Periodic Reporting for period 1 - ChRONAM-H (Chromatin Regulation Of Normal And Malignant Haematopoiesis)
Periodo di rendicontazione: 2020-10-01 al 2022-09-30
In this project, I have proposed to study how a family of proteins, called Chromatin Factors (CFs), regulate the developmental process that shapes the immune and blood systems called hematopoiesis and how these proteins behave in the abnormal hematopoietic process of leukemia.
Chromatin Factors and Transcription factors jointly regulate how the genomic information is decoded and expressed to shape cellular identities. However, even though Transcription Factors (TFs) have been extensively studied across different tissues and biological processes, Chromatin Factor's roles are much less known. This is, in part, related to a complex regulation of Chromatin Regulators via multi-valent interactions with different epigenetic layers.
Disruption of CF normal activity is connected to multiple diseases like cancerd, immunodeficiencies and neurological syndromes. In fact, Chromatin Factors are the most frequently mutated family of proteins in various cancers. In addition, Chromatin Factors are excellent targets for drug discovery, and a big proportion of the current anti-leukemic drugs in the market modulate the activity of Chromatin Factors. Thus, a comparative study of Chromatin Factors in healthy hematopoiesis and leukemia will pave the way for the development of novel anti-leukemic therapies, reflecting the strong societal impact of the project.
The present project is organized into three aims:
1) Use of Functional Genomics approaches to determine which CFs possess lineage-determining potential in hematopoiesis.
2) Application of different genomic profiling technologies to study how CFs access the genome to regulate cellular identities. Here, I have performed a comparative analysis between normal hematopoiesis and leukemia to detect corrupted mechanisms that are specific to leukemia and that can be therapeutically exploited.
3) Utilization of Single-cell technologies to study Chromatin Factor roles in vivo in both normal and leukaemic hematopoiesis. The goal of this approach is to measure with higher precision the cellular identities controlled by the CFs (identified in aim 1) in both normal and leukemic scenarios. This approach produces more precise information about the regulatory mechanisms orchestrated by CFs and connects the information from aims 1 and 2 to produce a general and comparative model describing CF roles in normal and leukaemic hematopoiesis. This is key to finding therapeutic avenues to cure leukemic diseases.
Chromatin Factors and Transcription factors jointly regulate how the genomic information is decoded and expressed to shape cellular identities. However, even though Transcription Factors (TFs) have been extensively studied across different tissues and biological processes, Chromatin Factor's roles are much less known. This is, in part, related to a complex regulation of Chromatin Regulators via multi-valent interactions with different epigenetic layers.
Disruption of CF normal activity is connected to multiple diseases like cancerd, immunodeficiencies and neurological syndromes. In fact, Chromatin Factors are the most frequently mutated family of proteins in various cancers. In addition, Chromatin Factors are excellent targets for drug discovery, and a big proportion of the current anti-leukemic drugs in the market modulate the activity of Chromatin Factors. Thus, a comparative study of Chromatin Factors in healthy hematopoiesis and leukemia will pave the way for the development of novel anti-leukemic therapies, reflecting the strong societal impact of the project.
The present project is organized into three aims:
1) Use of Functional Genomics approaches to determine which CFs possess lineage-determining potential in hematopoiesis.
2) Application of different genomic profiling technologies to study how CFs access the genome to regulate cellular identities. Here, I have performed a comparative analysis between normal hematopoiesis and leukemia to detect corrupted mechanisms that are specific to leukemia and that can be therapeutically exploited.
3) Utilization of Single-cell technologies to study Chromatin Factor roles in vivo in both normal and leukaemic hematopoiesis. The goal of this approach is to measure with higher precision the cellular identities controlled by the CFs (identified in aim 1) in both normal and leukemic scenarios. This approach produces more precise information about the regulatory mechanisms orchestrated by CFs and connects the information from aims 1 and 2 to produce a general and comparative model describing CF roles in normal and leukaemic hematopoiesis. This is key to finding therapeutic avenues to cure leukemic diseases.
My project Chromatin Regulation Of Normal And Malignant Haematopoiesis (ChRONAM-H) proposed a multidisciplinary framework to explore the functions of Chromatin Factors (CFs) during hematopoietic lineage commitment and malignant transformation.
Here is a summary of the main results achieved during this project:
First I have developed a methodology to interrogate the lineage specifying roles of Chromatin Factors (CFs) in hematopoiesis. This methodology relies on differentiation systems where cells are pushed into specific lineages using precise growth conditions and CRISPR is used to disrupt specific CFs in a high-throughput manner. This permits a large-scale interrogation of the relevance of different factors in the development of specific hematopoietic lineages. Using this methodology I have characterized the roles of 680 Chromatin Factors during hematopoiesis identifying 200 CFs as key lineage regulators; this represents the first comprehensive study of Chromatin Factors in a developmental process.
Next, I have used state-of-the-art genome profiling methods to study how key Chromatin Factors regulate the different hematopoietic lineages (progenitors, erythroid and myeloid) and how they operate in an abnormal leukemic setup. This has enabled me to dissect gene regulatory programs controlled by these CFs and to highlight the interactions between Transcription and Chromatin Factors that are key for cellular identities. Of note, I have identified two interactions with an applied potential in leukemia (Brd9-Cebp and Smarcb1-Stat5a)
Then, using single-cell technologies I have characterized in depth the cellular and molecular mechanisms regulated by Chromatin Factors during hematopoiesis and identify differential behaviors in leukemia. Key findings are an unexpected functional diversity for Chromatin Factors with activation roles, a common behavior for repressive factors as attenuators of excessive inflammatory responses - which can be exploited to treat inflammation-related diseases like lupus. And, the identification of chromatin factors that permit unlimited growth of leukemic cells that represent potential targets for treatment via small-molecule inhibition, highlighting this approach as an excellent tool for drug discovery.
In summary, I have generated a roadmap CFs roles in hematopoiesis and leukemia highlighting therapeutic targets.
The findings described above have been presented at three international conferences in 2022. In addition, a research article presenting this work is currently under revision in Nature Genetics and has received a very favorable reception and I expect this article to be published during the first trimester of 2023, which will be made available to the general public by following the Gold Open Access route.
Finally, we have identified several avenues to exploit the results obtained in this project. First, we have established partnerships with researchers from the University of Navarre Clinic to validate the translational potential of our findings in human leukaemias. Second, we have established a partnership with Relation Therapeutics (London), a start-up company applying machine learning to discover novel therapeutic targets. In both initiatives, we have protected the Intellectual Property (IP) of the findings.
Here is a summary of the main results achieved during this project:
First I have developed a methodology to interrogate the lineage specifying roles of Chromatin Factors (CFs) in hematopoiesis. This methodology relies on differentiation systems where cells are pushed into specific lineages using precise growth conditions and CRISPR is used to disrupt specific CFs in a high-throughput manner. This permits a large-scale interrogation of the relevance of different factors in the development of specific hematopoietic lineages. Using this methodology I have characterized the roles of 680 Chromatin Factors during hematopoiesis identifying 200 CFs as key lineage regulators; this represents the first comprehensive study of Chromatin Factors in a developmental process.
Next, I have used state-of-the-art genome profiling methods to study how key Chromatin Factors regulate the different hematopoietic lineages (progenitors, erythroid and myeloid) and how they operate in an abnormal leukemic setup. This has enabled me to dissect gene regulatory programs controlled by these CFs and to highlight the interactions between Transcription and Chromatin Factors that are key for cellular identities. Of note, I have identified two interactions with an applied potential in leukemia (Brd9-Cebp and Smarcb1-Stat5a)
Then, using single-cell technologies I have characterized in depth the cellular and molecular mechanisms regulated by Chromatin Factors during hematopoiesis and identify differential behaviors in leukemia. Key findings are an unexpected functional diversity for Chromatin Factors with activation roles, a common behavior for repressive factors as attenuators of excessive inflammatory responses - which can be exploited to treat inflammation-related diseases like lupus. And, the identification of chromatin factors that permit unlimited growth of leukemic cells that represent potential targets for treatment via small-molecule inhibition, highlighting this approach as an excellent tool for drug discovery.
In summary, I have generated a roadmap CFs roles in hematopoiesis and leukemia highlighting therapeutic targets.
The findings described above have been presented at three international conferences in 2022. In addition, a research article presenting this work is currently under revision in Nature Genetics and has received a very favorable reception and I expect this article to be published during the first trimester of 2023, which will be made available to the general public by following the Gold Open Access route.
Finally, we have identified several avenues to exploit the results obtained in this project. First, we have established partnerships with researchers from the University of Navarre Clinic to validate the translational potential of our findings in human leukaemias. Second, we have established a partnership with Relation Therapeutics (London), a start-up company applying machine learning to discover novel therapeutic targets. In both initiatives, we have protected the Intellectual Property (IP) of the findings.
During the time assigned to this project I have reached the vast majority of the goals presented in the original proposal which has crystallized in an article (currently under revision in a top journal), dissemination activities, and partnerships with both academia and industry to exploit the results obtained in ChRONAM-H.
The publication of the project findings in a top journal (expected in early 2023) will have a profound impact on the scientific community. Our study shows how cutting-edge technologies can be applied to study diseases by comparing these to their normal counterparts (hematopoiesis vs leukemia in this case). I expect that this will result in adopting our strategy to study key diseases.
Second, this project shows that Chromatin Factors are key regulators of cellular identities and highlights the association between Chromatin Factors and Transcription Factors as a key aspect of ensuring healthy cellular behaviors. I expect this principle (TF-CF associations) will be applied to other processes and diseases, paving the way for novel and more specific therapeutic approaches that hold a strong societal impact. Specifically in this project, I have identified two TF-CF associations that can be modulated to treat leukemia and that we plan to exploit through partnerships with the academia and industry mentioned above.
Finally, these partnerships will ensure that this project will have continuity and produce a strong societal impact by developing novel methodologies for drug discovery and by exploiting the targets identified in the project to develop novel anti-leukemic treatments.
The publication of the project findings in a top journal (expected in early 2023) will have a profound impact on the scientific community. Our study shows how cutting-edge technologies can be applied to study diseases by comparing these to their normal counterparts (hematopoiesis vs leukemia in this case). I expect that this will result in adopting our strategy to study key diseases.
Second, this project shows that Chromatin Factors are key regulators of cellular identities and highlights the association between Chromatin Factors and Transcription Factors as a key aspect of ensuring healthy cellular behaviors. I expect this principle (TF-CF associations) will be applied to other processes and diseases, paving the way for novel and more specific therapeutic approaches that hold a strong societal impact. Specifically in this project, I have identified two TF-CF associations that can be modulated to treat leukemia and that we plan to exploit through partnerships with the academia and industry mentioned above.
Finally, these partnerships will ensure that this project will have continuity and produce a strong societal impact by developing novel methodologies for drug discovery and by exploiting the targets identified in the project to develop novel anti-leukemic treatments.