Site-specific integration of Lmx1a, FoxA2, & Otx2 to optimize dopaminergic differentiation

Dopaminergic (DA) neurons of the midbrain are the main source of dopamine in the mammalian central nervous system. Their loss is associated with a prominent human neurological disorder, Parkinson's disease (PD). There is no cure for PD, nor are there any good long-term therapeutics without deleterious side effects. Therefore, there is a great need for novel therapies to halt or reverse the disease. The objective of this study is to develop a new technology to obtain a purer, more abundant population of midbrain DA neurons in a culture dish. Such cells would be useful for disease modeling, drug screening, and development of cell therapies. Recent discoveries allow us to use adult human skin cells, introduce specific genes into them, and generate cells, termed induced pluripotent stem cells (iPSC), that exhibit the characteristics of embryonic stem cells. These iPSC, when derived from PD patient skin cells, can be used as an experimental model to study disease mechanisms that are unique to PD. When differentiated into DA neurons, and these cells are actually pathologically affected with PD. The current methods for directed DA neuronal differentiation from iPSC are inadequate in terms of efficiency and reproducibility. This situation hinders the ability to establish a robust model for PD-related neurodegeneration. In this study, we use a new, efficient gene integration technology to induce expression of midbrain-specific genes in iPSC lines derived from a patient with PD and a normal sibling. Forced expression of these midbrain transcription factor genes directs iPSC to differentiate into DA neurons in cell culture. A purer population of midbrain DA neurons may lay the foundation for successfully modeling PD and improving hit rates in drug screening approaches. The milestones for the first year of the project were to establish PD-specific iPSC lines that contain genomic “docking” sites, termed “attP” sites. In year 2, these iPSC/attP cell lines will be used to insert midbrain-specific transcription factors with high efficiency, mediated by enzymes called integrases. We previously established an improved, high-efficiency, site-specific DNA integration technology in mice. This technology combines the integrase system with newly identified, actively expressed locations in the genome and ensures efficient, uniform gene expression. The PD patient-specific iPSC lines we used were PI-1754, which contains a severe mutation in the SNCA (synuclein alpha) gene, and an unaffected sibling line, PI-1761. The SNCA mutation causes dramatic clinical symptoms of PD, with early-onset progressive disease. We use a homologous recombination-based procedure to place the “docking” site, attP, at well-expressed locations in the SNCA and control iPSC lines (Aim 1.1). We also included a human embryonic stem cell line, H9, to monitor our experimental procedures. The genomic locations we chose for placement of the attP sites included a site on chromosome 22 (Chr22) and a second, backup site on chromosome 19 (Chr19). These two sites were chosen based on mouse studies, in which mouse equivalents of both locations conferred strong gene expression. In order to perform recombination, we constructed targeting vectors, each containing an attP cassette flanked by 5’ and 3’ homologous fragments corresponding to the human genomic location we want to target. For the Chr22 locus, we were able to obtain all 3 targeting constructs for the PI-1754, PI-1761 and H9 cell lines. For technical reasons, we were not able to obtain constructs for the Chr19 location Thus, we decided to focus on the Chr22 locus and move to the next step. We introduced the targeting vectors into the cells and selected for positive clones by both drug selection and green fluorescent protein expression. For the H9 cells, we obtained 110 double positive clones and analyzed 98 of them. We found 8 clones that had targeted the attP site precisely to the Chr22 locus. For the PI-1761 sibling control line, we obtained 44 clones, and 1 of them had the attP site inserted at the Chr22 locus. The PI-1754 SNCA mutant line, on the other hand, grows slowly in cell culture. We are in the process of obtaining enough cells to perform the recombination experiment in that cell line. In summary, we demonstrated that the experimental strategy proposed in the grant indeed worked. We were successful in obtaining iPSC lines with a “docking” site placed in a pre-selected human genomic location. These cell lines are the necessary materials that set the stage for us to fulfill the milestones of year 2.

Parkinson's disease (PD) is caused by the loss of dopaminergic (DA) neurons in the midbrain. These DA neurons are the main source of dopamine, an important chemical in the central nervous system. PD is a common neurological disorder, affecting 1% of those at 60 years old and 4% of those over 80. Unfortunately, there is no cure for PD, nor are there any long-term therapeutics without harmful side effects. Therefore, there is a need for new therapies to halt or reverse the disease. The goal of this study is to develop a new technology that helps us obtain a purer, more abundant population of DA neurons in a culture dish and to characterize the resulting cells. These cells will be useful for studying the disease, screening potential drugs, and developing cell therapies. Due to recent discoveries, we can introduce specific genes into adult human skin cells and generate cells similar to embryonic stem cells, termed induced pluripotent stem cells (iPSC). These iPSC, when derived from PD patients, can be used as an experimental model to study disease mechanisms that are unique to PD, because when differentiated into DA neurons, these cells are actually pathologically affected with PD. We are using a PD iPSC line called PI-1754 derived from a patient with a severe mutation in the SNCA gene, which encodes alpha-synuclein. The SNCA mutation causes dramatic clinical symptoms of PD, with early-onset progressive disease. For comparison we are using a normal, unaffected sibling iPSC line PI-1761. We are also using a normal human embryonic stem cell (ESC) line H9 as the gold standard for differentiation. The current methods for differentiating iPSC into DA neurons are not adequate in terms of efficiency and reliability. Our hypothesis is that forced expression of certain midbrain-specific genes called transcription factors will direct iPSC to differentiate more effectively into DA neurons in cell culture. We use transcription factors called Lmx1a, Otx2, and FoxA2, abbreviated L, O, and F. In this project, we have developed a new, efficient gene integration technology that allows us rapidly to introduce and express these transcription factor genes in various combinations, in order to test whether they stimulate the differentiation of iPSC into DA neurons. In the first year of the project, we began establishing iPSC and ESC lines that contained a genomic “landing pad” site for insertion of the transcription factor genes. We carefully chose a location for placement of the genes based on previous work in mouse that suggested that a site on human chromosome 22 would provide strong and constant gene expression. We initially used ordinary homologous recombination to place the landing pad into this site. By the end of year 1 of the project, this method was successful in the normal iPSC and in the ESC, but not in the more difficult-to-grow PD iPSC. To solve this problem, in year 2 we introduced a new and more powerful recombination technology, called TALENs, and were successful in placing the landing pad in the correct position in all three of the lines, including the PD iPSC. We were now in a position to insert the midbrain-specific transcription factor genes with high efficiency. For this step, we developed a new genome engineering methodology called DICE, for dual integrase cassette exchange. In this technology, we use two site-specific integrase enzymes, called phiC31 and Bxb1, to catalyze precise placement of the transcription factor genes into the desired place in the genome. We constructed gene cassettes carrying all pair-wise combinations of the L, O, and F transcription factors, LO, LF, and OF, and the triple combination, LOF. We successfully demonstrated the power of this technology by rapidly generating a large set of iPSC and ESC that contained all the above combinations of transcription factors, as well as lines that contained no transcription factors, as negative controls for comparison. Two examples of each type of line for the 1754 and 1761 iPSC and the H9 ESC were chosen for differentiation and functional characterization studies. Initial results from these studies have demonstrated correct differentiation of neural stem cells and expression of the introduced transcription factor genes. In summary, we were successful in obtaining ESC and iPSC lines from normal and PD patient cells that carry a landing pad in a pre-selected genomic location chosen and validated for strong gene expression. These lines are valuable reagents. We then modified these lines to add DA-associated transcription factors in four combinations. All these lines are currently undergoing differentiation studies in accordance with the year two and three timelines. During year three of the project, the correlation between expression of various transcription factors and the level of DA differentiation will be established. Furthermore, functional studies with the PD versus normal lines will be carried out.

The objective of this project is to develop approaches and technologies that will improve neuronal differentiation of stem cells into midbrain dopaminergic (DA) neurons. DA neurons are of central importance in the project, because they are that cells that are impaired in patients with Parkinson’s disease (PD). Current differentiation methods typically produce low yields of DA neurons. The methods also give variable results, and cell populations contain many types of cells. These impediments have hampered the study of disease mechanisms for PD, as well as other uses for the cells, such as drug screening and cell replacement therapy. Our strategy is to develop a novel method to introduce genes into the genome at a specific place, so we can rapidly add genes that might help in the differentiation of DA neurons. The genes we would like to add are called transcription factors, which are proteins involved differentiation of stem cells into DA neurons. We have placed the genes for three transcription factors into a safe, active position on human chromosome 22 in the cell lines we are studying. These cells, called pluripotent stem cells, have the potential to differentiate into almost any type of cell. We are using embryonic stem cells in our study, as well as induced pluripotent stem cells (iPSC), which are similar, but are derived from adult cells, rather than an embryo. We are using iPSC derived from a PD patient, as well as iPSC from a normal person, for comparison. By forced expression of these neuronal transcription factors, we may achieve more efficient and reproducible generation of DA neurons. The effects of expressing different combinations of the three transcription factors called Lmx1a, FoxA2, and Otx2 on DA neuronal differentiation will be evaluated in the context of embryonic stem cells (ESC) as the gold standard, as well as in iPSC derived from a PD patient with a severe mutation in alpha-synuclein and iPSC derived from a normal control. Comparative functional assays of the resulting DA neurons will complete the analysis. To date, this project has created a novel technology for modifying the genome. The strategy developed out of the one that we originally proposed, but contains several innovations that make it more powerful and useful. The new methodology, called DICE for Dual Integrase Cassette Exchange, allowed us to generate “master” or recipient cell lines for ESC, normal iPSC, and PD iPSC. These recipient cell lines contain a “landing pad” placed into a newly-identified actively-expressed location on human chromosome 22 called H11 that permits robust expression of genes placed into it. We then generated a series of cell lines by "cassette exchange" at the H11 locus. In cassette exchange, the new genes we want to add take the place of the landing pad we originally put into the cells. Cassette exchange is a good way to introduce various genes into the same place in the chromosomes. We created cell lines expressing three neuronal transcription factors suspected to be involved in DA neuronal differentiation, in all pair-wise combinations, including lines with expression of all three factors, and negative control lines with no transcription factors added. This collection of modified human pluripotent stem cell lines is now being used to study neural differentiation. The modified ESC have undergone differentiation into DA neurons and are being evaluated for the effects of the different transcription factor combinations on DA neuronal differentiation. During the final year of the project, this differentiation analysis will be completed, and we will also analyze functional properties of the differentiated DA neurons, with special emphasis on disease-related features of the cells derived from PD iPSC.

The objective of this project is to develop technologies and approaches that will improve differentiation of stem cells into midbrain dopaminergic (DA) neurons. DA neurons are of central importance in the project, because they are the cells that are impaired in patients with Parkinson’s disease (PD). It appears that midbrain dopaminergic neurons have an enormous energy requirement, which might help explain their vulnerability to degeneration in PD. Current differentiation methods typically produce low yields of DA neurons. The methods also give variable results, and cell populations contain many types of cells. These impediments have hampered the study of disease mechanisms for PD, as well as other uses for the cells, such as drug screening and cell replacement therapy. Our strategy is to develop a novel method to introduce genes into the genome at a specific place, so we can rapidly add genes that might help in the differentiation of DA neurons. The genes we would like to add are called transcription factors, which are proteins involved in differentiation of stem cells into DA neurons. We have placed the genes for three transcription factors into a safe, active position on human chromosome 22 in the cell lines we are studying. These cells, called pluripotent stem cells, have the ability to differentiate into almost any type of cell. We are using embryonic stem cells in our study, as well as induced pluripotent stem cells (iPSC), which are similar, but are derived from adult cells, rather than an embryo. We are using iPSC derived from a PD patient, as well as iPSC from a normal person, for comparison. By forced expression of neuronal transcription factors, we may achieve more efficient and reproducible generation of DA neurons. We want to evaluate the effects of expressing different combinations of three transcription factors called Lmx1a, FoxA2, and Otx2 on DA neuronal differentiation in the context of embryonic stem cells (ESC) as the gold standard, as well as in iPSC derived from a PD patient with a severe mutation in alpha-synuclein, and in iPSC derived from a normal person without PD. Comparative functional assays of the resulting DA neurons will complete the analysis. To date, this project created a novel technology for modifying the genome. The strategy developed out of the one that we originally proposed, but contains several innovations that make it more powerful and useful. The new methodology, called DICE for Dual Integrase Cassette Exchange, allowed us to generate “master” or recipient cell lines for ESC, normal iPSC, and PD iPSC. These recipient cell lines contain a “landing pad” placed into a newly-identified actively-expressed location on human chromosome 22 called H11 that permits robust expression of genes placed into it. We then generated a series of cell lines by "cassette exchange" at the H11 locus. In cassette exchange, the new genes we want to add take the place of the landing pad we originally put into the cells. Cassette exchange is a good way to introduce various genes into the same place in the chromosomes. We created cell lines expressing three neuronal transcription factors suspected to be involved in DA neuronal differentiation, in all pair-wise combinations, including lines with expression of all three factors, and negative control lines with no transcription factors added. This collection of modified human pluripotent stem cell lines is being used to study neural differentiation. The modified ESC were used to form embryoid bodies, which are spherical aggregations of stem cells similar to an embryo that are favorable for producing differentiated cells. We found that the embyroid bodies underwent a rapid process of spontaneous differentiation into DA neurons. The differentiation was stimulated in the cells that expressed inserted transcription factors, and some combinations of transcription factors were better than others in bringing about DA neuronal differentiation. We obtained the best differentiation in the lines that expressed the LMX1A and OTX2 transcription factors. In continuing studies, we will analyze functional properties of the differentiated DA neurons, with special emphasis on disease-related features of the cells derived from PD iPSC.