Final Proposal - Team 10
Final Proposal - Team 10
Final Proposal - Team 10
1
Proposal Keywords:
1. Cystic Fibrosis
2. CRISPR/cas9
3. Gene editing
4. CFTR gene
5. Homology-directed gene repair
Summary:
Individuals with Cystic Fibrosis (CF) face significant health challenges, and shortened life
spans due to respiratory and digestive complications1. Our study is needed because it
addresses a critical medical need by offering a potential cure for this devastating disease. This
genetic recessive disorder is most commonly caused by a deletion of the F508 amino acid on
the CFTR gene which produces a full-length but misfolded gene that gets degraded in the
endoplasmic reticulum. Despite advancements in gene therapy, there are still challenges in
delivering therapeutic genes to the target epithelial lung cells efficiently and safely2. Our project
aims to use a CRISPR/cas9 system for the targeted insertion of a full-length CFTR cDNA into
the CFTR locus to replace the endogenous CFTR through directed homologous gene repair. To
do this, we will first obtain CRISPR/cas9 DNA, CFTR template strand, GFP, and sgRNA
biobricks. Then, we will insert the CFTR template strand and GFP into a biobrick plasmid that
has chloramphenicol resistance and the sgRNA and cas9 into a separate biobrick plasmid also
treated with antibiotic resistance. Then, Sanger Sequencing will verify if the genes were
successfully implemented into the plasmids. The plasmids will then be transfected into epithelial
cells, grown on a chloramphenicol-treated plate, detected for fluorescence, and lysed to extract
the DNA. If fluorescence is detected, the cells will glow when exposed to UV light. Then, we will
perform PCR genotyping on our plasmids to confirm the knockin gene is present. We will finally
run gel electrophoresis and see if there is a strong band presence where our gene should be.
Following this, we will use the modified solvent evaporation method to get both plasmids into the
lipid nanoparticles (LNPs) to then suspend in solution, freeze dry, and lyophilize3. We will end by
taking our lyophilized solution, which now has fragile or easily breakable LNPs, suspend them in
2
an aerosol solution, and deliver them through a pulmonary inhaler. The CRISPR/cas9 plasmid
and the CFTR plasmid in solution will travel through the pulmonary system to be delivered to
epithelial cells, specifically the HSAEC1-KT cells from the hTERT-immortalized cell line before
moving to living organisms. Our initial studies will include mice until we can validate the
treatment's safety and efficacy for humans. Our project will have significant benefits for patients
suffering from CF if our design works as planned. Successful completion of our study will
treating genetic diseases like CF. This approach could pave the way for developing similar
gene-editing therapies for other genetic disorders, thus advancing the field of genetic medicine.
Each patient's genetic mutation can be specifically targeted and corrected, allowing for tailored
therapeutic interventions that address the underlying cause of the disease, therefore bettering
the medical solution for CF. If successful, rather than relying solely on symptomatic
management, patients could experience long-term relief from respiratory and digestive
3
Figure 1. Graphical Abstract The general process of our proposed plan and a depiction of how
Proposal Background:
The debilitating autosomal recessive genetic disease known as Cystic Fibrosis (CF) is
most distinguished by its severe effects on the respiratory system. It causes thick, sticky mucus
to accumulate in the airways, which worsens lung damage over time and results in recurring
infections and chronic inflammation. The CFTR gene, which codes for a protein essential for
controlling chlorine ion transport across cell membranes in many tissues, including the lungs, is
cystic fibrosis transmembrane conductance regulator (CFTR) genes in individuals with CF. The
protein cannot assist in transferring chloride- the primary component in salt- to the cell surface
when it is malfunctioning. Without chloride, which draws water to the cell surface, mucus in
different organs gets thick and sticky. Over two thousand gene variants related to the conditions
4
have been found, with the F509del mutation being the most common4. The mucus clogs the
airways in the lungs and holds onto bacteria and other germs, which can cause infections,
inflammation, respiratory failure, and other problems. Because of this, staying away from
A 2022 analysis estimates that 162,428 people with CF reside in 94 countries5. The
illness, which is more common among Caucasian people, affects approximately 30,000 people
in the United States5. Although non-Hispanic white people are disproportionately affected by CF,
the condition is becoming more common among racial and ethnic minorities. Minority groups
with CF frequently have worse health outcomes than non-Hispanic whites, including lower lung
function and more excellent mortality rates, despite having equal socioeconomic status6. These
(AAV2), to deliver CFTR cDNA to the human lungs and nasal cavities in the early 2000s
revealed no clinically meaningful effect regarding lung function restoration7. However, the trials
were safe. Challenges included low transduction effectiveness in airway epithelial cells and
difficulties and prevented AAV-based treatments from being administered again because of
preexisting or developed immunity. Although AAV-based gene treatments showed promise for
treating CF, their success depends on overcoming immunogenicity and temporary expression
concerns.
Precision medicine could also be possible if gene editing technologies could correct
CFTR gene mutations and return them to normal functions. Early research on human intestinal
stem cell organoids and induced pluripotent stem cells produced from CF patients has shown
that CFTR function can be successfully restored. Recent developments included using an
5
AAV-delivered CRISPR/cas9 platform to fix CFTR mutations in patient-derived airway basal
cells, resulting in nearly normal levels of CFTR activity7. However, despite these developments,
difficulties still exist because gene editing techniques are specialized to particular mutations,
necessitating customized repair for each mutation. However, these studies did show that
CRISPR can successfully repair a variety of CFTR abnormalities like slicing mutations and
premature termination codons, and it also holds promise for the advancement of cell-based
In recent years, there have been notable developments in CFTR-modifying therapy. With
the advent of ivacaftor, lumacaftor, and tezacaftor, approximately 50% more CF patients are
now eligible for CFTR-modifying medication ⁸. Regardless of their second mutation, CF patients
12 and older with at least one F508del mutation have hope. To improve CFTR protein function,
ivacaftor, a potentiator is combined with tezacaftor and elexacaftor, both correctors. However, a
major obstacle to access is its cost of approximately $24,000 each month8. One of our top
priorities is to create a more affordable and inclusive treatment for patients with cystic fibrosis.
Although current medications have improved the management of CF, certain patients
may not benefit from them due to specific mutation classes that are not impacted by current
these restrictions and help CF patients return to normalcy, researchers need to look into
Even though CF is currently incurable and has a substantial negative influence on life
expectancy, improvements in therapy have caused the average survival age to rise dramatically
to more than 40 years old9. As a result, CF is now acknowledged to impact both children and
adults and is no longer only thought to be a childhood illness. Since active therapy has been
demonstrated to improve quality of life, prolong life span, and improve prognosis, over half of
CF patients are now adults. In order to maximize the quality of life and long-term survival for CF
6
CF is a severely life-hindering condition with persistent differences in treatment
potential for better treatment outcomes and precision medicine methodologies. However,
guaranteeing fair access to care for all CF patients will require addressing problems like
excessive treatment costs and healthcare inequalities. For the field to advance and for the lives
of those who live with cystic fibrosis to improve, more research and innovation are essential.
We are proposing to create a gene therapy for patients living with Cystic Fibrosis, a
recessive genetic disorder that damages a person's lungs, pancreas, and other organs. Our
proposed project aims to use a CRISPR/Cas9 system for targeted insertion of a full-length
CFTR cDNA into the CFTR locus to replace the endogenous CFTR. This will be done through
directed homologous gene repair. The faulty CFTR gene is caused by deleting the F508 amino
acid on the gene that produces a full-length but misfolded CFTR gene degrading in the
endoplasmic reticulum. Our study is important because there are close to 40,000 children and
adults living with CF in the United States, and CF can affect people of every racial and ethnic
group¹⁰, so we need to find a solution for these people. Our study is also needed because it
addresses a critical medical need by offering a potential cure for this devastating disease.
Despite advancements in gene therapy, there are still challenges in delivering therapeutic genes
to the target cells efficiently and safely⁸. Our study is also needed because it addresses a critical
barrier to progress in gene therapy for CF and other genetic disorders. This project addresses a
significant problem in the field of CF treatment and offers a potential solution that could
revolutionize how this disease is managed and treated. Our project will be extremely impactful if
it works as expected. Successful completion of our study will significantly advance our
understanding of CRISPR/Cas9 technology and its application in treating genetic diseases like
7
CF. Also, If successful, this approach could pave the way for developing similar gene-editing
therapies for other genetic disorders, thus advancing the field of genetic medicine. Each
patient's genetic mutation can be specifically targeted and corrected, allowing for tailored
therapeutic interventions that address the underlying cause of the disease, therefore bettering
the medical solution for CF. If this project works, rather than relying solely on symptomatic
management, patients could experience long-term relief from respiratory and digestive
Proposal Approach:
Our project aims to utilize CRISPR/Cas9 technology for targeted gene editing to address
cystic fibrosis (CF). We plan to insert a corrected CFTR gene into affected cells, replacing the
8
faulty gene responsible for the disease. Initially, we will design and construct the necessary
genetic components, including the CRISPR/Cas9 system and the corrected CFTR gene. After
using Gibson Assembly and verifying their successful plasmid implementation, we will introduce
these constructs into target cells and confirm their uptake and expression. Following validation,
we will encapsulate these genetic constructs into nanoparticles for delivery. These
nanoparticles, designed to be easily administered via aerosol inhalation, will carry the corrective
Our proposed project aims to use a CRISPR/cas9 system for targeted insertion of a
full-length CFTR cDNA into the CFTR locus to replace the endogenous CFTR. This will be done
through directed homologous gene repair. This targeted gene repair approach addresses a
deletion mutation of the F508 amino acid, producing a misfolded CFTR protein prone to
degradation in the endoplasmic reticulum. CRISPR/Cas9 DNA, CFTR template strand, GFP,
and sgRNA biobricks will be obtained initially. The CFTR template strand and GFP will be
inserted into a biobrick plasmid with chloramphenicol resistance. In contrast, the CRISPR/Cas9
will be inserted into a separate plasmid with the same resistance marker. One biological part we
will be using from the registry of standard biological parts is BBa_K1218011, which is the cas9
enzyme needed to cleave the mutated gene. Another biological part that will be used from the
registry of standard biological parts is BBa_k2061002, which is the gRNA needed to bring the
enzyme and corrected gene to the point of mutation in the CFTR gene.
To make all the parts needed for our project work as a system after including them on
the plasmids mentioned above, we will perform the following steps to ensure successful
implementation. Sanger Sequencing will confirm successful gene implementation. The plasmids
will then be transfected into epithelial cells, grown on a chloramphenicol-treated plate, detected
for fluorescence, and lysed to extract DNA. If fluorescence is detected, the cells will glow when
exposed to UV light. Then, we will perform PCR genotyping on plasmids to confirm the knockin
gene is present. We will finally run gel electrophoresis and see if there is a strong band where
9
our gene should appear. Subsequently, both plasmids will be incorporated into nanoparticles
using the modified solvent evaporation method. We will then suspend them in a solution that
freezes them dry and lyophilized them. Then we will take the brittle matrix, the now fragile or
easily breakable nanoparticles, and suspend them in aerosol solution and deliver it through a
pulmonary inhaler. The nanoparticles' CRISPR/Cas9 and CFTR plasmids will target lung
epithelial cells, offering a potential therapeutic strategy. Mouse models will be utilized for in vivo
testing.
Figure 2 Precise Design. This figure shows the creation of our CRISPR/cas9 plasmid made of
sgRNA, cas9, CFTR Gene, and Chloramphenicol Antibiotic Resistance. The plasmid will then
be injected into nanoparticles which will give us our PEGylated CRISPR/cas9 lipid nanoparticles
(LNPs).
10
Figure 3 Flowchart depicting our proposed approach in step-by-step detail.
Some expected outcomes are that we should see a strong band on the gel representing
our gene of interest for the PCR genotyping. The band size should be similar to that of the
control for a CFTR gene. Also, in cell culture, we would see the cells with our plasmid
fluorescence due to the expression of GFP. We should see that the CRISPR system works
inside cells and can cut out the mutated CFTR gene and replace it with a functioning copy. We
do this by looking at the protein expression from a western blot and DNA sequence from Sanger
11
Sequencing. For Sanger Sequencing, we would see the corrected sequence if it worked and for
the Western blot, we would see a larger band representing the full CFTR protein.
debugged correctly and works as designed. We will start by verifying that our recombinant
plasmids are successful through Sanger Sequencing. Our PCR genotyping and gel
electrophoresis experiment will confirm if our plasmid was transfected into the epithelial cells.
HPLC can be used to quantify the amount of plasmid encapsulated within each nanoparticle.
Finally, to ensure the CRISPR/cas9 system successfully cut and added the new gene, western
blot can confirm protein expression from the edited gene, and Sanger Sequencing can be used
to sequence the PCR products generated from the target region. If a new gene has been
successfully inserted, Sanger Sequencing will confirm its presence and sequence. We will also
have a negative control while optimizing our transfection conditions by removing the Cas
nuclease and only delivering the gRNA. This would mean the component that cuts DNA is not
Literature Examples:
12
Figure 4:
The figure depicts the validation of CRISPR/Cas9-mediated gene correction in primary cultured
intestinal stem cells derived from cystic fibrosis (CF) patients. Using forskolin-induced swelling
assays, the researchers confirmed the loss of CFTR function in CF patient-derived organoids.
Subsequently, CRISPR/Cas9 was employed to correct the CFTR mutation, resulting in restored
CFTR function, as evidenced by significant expansion of organoid surface area upon forskolin
treatment. This restoration of CFTR function was further validated through sensitivity to CFTR
inhibition, confirming the functional rescue of the CFTR phenotype in the corrected organoids. In
13
this figure, F508del represents uncorrected control organoids, and SI_c1 and SI_c2 represent
clones derived from SI organoids corrected by cleavage with sgRNA1 and sgRNA2,
respectively. As seen in Figures A, C, and D10, the F508del patient organoids did not expand
their surface area, while the SI_c1 and SI_c2 without the CFTR inhibitor showed an increase in
the surface area. This means that the corrected CFTR genes in SI_c1 and SI_c2 worked
because of the increased surface area shown. You can also see that in Figures 2E and 2F,
where the error bars show a significant difference in surface area for both SI_c1 and SI_c2
when they have the CFTR inhibitor versus when they do not. This shows that without the CFTR
inhibitor, the surface area is significantly larger from the swelling. In Figures E and F for the
F508del, there is no significant difference between with and without the inhibitor of the CFTR
gene because there was no correction as this was the control group10.
The results of our study will be compared to Figure 4, which shows whether or not the
CFTR gene was corrected efficiently. Our study will use CRISPR/cas9 to cut out the faulty
CFTR gene and replace it with a correct copy of the CFTR gene. The study will also determine if
the CFTR gene was correctly replaced through experimentation. The difference will be that our
study will confirm if our CRISPR system worked by looking at the protein expression from a
14
Figure 5. Shows the size, PDI and zeta potential of dry powder formulations. A-C shows the size
and PDI of TFFD formulations and D-F shows the zeta potential of TFFD formulations
A second piece of literature we consulted was an article that looked into the best ways to
deliver gene editing modalities pulmonarily³. This study looked at gene editing dry powder
pulmonary system would allow for enhanced regional targeting and avoidance of biological
barriers that limit the efficiency of systemically (blood) administered therapeutics. Overall, this
study concluded that PEGylated chitosan/CRISPR-Cas9 nano complexes in dry powder are
suitable for inhalation and were best deployed using 3% of mannitol as the cryoprotectant
through TFFD. This DPI and TFFD process could be the delivery mechanism we employ to get
our CRISPR device into the patient’s lungs. Before even getting to the patient, we can even test
our method in a mouse model to study the safety and efficacy. While a mouse model would not
15
be the exact match for how our pulmonary system works, it would give us a good early
One technical limitation is the efficiency of nanoparticle delivery and endosomal escape.
Epithelial cells have barriers like the cell membrane that nanoparticles need to penetrate to
deliver the plasmid. Once inside the cells, the nanoparticle may get sequestered within
endosomes, limiting the release of the CRISPR/Cas9 into the cytoplasm, where it needs to act.
To overcome this, biocompatible materials like lipids can be used for our nanoparticle
fabrication, and incorporating components that promote endosomal escape, like pH-responsive
polymers or membrane-disruptive peptides into our nanoparticle formulation can facilitate the
release of CRISPR/cas9.
modified cells. We can mitigate contamination when working with these plasmids by wearing the
appropriate PPE, including lab coats, gloves, and safety glasses, and in biosafety cabinets. We
will also ensure all waste products are autoclaved with any biological substance or
contamination. We will also ensure that any human cell lines we are working with have been
screened & cleared to be free of pathogenic viruses & bacteria. Another biosafety issue is
ensuring the CRISPR/cas9 system does not mutate the wrong gene. We ensure this won’t
happen by doing a triple check to ensure the correct gene is placed into the DNA. This is seen
in our project, which used Sanger Sequencing, PCR, and gel electrophoresis.
Proposed budget/cost:
16
HSAEC1-KT cells Model delivery of ATCC $6,000
organism trials.
/product/K210014?IC
ID=cvc-pdna-midipre
p-c1b3
cells
https://www.ncbi.nlm.
nih.gov/pmc/articles/
PMC3776838/
er.com/products-servi
ces/service/adenoviru
s-packaging.html
17
LNPs For encapsulation of VectorBuilder n/a (quote needed)
er.com/products-servi
ces/service/mRNA-so
lutions.html
Antibiotic Resistance
Western plot
experiments
Proposed Timeline:
18
Human Practices:
One stakeholder for our proposed project is patients and patient advocacy groups. From
their perspective, the proposed use of CRISPR/Cas9 for targeted gene editing offers hope for a
potential cure or significant improvement in managing CF. They may be eager for
advancements in genetic therapies that could alleviate symptoms, improve quality of life, and
extend the lifespan of individuals affected by CF. However, they may also have concerns about
the safety, accessibility, and ethical implications of such treatments and issues related to
affordability and equitable access to emerging therapies. Another stakeholder for our proposed
project could be regulatory authorities and policymakers at the national and international levels.
From their perspective, using CRISPR/Cas9 technology for gene editing raises important
regulatory and ethical considerations. They are responsible for evaluating the safety and
efficacy of new therapies and establishing guidelines and regulations to govern their
development, approval, and implementation. They must balance the potential benefits of
innovative genetic treatments with the need to ensure patient safety, ethical standards, and
19
societal acceptance. They may also need to consider issues related to intellectual property
rights, healthcare infrastructure, and public funding for research and development in this field.
Cystic fibrosis (CF) is a genetic disorder that affects multiple organ systems, primarily
the lungs and digestive system, and is caused by mutations in the CFTR gene. Over the years,
significant progress has been made in understanding the molecular basis of CF and developing
treatments to manage its symptoms. However, there remains a critical need for more effective
therapies that address the underlying genetic cause of the disease. Recent advances in
genome editing technologies, particularly CRISPR/Cas9, have opened up new possibilities for
treating genetic disorders like CF. Researchers and organizations in the social sciences and
public health have been actively exploring the societal implications of these emerging genetic
therapies.
CRISPR/Cas9 for human gene editing. Questions arise regarding the potential for unintended
off-target effects, the long-term safety of genetic modifications, and the implications of germline
editing for future generations13. Another societal concern is the accessibility and affordability of
CRISPR-based therapies13. As with many innovative medical treatments, there are challenges
related to equitable access to these therapies, particularly for marginalized and underserved
populations. Issues such as healthcare disparities, insurance coverage, and the high cost of
genetic therapies must be addressed to ensure that all individuals affected by CF have access
Furthermore, public perception and attitudes toward genetic engineering and gene
editing significantly shape the regulatory landscape and public policy surrounding these
technologies. Public engagement efforts, education initiatives, and stakeholder dialogues are
essential for fostering informed decision-making and building trust in the ethical and responsible
20
While CRISPR/Cas9 holds great promise for treating genetic disorders like CF, it is
crucial to consider the broader societal implications and engage stakeholders such as patients
and authorities in discussions about the ethical, legal, social, and policy aspects of this rapidly
evolving field. Collaborative efforts between researchers, policymakers, advocacy groups, and
the public are essential for navigating the complex challenges and opportunities presented by
21
References:
1.McBennett KA, Davis PB, Konstan MW. Increasing life expectancy in cystic fibrosis: Advances
and challenges. Pediatr Pulmonol. 2022;57 Suppl 1(Suppl 1):S5-S12. doi:10.1002/ppul.25733
2. Gonçalves GAR, Paiva RMA. Gene therapy: advances, challenges and perspectives. Einstein
(Sao Paulo). 2017;15(3):369-375. doi:10.1590/S1679-45082017RB4024
5. Gill K, Fletch J. How Common Is Cystic fibrosis? Statistics and Risk Factors.
www.medicalnewstoday.com. Published September 20, 2023.
https://www.medicalnewstoday.com/articles/how-common-is-cystic-fibrosis#Learn-more
6. McBennett KA, Davis PB, Konstan MW. Increasing Life Expectancy in Cystic fibrosis: Advances
and Challenges. Pediatric Pulmonology. 2021;57(S1). doi:https://doi.org/10.1002/ppul.25733
7. Allan KM, Farrow N, Donnelley M, Jaffe A, Waters SA. Treatment of Cystic Fibrosis: From
Gene- to Cell-Based Therapies. Frontiers in Pharmacology. 2021;12(12).
doi:https://doi.org/10.3389/fphar.2021.639475
9. Chen Q, Shen Y, Zheng J. A Review of Cystic Fibrosis: Basic and Clinical Aspects. Animal
Models and Experimental Medicine. 2021;4(3):220-232.
doi:https://doi.org/10.1002/ame2.12180
22
12.Human genome editing.; 2017. doi:10.17226/24623
14. Shinwari ZK, Tanveer F, Khalil AT. Ethical Issues Regarding CRISPR Mediated Genome
Editing. Curr Issues Mol Biol. 2018;26:103-110. doi:10.21775/cimb.026.103
23