinedata.tsx @@ -414,6 +414,8 @@ export const timelinedata: Array<TimelineDatenpunkt> = [ interviewtabid: "weber", cardtext: "", language: "en", + quoteNachname:"Weber", + quoteVorname: "Prof. Dr. Wolf-Michael", quote: "This is also an innovative step that you have developed yourselves. That's the part that's really new and significant. A clever and exciting approach with great potential.", aimofcontact: [<p>The aim of the interview was to gain expert insights on optimizing the delivery of CFTR-mRNA via lung-targeted lipid nanoparticles (LNPs) for Cystic Fibrosis (CF) treatment. Specifically, the goal was to explore potential cell targets, challenges in delivery mechanisms, and technical tools for assessing the effectiveness of mRNA therapies like the Ussing chamber system. </p>], @@ -1239,8 +1241,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [ <QaBox q="Is it advisable to modify the lipid components in an existing LNP formulation?" a="It is generally advisable to consider alternative lipid components, as different lipids may offer improved stability or efficacy. However, the specific needs of the project will dictate whether changes are necessary."/> <QaBox q="Is it possible to incorporate antibodies into LNPs, and what is the recommended approach?" a="Yes. Incorporation of antibodies into LNPs is possible. This can be achieved either during the initial preparation phase or by incubating antibodies with LNPs after their formation, depending on whether surface or internal localization of antibodies is desired. Reference to specific studies may provide further guidance."/> <QaBox q="What is Corden Pharma's position on projects involving gene therapy?" a="Corden Pharma operates as a service provider, focusing on the manufacturing of active pharmaceutical ingredients (APIs) and excipients rather than developing therapeutic products. Consideration should be given to the intellectual property status of the lipids used in LNP formulations, particularly for commercial applications."/> - <QaBox q="Is it possible to obtain a discount on LNP starter kits or establish a collaborative relationship with Corden Pharma?" a="We would need to discuss this internally but generally we would be open to potential collaborations that could involve recognition in publications or other forms of acknowledgment, pending approval from relevant management."/> - </>, + </>, summary: "The primary goal of the communication with Steffen Bira and Serra Gürcan from Corden Pharma was to explore the use of Lipid Nanoparticles (LNPs) in gene therapy and inhalation treatments. Corden Pharma recommended consulting specialists for assessing spray drying feasibility, while highlighting the importance of testing LNP stability under various conditions. Their LNP starter kits are optimized for stability and encapsulation efficiency, with potential for lipid modifications to enhance cellular uptake. They also confirmed that antibodies can be incorporated into LNPs and emphasized considering intellectual property when selecting lipids. Based on Corden Pharma’s insights, we switched to their kit #2 for our project, hoping to improve the stability and efficiency of our LNP formulations. Their guidance also opened opportunities for targeted therapies and collaborations. This feedback will continue to enhance our testing and therapeutic approaches.", months: "july", pictureurl_interview:"https://static.igem.wiki/teams/5247/photos/hp/hp-corden-zoom.png" @@ -1339,6 +1340,8 @@ export const timelinedata: Array<TimelineDatenpunkt> = [ tag: "Other", heading: "Cooperation to create a Lipid Delivery System Handbook", interviewtabid: "handbook", + job: "iGEM Team", + affiliation: "Linköping", cardtext: "", quoteVorname: "Kaya", quoteNachname: "Lange",