Periodic Reporting for period 4 - EpiTune (Epigenetic fine-tuning of T cells for improved adoptive cell therapy)
Período documentado: 2023-07-01 hasta 2024-12-31
Adoptive T cell therapy is a promising approach in various clinical settings, from target-specific immune reconstitution fighting cancer and chronic infections to combating undesired immune reactivity during auto-immunity and after organ transplantation. While first promising therapies are now available in the oncological field, several limitations have still to be overcome in order to unfold the full potential of this precision medicine approach. Among them is 1) the acquisition of senescence of T cells during the required in vitro expansion phase which limits their survival and fitness after infusion into the patient, and 2) the functional plasticity of T cells, which is sensitive to the inflammatory environment they encounter after transfusion and which might result in a functional switch from the desired effect (e.g. immunosuppressive) to the opposite one (pro-inflammatory).
In this project, we want to tackle these obstacles from a new molecular angle, utilizing the profound impact of epigenetic mechanisms on the senescence process as well as on the functional imprinting of T lymphocytes. We propose to equip T lymphocytes with the required properties for their successful and safe therapeutic application, including their functional fine-tuning according to the clinical need by directed modifications of the epigenome ('Epi-tuning').
To reach these goals we want to: 1) clarify the epigenetic mechanisms in the acquisition of proliferation-induced cellular senescence to reveal strategies for their directed prevention and 2) identify epigenetic regions involved in stable functional imprinting of T cells in order to address them as molecular switches for the functional optimization of T cell products using state-of-the-art CRISPR/dCas9-mediated epigenetic editing approaches.
These innovative epigenetic "one-shot" manipulations during the in vitro expansion phase of T cell products should advance T cell therapy towards improved efficiency, stability as well as safety.
In this project, we want to tackle these obstacles from a new molecular angle, utilizing the profound impact of epigenetic mechanisms on the senescence process as well as on the functional imprinting of T lymphocytes. We propose to equip T lymphocytes with the required properties for their successful and safe therapeutic application, including their functional fine-tuning according to the clinical need by directed modifications of the epigenome ('Epi-tuning').
To reach these goals we want to: 1) clarify the epigenetic mechanisms in the acquisition of proliferation-induced cellular senescence to reveal strategies for their directed prevention and 2) identify epigenetic regions involved in stable functional imprinting of T cells in order to address them as molecular switches for the functional optimization of T cell products using state-of-the-art CRISPR/dCas9-mediated epigenetic editing approaches.
These innovative epigenetic "one-shot" manipulations during the in vitro expansion phase of T cell products should advance T cell therapy towards improved efficiency, stability as well as safety.
Regulatory T cells (Tregs) are a special type of immune cell with the remarkable ability to suppress excessive inflammation. This makes them promising candidates in adoptive cell therapies – ‘living drugs’ for treating autoimmune diseases, chronic inflammatory conditions, and transplant rejection. However, a major challenge in Treg-based therapies is ensuring these cells remain functional after being expanded in the lab to generate therapeutic products and transfer into patients. The EpiTune project set out to address this issue from a new molecular angle, by investigating how epigenetic mechanisms—chromatin switches that regulate gene activity—affect Treg function and stability.
Our research identified key epigenetic changes that occur during Treg product manufacturing, which can compromise their therapeutic effectiveness. One major discovery was that epigenetic stabilizer elements - regions of the genome essential for Treg identity—undergo modifications over time, reducing their function. We also found that heterochromatin, an inactivated part of the genome, loses important regulatory marks during cell expansion. This destabilization can lead to harmful gene activation and limit the long-term effectiveness of Treg therapies.
To counteract these effects, we developed a CRISPR-based epigenetic editing tool that allows us to precisely modify genetic regulatory elements and restore lost function. By refining our technique, we successfully reprogrammed pro-inflammatory T cells into functional, immunosuppressive Tregs - essentially generating Tregs ‘from scratch’. This breakthrough could significantly expand the number of patients who can benefit from Treg therapy, including those who lack a natural population of functional Tregs. Additionally, this technology holds promise for converting harmful autoreactive immune cells into regulatory cells, opening up new possibilities for personalized medicine.
In parallel, we also tackled the loss of epigenomic stability during cell manufacturing. We uncovered the molecular cause behind this phenomenon and developed a pharmacological intervention approach to preserve the epigenetic identity of Tregs during expansion. This method not only improved Treg functionality but has potential applications in other cell therapies, including cancer immunotherapies and regenerative medicine.
The impact of these findings is already being recognized: our host institution has initiated patent applications to secure intellectual property rights, ensuring these technologies can be translated into real-world treatments. With our discoveries, we are paving the way for more effective, stable, and accessible cell-based therapies - bringing us closer to harnessing the full potential of Tregs in medicine.
Our research identified key epigenetic changes that occur during Treg product manufacturing, which can compromise their therapeutic effectiveness. One major discovery was that epigenetic stabilizer elements - regions of the genome essential for Treg identity—undergo modifications over time, reducing their function. We also found that heterochromatin, an inactivated part of the genome, loses important regulatory marks during cell expansion. This destabilization can lead to harmful gene activation and limit the long-term effectiveness of Treg therapies.
To counteract these effects, we developed a CRISPR-based epigenetic editing tool that allows us to precisely modify genetic regulatory elements and restore lost function. By refining our technique, we successfully reprogrammed pro-inflammatory T cells into functional, immunosuppressive Tregs - essentially generating Tregs ‘from scratch’. This breakthrough could significantly expand the number of patients who can benefit from Treg therapy, including those who lack a natural population of functional Tregs. Additionally, this technology holds promise for converting harmful autoreactive immune cells into regulatory cells, opening up new possibilities for personalized medicine.
In parallel, we also tackled the loss of epigenomic stability during cell manufacturing. We uncovered the molecular cause behind this phenomenon and developed a pharmacological intervention approach to preserve the epigenetic identity of Tregs during expansion. This method not only improved Treg functionality but has potential applications in other cell therapies, including cancer immunotherapies and regenerative medicine.
The impact of these findings is already being recognized: our host institution has initiated patent applications to secure intellectual property rights, ensuring these technologies can be translated into real-world treatments. With our discoveries, we are paving the way for more effective, stable, and accessible cell-based therapies - bringing us closer to harnessing the full potential of Tregs in medicine.
One of the most significant advancements is the de novo generation of immunosuppressive Tregs without relying on patient-derived Treg populations, using our targeted epigenetic editing approach. With this, patients lacking a functional Treg populations could now benefit from adoptive Treg therapies. In addition, this novel technique allows antigen-specific immunosuppressive ‘living drugs’ to be created from a patient’s own pathogenic T cells, enabling personalized precision medicine for autoimmune diseases. This success can be further advanced towards the next breakthrough of making Tregs available “off-the-shelf”, based on generated Treg products from third party donors.
A second key advancement is the development of a CRISPR-Cas9-based epigenetic editing platform, enabling precise modification of epigenetic patterns in primary human T cells in a GMP-compatible and thus, clinically applicable manner. This represents a major step forward in cellular engineering, providing a versatile tool not only for adoptive Treg therapy but also for improving other cell products used in immunotherapy and regenerative medicine.
Additionally, the project identified a previously unknown interdependent mechanism regulating epigenomic integrity and cellular plasticity during cell proliferation. We discovered a tunable regulator that controls proliferation-associated epigenetic changes, shedding light on fundamental processes linked to aging and cellular senescence. By intervening in this mechanism, we developed a pharmacological approach to prevent proliferation-induced epigenetic changes, which otherwise leads to functional decline in expanded cell populations. This breakthrough not only enhances the quality of Treg therapy products but also opens new therapeutic avenues for promoting healthy aging and improving a variety of cell-based therapies.
In summary, this project has pushed the boundaries of adoptive cell therapy using a transdisciplinary approach of epigenomics and T cell immunology, offering groundbreaking insights into cellular ageing processes and innovative solutions for cell therapy approaches fighting autoimmune diseases, chronic inflammation and supporting regenerative medicine. These advances set the stage for next-generation personalized and off-the-shelf cell therapies with improved stability, efficacy, and accessibility.
A second key advancement is the development of a CRISPR-Cas9-based epigenetic editing platform, enabling precise modification of epigenetic patterns in primary human T cells in a GMP-compatible and thus, clinically applicable manner. This represents a major step forward in cellular engineering, providing a versatile tool not only for adoptive Treg therapy but also for improving other cell products used in immunotherapy and regenerative medicine.
Additionally, the project identified a previously unknown interdependent mechanism regulating epigenomic integrity and cellular plasticity during cell proliferation. We discovered a tunable regulator that controls proliferation-associated epigenetic changes, shedding light on fundamental processes linked to aging and cellular senescence. By intervening in this mechanism, we developed a pharmacological approach to prevent proliferation-induced epigenetic changes, which otherwise leads to functional decline in expanded cell populations. This breakthrough not only enhances the quality of Treg therapy products but also opens new therapeutic avenues for promoting healthy aging and improving a variety of cell-based therapies.
In summary, this project has pushed the boundaries of adoptive cell therapy using a transdisciplinary approach of epigenomics and T cell immunology, offering groundbreaking insights into cellular ageing processes and innovative solutions for cell therapy approaches fighting autoimmune diseases, chronic inflammation and supporting regenerative medicine. These advances set the stage for next-generation personalized and off-the-shelf cell therapies with improved stability, efficacy, and accessibility.