Periodic Reporting for period 1 - MM_BH3_CutTag (Parallel epigenomic and apoptotic profiling to identify targetable sensitivities in Multiple Myeloma)
Reporting period: 2022-09-01 to 2024-08-31
Multiple Myeloma (MM) is an incurable disease with an extremely poor 10-year survival rate (~30%) (Cancer research UK, Survival for Myeloma). In 2022 in the EU alone, 22,000 people died of MM (European Cancer Information System Data Explorer). Over the last decade there have been several advances in MM treatment, such as the development of immunomodulators and proteasome inhibitors which have improved overall survival rates. However, MM remains incurable, as continuous treatment leads to the emergence of drug-resistant clones, eventually causing relapse. High levels of inter- and intra-patient genetic heterogeneity contribute to the failure of broadly targeted therapies. Therefore, it is imperative to generate novel, alternative strategies to treat this intractable disease that is specifically targeted at individual patients.
BCL-2 is an anti-apoptotic protein that blocks cell death. Increased reliance on BCL-2 family proteins as well as altered epigenetic landscapes are mechanisms by which MM cells become resistant to drug treatment.
Growing evidence across the field of oncology supports epigenetic regulation promoting cancer progression and treatment resistance. In fact, non-mutational epigenetic dysregulation is now considered an emerging hallmark of cancer. Therefore, a burgeoning opportunity for circumventing therapeutic resistance is through epigenetic drugs, particularly as there has been huge developments in the range of small molecule compounds targeting epigenetic regulatory proteins.
The aims of this project are:
1) To establish a mechanism of epigenetic mapping (CUT&Tag), in combination with BH3 profiling (a technique to identify BCL-2 dependency profiles), that can be applied to primary MM patient samples in order to understand the basal epigenetic profile of BCL- 2 dependent MM.
2) Identify the basal landscape/distribution of inter- and intra-MM patient histone post-translational modifications (PTMs) using CUT&Tag
3) Assess sensitivity to epigenetic modifiers in patient MM samples, therefore identifying candidate drugs for future MM therapy.
The significance of this project is to improve existing MM therapy (BCL-2 inhibition) by combining this treatment with epigenetic inhibitors that regulate different BCL-2 dependency profiles.
BCL-2 is an anti-apoptotic protein that blocks cell death. Increased reliance on BCL-2 family proteins as well as altered epigenetic landscapes are mechanisms by which MM cells become resistant to drug treatment.
Growing evidence across the field of oncology supports epigenetic regulation promoting cancer progression and treatment resistance. In fact, non-mutational epigenetic dysregulation is now considered an emerging hallmark of cancer. Therefore, a burgeoning opportunity for circumventing therapeutic resistance is through epigenetic drugs, particularly as there has been huge developments in the range of small molecule compounds targeting epigenetic regulatory proteins.
The aims of this project are:
1) To establish a mechanism of epigenetic mapping (CUT&Tag), in combination with BH3 profiling (a technique to identify BCL-2 dependency profiles), that can be applied to primary MM patient samples in order to understand the basal epigenetic profile of BCL- 2 dependent MM.
2) Identify the basal landscape/distribution of inter- and intra-MM patient histone post-translational modifications (PTMs) using CUT&Tag
3) Assess sensitivity to epigenetic modifiers in patient MM samples, therefore identifying candidate drugs for future MM therapy.
The significance of this project is to improve existing MM therapy (BCL-2 inhibition) by combining this treatment with epigenetic inhibitors that regulate different BCL-2 dependency profiles.
1. We successfully implemented CUT&Tag in both MM cell lines and primary MM patient samples, in combination with full BH3 profiling. We have generated CUT&Tag-BH3 profiling data for 8 patient samples (WP1 and WP2 complete).
2. We have generated high-quality data from these patient samples, and are in the process of integrating the results from our CUT&Tag and BH3 profiles in these patients to identify key epigenetic profiles alongside key genotype data for these samples.
3. In addition to these aims, we were also able to obtain transcriptomic data from 2 of these patient samples (RNAseq), which we are also integrating with our results, to further understand the epigenomic and transcriptomic profiles for indiviudal BCL-2 dependencies.
2. We have generated high-quality data from these patient samples, and are in the process of integrating the results from our CUT&Tag and BH3 profiles in these patients to identify key epigenetic profiles alongside key genotype data for these samples.
3. In addition to these aims, we were also able to obtain transcriptomic data from 2 of these patient samples (RNAseq), which we are also integrating with our results, to further understand the epigenomic and transcriptomic profiles for indiviudal BCL-2 dependencies.
WP 1: Establish CUT&Tag with BH3 profiling to understand the basal epigenetic profile of BCL-2-dependent multiple myeloma (MM)
Progress Summary: This work package has been successfully completed. We have developed and optimised robust protocols for both CUT&Tag and BH3 profiling, tailored to the study of MM cell lines. BH3 profiling has been finalized across key MM cell lines, allowing us to assess mitochondrial apoptotic priming and BCL-2 dependency. CUT&Tag profiling is ongoing and has already yielded preliminary epigenetic data that complements the BH3 findings. These methods are now fully integrated into our laboratory workflows, setting the stage for broader profiling in future studies.
WP 2: Identify the basal distribution of histone post-translational modifications (PTMs) in MM patient samples using CUT&Tag
Progress Summary: We have completed CUT&Tag profiling for four critical histone modifications—H3K4me1, H3K4me3, H3K27ac, and H3K27me3—as well as IgG controls in seven patient-derived MM samples. These marks were selected for their relevance in chromatin accessibility, transcriptional activation, and repression. The analysis of these datasets is ongoing, with promising initial insights into both inter-patient and intra-tumoral heterogeneity. In parallel, I have trained an additional postdoctoral researcher in the CUT&Tag protocol to increase throughput and reproducibility. We are actively expanding our patient cohort to strengthen statistical power and clinical relevance.
WP3: Assess sensitivity of MM patient samples to epigenetic modifiers (WP3)
Progress Summary: We have made significant progress in identifying epigenetic drug vulnerabilities in MM. A key outcome of this work is a recent publication in Haematologica (Flanagan et al., 2024), where we demonstrated a strong synergistic effect between the DNA methyltransferase inhibitor 5-azacitidine and the BCL-2 inhibitor venetoclax. Building on this, we have observed compelling synergistic activity between the H3K27 demethylase inhibitor GSK-J4 and venetoclax across a panel of MM cell lines, regardless of their BCL-2 dependency status. This highlights a potentially broad therapeutic application. These studies are ongoing, with further in-depth mechanistic and functional assays underway.
Work Package 4: Project management
Throughout the duration of the project, I maintained regular and structured communication with my supervisor through weekly one-on-one meetings. In addition to these sessions, I presented ongoing research updates during bi-monthly laboratory meetings, as well as at departmental seminars held twice a year within the Department of Physiology and Medical Physics.
To ensure clinical relevance and foster interdisciplinary collaboration, I met with Prof. Siobhan Glavey (Haematology) on a biannual basis to discuss research progress and potential clinical implications. I also disseminated key findings by presenting at the RCSI Research Day, engaging with a broader institutional audience.
From a financial management perspective, I oversaw the procurement of consumables and equipment related to the project. All purchases were processed through the RCSI Agresso system and received prior approval from the Principal Investigator, in line with institutional and MSCA financial guidelines.
Work Package 5: Training and Knowledge Transfer.
Transfer of Knowledge
During the fellowship, I contributed significantly to the sustainability and dissemination of technical skills within the host institution. I provided hands-on training in CUT&Tag techniques to two PhD students and one postdoctoral researcher in the Ni Chonghaile laboratory. This training—delivered over a cumulative six days—has enabled ongoing CUT&Tag profiling of patient samples, supporting continuity of this research stream. I continue to collaborate closely with both the Ní Chonghaile and Mahony groups to guide analysis and interpretation of these datasets.
In parallel, I received specialised training in BH3 profiling and applied this expertise in a collaborative project, culminating in a manuscript entitled "Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer." Following positive peer review, the manuscript is currently under resubmission to Nature Metabolism.
Teaching Activities
I contributed to institutional teaching efforts by delivering a lecture to Graduate Entry Medicine students at RCSI. This lecture, part of the GEM REB2 course, focused on the topic of Glomerular Filtration, providing foundational renal physiology instruction to medical trainees.
Mentoring: I Mentored one summer undergraduate research student for two weeks (July 2022)
Grant Writing and Career Development
As part of my professional development, I wrote a successful application for the Science Foundation Ireland (SFI) Pathway Grant, which facilitated my transition to an independent research role. This achievement has enabled me to establish my own research group at University College Dublin (UCD), marking a significant milestone in my academic career trajectory. Which was likely greatly facilitated by the MSCA postdoctoral fellowship.
Work Package 6: Dissemination, exploitation and Communication
Conference Participation and Scientific Dissemination
During the fellowship, I actively disseminated my research findings to the scientific community through conference presentations and seminars:
• BCNI 2023 – Poster Presentation
• TSJCI Conference 2022 – Poster Presentation
• ERN 2022 – Poster Presentation
• University College Dublin (UCD) – Invited Oral Seminar (October 2, 2023)
• IACR/EACR Joint Conference 2024 – Poster Presentation (February 2024)
These engagements enabled meaningful scientific exchange and feedback, particularly within the cancer biology and epigenetics research communities.
Scientific Publication
I contributed as a co-author to a peer-reviewed publication in the open-access journal Haematologica:
Flanagan L, Coughlan A., Cosgrove N., Roe A., Wang Y., Gilmore S., Drozdz I., Comerford C., Ryan J., Minihane E., Parvin S., O’Dwyer M., Quinn J., Murphy P., Furney S., Glavey S., Ní Chonghaile T. “Steroid-free combination of 5-azacytidine and venetoclax for the treatment of multiple myeloma.” Haematologica, 109(9): 2930–2943, 2024. DOI: 10.3324/haematol.2023.283771
This study received substantial media coverage, being highlighted by 16 international and national news outlets, including:
• The Irish Independent
• Science Daily
• MSN
• The Medical Independent
• Pharmacy Times
• eCancer
This reflects the translational significance and broad interest in the research findings.
Public Communication and Online Engagement
I actively communicate my research to both scientific and public audiences through social media and digital platforms, including:
• X (formerly Twitter): @aisling1751
• LinkedIn: linkedin.com/in/aisling-coughlan-9a4b8465
• Lab Website: www.coughlan-lab.com
These platforms are used to share research updates, publications, job opportunities, and educational content, enhancing the visibility and accessibility of our work.
Secondment
Due to my early appointment as Group Leader at University College Dublin, I was unable to complete the planned secondment at Almac. While the secondment was a valuable component of the proposal, this career progression marked a significant outcome of the fellowship, facilitating continued academic leadership and research translation.
IMPACT
Scientific Impact
Significant scientific progress has been achieved in alignment with the project's objectives. I successfully established the CUT&Tag technique at RCSI, overcoming key technical challenges associated with profiling the epigenome in low-yield multiple myeloma (MM) patient samples. Importantly, I trained two additional researchers in this method, ensuring continuity and capacity-building within the host lab. This represents a lasting technical advancement for MM research at the institution. Our work contributed to the field’s understanding of epigenetic vulnerabilities in MM.
Notably, I co-authored a peer-reviewed, open-access publication in Haematologica:
Flanagan et al. “Steroid-free combination of 5-azacytidine and venetoclax for the treatment of multiple myeloma.” Haematologica, 109(9): 2930–2943, 2024. DOI: 10.3324/haematol.2023.283771
This publication highlights a promising therapeutic combination and received widespread attention across 16 media outlets, underlining its translational potential.
I am also a co-author on a second impactful manuscript currently under review at Nature Metabolism: Moss et al. “Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer.” Currently available on bioRxiv: 2024.09.12.611189
In parallel, I am began efforts to validate a novel epigenetic synergy between the H3K27 demethylase inhibitor GSK-J4 and venetoclax. Our integrative analysis (RNA-seq, BH3 profiling, CUT&Tag, and SCENITH) aims to elucidate how GSK-J4 may enhance BCL-2 dependency in MM. If successful, this line of investigation could offer a new therapeutic avenue for MM patients, with high potential for clinical and societal benefit.
Societal Impact:
The previously mentioned Haematologica study has generated significant public interest and dissemination beyond academic circles, with coverage in national and international media including The Irish Independent, MSN, Science Daily, and Pharmacy Times. This indicates the broader relevance of our findings and supports the translation of bench-side science to public awareness and potential clinical practice.
I also engaged in science outreach activities, including hosting students from St. Andrew’s School and mentoring transition year students in the lab. These interactions help stimulate interest in STEM fields among secondary-level students and contribute to long-term societal impact by fostering the next generation of researchers.
Environmental Sustainability
The Department of Physiology and Medical Physics at RCSI was awarded Platinum Certification under the My Green Lab program, reflecting a commitment to environmentally responsible laboratory practices. As part of this department, I contributed to and supported this sustainability ethos throughout the fellowship.
Supervision, Collaboration & Career Development
Regular supervision and strategic mentorship played a vital role in project delivery. I held weekly one-on-one meetings with my supervisor, Prof. Tríona Ní Chonghaile, and met biannually with clinical collaborator Prof. Siobhán Glavey to ensure alignment with translational goals. I also engaged with Dr. Simon Furney and Prof. Shaun Mahony for guidance on bioinformatics strategy.
These interactions directly contributed to my successful application for a Science Foundation Ireland (SFI) Pathway Grant, which supported my transition to an independent research position. I have since been appointed Ad Astra Fellow and Group Leader at University College Dublin, marking a key milestone in my scientific career and ensuring continued exploitation of project outputs.
Progress Summary: This work package has been successfully completed. We have developed and optimised robust protocols for both CUT&Tag and BH3 profiling, tailored to the study of MM cell lines. BH3 profiling has been finalized across key MM cell lines, allowing us to assess mitochondrial apoptotic priming and BCL-2 dependency. CUT&Tag profiling is ongoing and has already yielded preliminary epigenetic data that complements the BH3 findings. These methods are now fully integrated into our laboratory workflows, setting the stage for broader profiling in future studies.
WP 2: Identify the basal distribution of histone post-translational modifications (PTMs) in MM patient samples using CUT&Tag
Progress Summary: We have completed CUT&Tag profiling for four critical histone modifications—H3K4me1, H3K4me3, H3K27ac, and H3K27me3—as well as IgG controls in seven patient-derived MM samples. These marks were selected for their relevance in chromatin accessibility, transcriptional activation, and repression. The analysis of these datasets is ongoing, with promising initial insights into both inter-patient and intra-tumoral heterogeneity. In parallel, I have trained an additional postdoctoral researcher in the CUT&Tag protocol to increase throughput and reproducibility. We are actively expanding our patient cohort to strengthen statistical power and clinical relevance.
WP3: Assess sensitivity of MM patient samples to epigenetic modifiers (WP3)
Progress Summary: We have made significant progress in identifying epigenetic drug vulnerabilities in MM. A key outcome of this work is a recent publication in Haematologica (Flanagan et al., 2024), where we demonstrated a strong synergistic effect between the DNA methyltransferase inhibitor 5-azacitidine and the BCL-2 inhibitor venetoclax. Building on this, we have observed compelling synergistic activity between the H3K27 demethylase inhibitor GSK-J4 and venetoclax across a panel of MM cell lines, regardless of their BCL-2 dependency status. This highlights a potentially broad therapeutic application. These studies are ongoing, with further in-depth mechanistic and functional assays underway.
Work Package 4: Project management
Throughout the duration of the project, I maintained regular and structured communication with my supervisor through weekly one-on-one meetings. In addition to these sessions, I presented ongoing research updates during bi-monthly laboratory meetings, as well as at departmental seminars held twice a year within the Department of Physiology and Medical Physics.
To ensure clinical relevance and foster interdisciplinary collaboration, I met with Prof. Siobhan Glavey (Haematology) on a biannual basis to discuss research progress and potential clinical implications. I also disseminated key findings by presenting at the RCSI Research Day, engaging with a broader institutional audience.
From a financial management perspective, I oversaw the procurement of consumables and equipment related to the project. All purchases were processed through the RCSI Agresso system and received prior approval from the Principal Investigator, in line with institutional and MSCA financial guidelines.
Work Package 5: Training and Knowledge Transfer.
Transfer of Knowledge
During the fellowship, I contributed significantly to the sustainability and dissemination of technical skills within the host institution. I provided hands-on training in CUT&Tag techniques to two PhD students and one postdoctoral researcher in the Ni Chonghaile laboratory. This training—delivered over a cumulative six days—has enabled ongoing CUT&Tag profiling of patient samples, supporting continuity of this research stream. I continue to collaborate closely with both the Ní Chonghaile and Mahony groups to guide analysis and interpretation of these datasets.
In parallel, I received specialised training in BH3 profiling and applied this expertise in a collaborative project, culminating in a manuscript entitled "Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer." Following positive peer review, the manuscript is currently under resubmission to Nature Metabolism.
Teaching Activities
I contributed to institutional teaching efforts by delivering a lecture to Graduate Entry Medicine students at RCSI. This lecture, part of the GEM REB2 course, focused on the topic of Glomerular Filtration, providing foundational renal physiology instruction to medical trainees.
Mentoring: I Mentored one summer undergraduate research student for two weeks (July 2022)
Grant Writing and Career Development
As part of my professional development, I wrote a successful application for the Science Foundation Ireland (SFI) Pathway Grant, which facilitated my transition to an independent research role. This achievement has enabled me to establish my own research group at University College Dublin (UCD), marking a significant milestone in my academic career trajectory. Which was likely greatly facilitated by the MSCA postdoctoral fellowship.
Work Package 6: Dissemination, exploitation and Communication
Conference Participation and Scientific Dissemination
During the fellowship, I actively disseminated my research findings to the scientific community through conference presentations and seminars:
• BCNI 2023 – Poster Presentation
• TSJCI Conference 2022 – Poster Presentation
• ERN 2022 – Poster Presentation
• University College Dublin (UCD) – Invited Oral Seminar (October 2, 2023)
• IACR/EACR Joint Conference 2024 – Poster Presentation (February 2024)
These engagements enabled meaningful scientific exchange and feedback, particularly within the cancer biology and epigenetics research communities.
Scientific Publication
I contributed as a co-author to a peer-reviewed publication in the open-access journal Haematologica:
Flanagan L, Coughlan A., Cosgrove N., Roe A., Wang Y., Gilmore S., Drozdz I., Comerford C., Ryan J., Minihane E., Parvin S., O’Dwyer M., Quinn J., Murphy P., Furney S., Glavey S., Ní Chonghaile T. “Steroid-free combination of 5-azacytidine and venetoclax for the treatment of multiple myeloma.” Haematologica, 109(9): 2930–2943, 2024. DOI: 10.3324/haematol.2023.283771
This study received substantial media coverage, being highlighted by 16 international and national news outlets, including:
• The Irish Independent
• Science Daily
• MSN
• The Medical Independent
• Pharmacy Times
• eCancer
This reflects the translational significance and broad interest in the research findings.
Public Communication and Online Engagement
I actively communicate my research to both scientific and public audiences through social media and digital platforms, including:
• X (formerly Twitter): @aisling1751
• LinkedIn: linkedin.com/in/aisling-coughlan-9a4b8465
• Lab Website: www.coughlan-lab.com
These platforms are used to share research updates, publications, job opportunities, and educational content, enhancing the visibility and accessibility of our work.
Secondment
Due to my early appointment as Group Leader at University College Dublin, I was unable to complete the planned secondment at Almac. While the secondment was a valuable component of the proposal, this career progression marked a significant outcome of the fellowship, facilitating continued academic leadership and research translation.
IMPACT
Scientific Impact
Significant scientific progress has been achieved in alignment with the project's objectives. I successfully established the CUT&Tag technique at RCSI, overcoming key technical challenges associated with profiling the epigenome in low-yield multiple myeloma (MM) patient samples. Importantly, I trained two additional researchers in this method, ensuring continuity and capacity-building within the host lab. This represents a lasting technical advancement for MM research at the institution. Our work contributed to the field’s understanding of epigenetic vulnerabilities in MM.
Notably, I co-authored a peer-reviewed, open-access publication in Haematologica:
Flanagan et al. “Steroid-free combination of 5-azacytidine and venetoclax for the treatment of multiple myeloma.” Haematologica, 109(9): 2930–2943, 2024. DOI: 10.3324/haematol.2023.283771
This publication highlights a promising therapeutic combination and received widespread attention across 16 media outlets, underlining its translational potential.
I am also a co-author on a second impactful manuscript currently under review at Nature Metabolism: Moss et al. “Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer.” Currently available on bioRxiv: 2024.09.12.611189
In parallel, I am began efforts to validate a novel epigenetic synergy between the H3K27 demethylase inhibitor GSK-J4 and venetoclax. Our integrative analysis (RNA-seq, BH3 profiling, CUT&Tag, and SCENITH) aims to elucidate how GSK-J4 may enhance BCL-2 dependency in MM. If successful, this line of investigation could offer a new therapeutic avenue for MM patients, with high potential for clinical and societal benefit.
Societal Impact:
The previously mentioned Haematologica study has generated significant public interest and dissemination beyond academic circles, with coverage in national and international media including The Irish Independent, MSN, Science Daily, and Pharmacy Times. This indicates the broader relevance of our findings and supports the translation of bench-side science to public awareness and potential clinical practice.
I also engaged in science outreach activities, including hosting students from St. Andrew’s School and mentoring transition year students in the lab. These interactions help stimulate interest in STEM fields among secondary-level students and contribute to long-term societal impact by fostering the next generation of researchers.
Environmental Sustainability
The Department of Physiology and Medical Physics at RCSI was awarded Platinum Certification under the My Green Lab program, reflecting a commitment to environmentally responsible laboratory practices. As part of this department, I contributed to and supported this sustainability ethos throughout the fellowship.
Supervision, Collaboration & Career Development
Regular supervision and strategic mentorship played a vital role in project delivery. I held weekly one-on-one meetings with my supervisor, Prof. Tríona Ní Chonghaile, and met biannually with clinical collaborator Prof. Siobhán Glavey to ensure alignment with translational goals. I also engaged with Dr. Simon Furney and Prof. Shaun Mahony for guidance on bioinformatics strategy.
These interactions directly contributed to my successful application for a Science Foundation Ireland (SFI) Pathway Grant, which supported my transition to an independent research position. I have since been appointed Ad Astra Fellow and Group Leader at University College Dublin, marking a key milestone in my scientific career and ensuring continued exploitation of project outputs.