LDCRC WINTER 2024 NEWSLETTER

December 2024

Edition#5

LDCRC WINTER 2024 NEWSLETTER

RESEARCH NEWS & HIGHLIGHTS

READ MORE Limerick Cancer News LDCRC Anniversary HRI Update Research Week Aperio CS2 Scanner Sub Group Updates Publications March - Sept 2024 eHealth Hub Update

READ MORE Students at conferences LDCRC October Event Upcoming Funding Opportunities Upcoming Events and new staff November - Lung & Prostate Cancer Awareness Month Millin Lecture 2024 10x Genomics Update Join LDCRC

PAST & UPCOMING EVENTS

LIMERICK CANCER NEWS

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FULL ARTICLE HERE

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LIMERICK CANCER NEWS

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LDCRC 3RD ANNIVERSARY Since its establishment in 2021, the LDCRC has emerged as a hub of innovation, leveraging cutting-edge technologies such as single-cell molecular profiling, spatial proteomics, and artificial intelligence to transform cancer research. Lets celebrate the remarkable partnership and pioneering spirit of the Limerick Digital Cancer Research Centre (LDCRC). Together the Limerick Cancer community includes 28 research active principal investigators and clinical leaders, who span faculties and departments.

Together we have achieved incredibly over this short time-frame.

I look forward to

building our research strategy together to support and grow the LDCRC 2025-2028.

Some highlights & achievements in 2021-2024 Attracting over 11 million in research funding*, with over 19 awards, awarded to 15 PIs in 2023-2024. (*statistics were compiled Nov 2024) Between 3-6 meeting per year which have alternating between UL and UHL Establishment of a Cancer Patient PPI panel and CCRG Groups Launch of the LDCRC Single Cell and Sequencing that provides state-of-the-art facilities and services for advanced short, long read Next-generation DNA/RNA sequencing, Spatial proteomics using Akoya Phenocycler technology, Illumina NextSeq and Oxford Nanopore platforms, Flow cytometry and confocal microscopy for cellular analysis and Seahorse metabolomics for studying cellular metabolism This core facility is part of a national network for spatial biology (NaSPro) Hosting national & international meetings, membership of AICRI, building a national & international partnerships

AY202122

AY2022-23

AY202324*

Research Funding (Euros)

4,060,277

1,455,137

5,840,941

No Awards

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No PI

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ALL - CAN PHD PROGRAMME 2025 The LDCRC is pleased to announce that the HRB and US NCI funded ALL-CAN-TRAINING doctoral training program will be launched in 2025 and this programme will greatly expand our postgraduate training in cancer research. Any questions on the programme, please email ldcrc@ul.ie

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HRI UPDATE HRI Strategic Funding Calls The HRI is delighted to have introduced the following funding calls this year. Some are new; some repeated.

PhD Call- Spring 2024: Three PhDs awarded: Sinead Taylor: Development of a Core Outcome Set for cognition post-stroke.

Supervisor: Associate Professor Sara Hayes Nehal Nour: Evaluation of the Sláintecare Healthy Communities Programme (SCHC) for deprived communities. Supervisor: Dr Dervla Kelly Kelsi Gallati: Building 3D co-culture models of breast cancer to overcome endocrine therapy resistance. Supervisor: Dr Amira Mahdi HRI 10-Year Anniversary Bursaries- Summer 2024: Ten bursaries awarded (max. €2k each) to postdocs and postgrads.

HRI International Conference Call- opened October 1st for HRI members hosting international conferences on campus/UHL Travel (Conference Attendance) Call- currently open with a closing date of October 11th.

This is a biannual call- next call, February 2025, and is applicable to members who will attend a conference to present research findings at international or, occasionally, national conferences or will present a bid for that international conference to be hosted by University of Limerick at a future date.

Open Access Funding- continuous call for the coming academic year, while budget remains.

HRI Activities - Events and Training New Calendar of Activities: In progress. All available to view in the HRI Members’ SharePoint site Member Lunches: two per annum, that focus on networking with the previous lunch on November 14th covering the following areas Monthly Fundamentals of Health Research: continue monthly online with subjects such as Research Ethics, Research Integrity, Data Protection in Research Other Activities: Statistics training, project management workshops, critical skills appraisal training, and a research day for postgrads/postdocs- featuring a poster competition and elevator pitch presentations Good Clinical Practice training now complete for UHL colleagues; will be repeated for UL colleagues. This training was conducted by HRI colleagues in the HRI Clinical Research Support Unit (CRSU), located at CERC, UHL

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International Conferences HRI supported two international conferences on campus this year. Support provided was financial and operational.

1. 12th Scientific Meeting of the International Society for Research on Internet Interventions (June). Lead: Professor Pepijn Van de Ven 2. International Biochemistry of Exercise Conference (July). Lead: Professor Brian Carson HRI Postgraduate and Postdoctoral HUB New Committee now in place. Significant interest in pursuing an active role on the committee.

Current Focus: Increased collaboration with the Doctoral College.

Activities Calendar: In progress, with workshops planned to include a statistics session and new Members Introduction/Members refresher Statistical Support Dr Eleanor (Ellie) Fallon: Recruited as HRI Biostatistician, Summer 2024. Ellie is a graduate of the University of Limerick (UL), where she completed her PhD under the supervision of Professors Ailish Hannigan and Norma Bargary. Dr Fallon brings a wealth of expertise in biostatistics, enhancing members’ research capabilities and support for ongoing projects.

HRI Annual Report 2023 Annual Report launched May 2024.

Presented by HRI Director to URC on June 10th and Management Council on September 19th.

2024 Report: Planning has commenced with planned launch - May 2025.

HRI Membership Membership renewal process now complete, with all approved members now entitled to HRI Membership for next three years.

Covidence HRI is proud to co-fund the provision of Covidence software in the University in conjunction with the library. HRI and the Library hosted a face-to-face training and information session with Covidence personnel during October.

For more information on any of the above please reach out to hri@ul.ie

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Research Week - Festival of Science: Emerging Breakthroughs Advancing Cancer Research (HRI) On 29th April 2024 the LDCRC and the HRI held an event with an aim to explore the key themes of the research centre, Tumour Microenvironments and Genitourinary Disease and this event was facilitated by Dr James Brown, UL, and Professor Ruth Clifford UHL. The event was introduced by Professor Aedin Culhane and by Professor Ruth Clifford and a number of updates were heard on cancer research from members of the LDCRC such as Dr Eoghan Cunnane, Dr Jason Bennett, Dr Kieran McGourty and Dr Sinead O’Keeffe, Faculty of Science & Engineering, UL, Assistant Professor Amira Mahdi, Mr Michael Lynch and Dr Ciara Leahy, School of Medicine, UL, Ms. Christina Fleming Consultant of Colorectal Surgery and Dr Máire Lavelle, Lead Breast Histopathologist, UHL. It was an engaging event with several topics discussed in the panel sessions and we look forward to more LDCRC events in the future.

Left to right: Dr Ciara Leahy (PhD Student, School of Medicine), Ms Christina Fleming (Colorectal Surgery Consultant, UHL), Dr Máire Lavelle (Lead Breast Histopathologist, UHL) Dr Kieran McGourty, (Lecturer and Principal Investigator, Department of Chemical Sciences, UL) Dr Amira Mahdi (Assistant Professor of Biomedical Sciences, School of Medicine)

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Left to right: Colleagues from the Faculty of Science & Engineering, Dr Jason Bennett, Dr Sinead O’Keeffe and Dr Eoghan Cunnane

Aperio CS2 Pathology Scanner Demo at School of Medicine CERC Research Laboratory From September 6th to 16th, the LDCRC had the opportunity to test the capabilities of the Aperio CS2 Pathology Scanner (Leica) in the CERC research laboratory.

The Aperio CS2 is a cutting-edge scanner capable of digitizing up to five slides simultaneously, specifically designed for research applications. It provides high-quality imaging with magnifications of 20x and 40x, essential for conducting detailed analyses. This precision is particularly important for the accurate examination of histological samples in areas such as cancer research, and tissue pathology. More information available at this link: Aperio CS2 - Digital Pathology Slide Scanner (leicabiosystems.com) One of the key features highlighted during the demo was the scanner's user-friendly interface. The intuitive design allows even first-time users to efficiently manage data, store images, and share digital slides. The ability to quickly retrieve and share slides is particularly beneficial for multi-disciplinary teams engaged in collaborative projects, facilitating remote consultations and cross-site studies.

In addition to its high-performance imaging, the Aperio CS2 scanner supports streamlined data management through integration with software platforms for annotation and reporting, further enhancing research productivity.

Overall, the demo offered valuable insight into how the addition of this equipment can significantly enhance the progress and quality of ongoing research projects. The team is currently evaluating the benefits of integrating this technology into their future projects.

Your feedback and questions about this instrument are welcome. We would like to hear from all potential users, please email Elizabeth.Ryan@ul.ie with ‘LDCRC scanner’ in the subject line.

We thank Cecilia Soria, CERC lab and Tricia English, LDCRC for the organisation of the demo.

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SUB GROUP UPDATES

Breast Subgroup New member news: Kelsi Gallati has joined the Breast Research Subgroup this September as a PhD researcher. Kelsi will be working in the School of Medicine, UL. Her project is focused on building better in vitro models of breast cancer to understand and overcome endocrine therapy resistance. Welcome Kelsi!

"Hello, I’m Kelsi Gallati and I am starting my PhD in breast cancer research funded by the Health Research Institute at the UL School of Medicine supervised by Dr Amira Mahdi and cosupervised by Dr Kieran McGourty. The aim of my research is building 3-dimensional co-culture models to better represent the tumour microenvironment while using single-cell RNA-sequencing to study and overcome endocrine therapy resistance in estrogen receptor positive breast cancer.

In 2023 I finished my undergraduate studies in Bioscience at the University of Limerick. During my studies I gained research experience in reproductive studies supervised by Professor Sean Fair through a Health Research Board Summer Scholar program as well as my Final Year Project.

After graduating I spent a year working in the medical device industry at Boston Scientific, Clonmel."

PPI Subgroup The PPI Steering Committee, which comprises membership from members of the public, University Hospital Limerick and University of Limerick, has been focussed on developing a PPI Panel. This panel of patient and public members is available for involvement in research projects, grant applications, literature review and other such relevant activities. After some successful recruitment events in UHL Cancer Centre, several new members attended an induction programme in August, co-delivered by Margaret Carroll, Patient member PPI, Deirdre Hartigan, Cancer Research Nurse, Liz O'Leary, PALS Manager and Miriam McCarthy, Health Sciences Academy Manager and Chair of the PPI Steering Committee.

Resources to support the promotion of PPI in research and recruitment of new PPI members were also developed and shared, including a PPI Ignite-funded video explaining the importance of PPI in research, leaflets and a pull-up banner. All of this contributes to a greater awareness of the importance of PPI in research and supports the development of this inclusive culture.

Complimented by education and training, the role of PPI is growing. Other areas of PPI involvement include input into research grants, consultation on a lung cancer passport and involvement in several research subgroups. We look forward to a busy year ahead!

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Dr Elizabeth Ryan, Margaret Carroll and Deirdre Hartigan at the recent PPI Bursaries @ UL – Shining a Light on Public and Patient Involvement in Research event where the PPI Ignite funded video was highlighted. Please see the link here for the full video

Blood Subgroup The annual Haematology Summit took place in Dublin on Sept 6, 2024 to share recent insights into the diagnosis and treatment of multiple myeloma, chronic lymphocytic leukaemia (CLL) and acute myeloid leukaemia (AML).

Film Burkitt a new documentary on Dr Denis Burkitt, the Co Fermanagh man who discovered Burkitt’s lymphoma, will take place in Limerick in early 2025.

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CCRG Group

Scientific Lead

Clinical Lead

Status

Blood

Elizabeth Ryan

Ruth Clifford

Active, meeting monthly

Breast

James Brown

Chwanrow Baban

Active, meeting monthly

Colorectal

Kieran McGrourty

Christina Fleming

Restarting late 2024

Lung

Unfilled

Gregory Korpanty

On hold

GU/Prostate

Eoghan Cunnane

Niamh Peters

Active, meeting monthly

Allied Health (AHP)

Rose Galvin

Matthew O’ Brien

Active, meeting monthly

Cancer Nursing (CNS/ANP) Pauline Meskell

Nichola McNamara

Meeting 6-8 weekly

Biobanking

Ruth Clifford

Active, monthly meeting

Elizabeth Ryan

Publications from March - December 2024 from LDCRC

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Defects in NK cell immunity of pediatric cancer patients revealed by deep immune profiling.

Syrimi E, Khan N, Murray P, Willcox C, Haigh T, Willcox B, Masand N, Bowen C, Dimakou DB, Zuo J, Barone SM, Irish JM, Kearns P, Taylor GS. iScience. 2024 Aug 28;27(9):110837. doi: 10.1016/j.isci.2024.110837. eCollection 2024 Sep 20.

PMID: 39310750 Free PMC article.

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Harnessing PROTACs to combat H5N1 influenza: A new frontier in viral destruction.

Mukerjee N, Maitra S, Mukherjee D, Ghosh A, Alexiou AT, Thorat ND. J Med Virol. 2024 Sep;96(9):e29926. doi: 10.1002/jmv.29926.

PMID: 39295251 Review.

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Hodgkin/Reed-Sternberg cells induce GPNMB expression and release from macrophages to suppress T-cell responses to the Epstein-Barr virus-encoded LMP2A protein.

Masand N, Perry TA, Pugh M, Fennell E, Hennessy A, Wei W, Bouchalova K, Burns D, Kearns P, Taylor G, Vrzalikova K, Murray PG. Haematologica. 2024 Aug 22. doi: 10.3324/haematol.2024.285319.

Online ahead of print.

PMID: 39219456

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Mouse models to investigate in situ cell fate decisions induced by p53.

Lieschke E, Thomas AF, Kueh A, Atkin-Smith GK, Baldoni PL, La Marca JE, Young S, Huang AS, Ross AM, Whelan L, Kaloni D, Tai L, Smyth GK, Herold MJ, Hawkins ED, Strasser A, Kelly GL. EMBO J. 2024 Aug 19. doi: 10.1038/s44318-024-00189-z. Online ahead of print.

PMID: 39160273

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Intra-tumoral and peripheral blood TIGIT and PD-1 as immune biomarkers in nodular lymphocyte predominant Hodgkin lymphoma.

Gunawardana J, Law SC, Sabdia MB, Fennell É, Hennessy A, Leahy CI, Murray PG, Bednarska K, Brosda S, Trotman J, Berkahn L, Zaharia A, Birch S, Burgess M, Talaulikar D, Lee JN, Jude E, Hawkes EA, Jain S, Nath K, Snell C, Swain F, Tobin JWD, Keane C, Shanavas M, Blyth E, Steidl C, Savage K, Farinha P, Boyle M, Meissner B, Green MR, Vega F, Gandhi MK. Am J Hematol. 2024 Aug 17. doi: 10.1002/ajh.27459. Online ahead of print.

PMID: 39152767

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Evaluating the Cellular Roles of the Lysine Acetyltransferase Tip60 in Cancer: A Multi-Action Molecular Target for Precision Oncology.

Zohourian N, Coll E, Dever M, Sheahan A, Burns-Lane P, Brown JAL. Cancers (Basel). 2024 Jul 27;16(15):2677. doi: 10.3390/cancers16152677.

PMID: 39123405 Free PMC article. Review.

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Blood Cancer Network Ireland (BCNI) and National Cancer Registry Ireland (NCRI) collaboration: challenges and utility of an Enhanced Blood Cancer Outcomes Registry (EBCOR) pilot.

Millar SR, Mohamed MB, Mykytiv V, McMorrow R, Donnelly C, O'Leary E, Orfali N, Murphy P, Browne PV, Quinn J, O'Gorman P, Ryan MF, Clifford R, Hassadi EE, O'Shea D, Gilligan O, Krawczyk J, O'Dwyer ME, Szegezdi E, Cahill MR. Ir J Med Sci. 2024 Jul 20. doi: 10.1007/s11845-024-03756-9. Online ahead of print. PMID: 39030463

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Role of robot-assisted laparoscopy in deep infiltrating endometriosis with bowel involvement: a systematic review and application of the IDEAL framework.

Ong HI, Shulman N, Nugraha P, Wrenn S, Nally D, Peirce C, Mahmood U, McCormick J, Proud D, Warrier S, Fleming C, Mohan H. Int J Colorectal Dis. 2024 Jun 26;39(1):98. doi: 10.1007/s00384-024-04669-w.

PMID: 38922440 Free PMC article. Review.

Tumor microenvironment of Burkitt lymphoma: different immune signatures with different clinical behavior.

Siciliano MC, Bertolazzi G, Morello G, Tornambè S, Del Corvo M, Granai M, Sapienza MR, Leahy CI, Fennell E, Belmonte B, Arcuri F, Vannucchi M, Mancini V, Guazzo R, Boccacci R, Onyango N, Nyagol J, Santi R, Di Stefano G, Ferrara D, Bellan C, Marafioti T, Ott G, Siebert R, QuintanillaFend L, Fend F, Murray P, Tripodo C, Pileri S, Lazzi S, Leoncini L. Blood Adv. 2024 Aug 27;8(16):4330-4343. doi: 10.1182/bloodadvances.2023011506.

PMID: 38861355 Free PMC article.

Exosome-mediated PROTAC delivery for treatment of RNA viral infections and zoonosis.

Mukerjee N, Maitra S, Ghosh A, Alexiou A, Thorat ND. Drug Discov Today. 2024 Jul;29(7):104044. doi: 10.1016/j.drudis.2024.104044. Epub 2024 May 23. PMID: 38796097 Review.

Updated European guidelines for clinical management of familial adenomatous polyposis (FAP), MUTYH-associated polyposis (MAP), gastric adenocarcinoma, proximal polyposis of the stomach (GAPPS) and other rare adenomatous polyposis syndromes: a joint EHTG-ESCP revision.

Zaffaroni G, Mannucci A, Koskenvuo L, de Lacy B, Maffioli A, Bisseling T, Half E, Cavestro GM, Valle L, Ryan N, Aretz S, Brown K, Buttitta F, Carneiro F, Claber O, Blanco-Colino R, Collard M, Crosbie E, Cunha M, Doulias T, Fleming C, Heinrich H, Hüneburg R, Metras J, Nagtegaal I, Negoi I, Nielsen M, Pellino G, Ricciardiello L, Sagir A, Sánchez-Guillén L, Seppälä TT, Siersema P, Striebeck B, Sampson JR, Latchford A, Parc Y, Burn J, Möslein G. Br J Surg. 2024 May 3;111(5):znae070. doi: 10.1093/bjs/znae070. PMID: 38722804 Free PMC article.

The 1+Million Genomes Minimal Dataset for Cancer.

Riba M, Sala C, Culhane AC, Flobak Å, Patocs A, Boye K, Plevova K, Pospíšilová Š, Gandolfi G, Morelli MJ, Bucci G, Edsjö A, Lassen U, Al-Shahrour F, Lopez-Bigas N, Hovland R, Cuppen E, Valencia A, Poirel HA, Rosenquist R, Scollen S, Arenas Marquez J, Belien J, De Nicolo A, De Maria R, Torrents D, Tonon G. Nat Genet. 2024 May;56(5):733-736. doi: 10.1038/s41588-024-01721-x.

PMID: 38702538 No abstract available.

demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs. 13.

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Lynch MP, Wang Y, Ho Sui S, Gatto L, Culhane AC. Gigascience (IF: 6.52; Q1). 2024 Jan 2;13:giae090. doi: 10.1093/gigascience/giae090.PMID: 39607981 Free PMC article.

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Cancer Nanovaccines: Nanomaterials and Clinical Perspectives.

Desai N, Chavda V, Singh TRR, Thorat ND, Vora LK. Small. 2024 Aug;20(35):e2401631. doi: 10.1002/smll.202401631. Epub 2024 May 1.

PMID: 38693099 Review.

Putting the STING back into BH3-mimetic drugs for TP53-mutant blood cancers.

Diepstraten ST, Yuan Y, La Marca JE, Young S, Chang C, Whelan L, Ross AM, Fischer KC, Pomilio G, Morris R, Georgiou A, Litalien V, Brown FC, Roberts AW, Strasser A, Wei AH, Kelly GL. Cancer Cell. 2024 May 13;42(5):850-868.e9. doi: 10.1016/j.ccell.2024.04.004. Epub 2024 Apr 25.

PMID: 38670091

Current trends in clinical trials and the development of small molecule epigenetic inhibitors as cancer therapeutics.

Zohourian N, Brown JA. Epigenomics. 2024 Apr 19;16(9):671-80. doi: 10.2217/epi-2023-0443. Online ahead of print.

PMID: 38639711 Review.

Chitosan lecithin nanocomposite based electrochemical biosensor for glycine detection in biological matrices.

Saini N, Yadav D, Shirolkar M, Murugappan S, Thorat N, Kulkarni A. Colloids Surf B Biointerfaces. 2024 Jun;238:113901. doi: 10.1016/j.colsurfb.2024.113901. Epub 2024 Apr 10.

PMID: 38608466

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Targeted therapies for HPV-associated cervical cancer: Harnessing the potential of exosomebased chipsets in combating leukemia and HPV-mediated cervical cancer.

Maitra S, Mukerjee N, Alharbi HM, Ghosh A, Alexiou A, Thorat ND. J Med Virol. 2024 Apr;96(4):e29596. doi: 10.1002/jmv.29596.

PMID: 38590017

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Aflatoxin B1 and Epstein-Barr virus-induced CCL22 expression stimulates B cell infection.

Maroui MA, Odongo GA, Mundo L, Manara F, Mure F, Fusil F, Jay A, Gheit T, Michailidis TM, Ferrara D, Leoncini L, Murray P, Manet E, Ohlmann T, De Boevre M, De Saeger S, Cosset FL, Lazzi S, Accardi R, Herceg Z, Gruffat H, Khoueiry R. Proc Natl Acad Sci U S A. 2024 Apr 16;121(16):e2314426121. doi: 10.1073/pnas.2314426121.

Epub 2024 Apr 4.

PMID: 38574017

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Mass-manufacturable scintillation-based optical fiber dosimeters for brachytherapy.

Gierej A, Baghdasaryan T, Martyn M, Woulfe P, Mc Laughlin O, Prise K, Workman G, O'Keeffe S, Rochlitz K, Verlinski S, Giaz A, Santoro R, Caccia M, Berghmans F, Van Erps J. Biosens Bioelectron. 2024 Jul 1;255:116237. doi: 10.1016/j.bios.2024.116237. Epub 2024 Mar 21.

PMID: 38537429

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Pre-operative prediction of BCR-free survival with mRNA variables in prostate cancer.

O'Donnell A, Cronin M, Moghaddam S, Wolsztynski E.PLoS One (IF: 3.24; Q2). 2024 Oct 1;19(10):e0311162. doi: 10.1371/journal.pone.0311162. eCollection 2024.PMID: 39352906 Free PMC article.

Revolutionizing Cancer Treatment: The Promising Horizon of Zein Nanosystems.

Preetam S, Duhita Mondal D, Mukerjee N, Naser SS, Tabish TA, Thorat N. ACS Biomater Sci Eng. 2024 Apr 8;10(4):1946-1965. doi: 10.1021/acsbiomaterials.3c01540. Epub 2024 Mar 1. PMID: 38427627 Free PMC article. Review.

Genome-scale clustered regularly interspaced short palindromic repeats screen identifies nucleotide metabolism as an actionable therapeutic vulnerability in diffuse large B-cell lymphoma.

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Davies N, Francis T, Oldreive C, Azam M, Wilson J, Byrd PJ, Burley M, Sharma-Oates A, Keane P, Alatawi S, Higgs MR, Rudzki Z, Ibrahim M, Perry T, Agathanggelou A, Hewitt AM, Smith E, Bonifer C, O'Connor M, Forment JV, Murray PG, Fennell E, Kelly G, Chang C, Stewart GS, Stankovic T, Kwok M, Taylor AM. Haematologica (IF: 9.94; Q1). 2024 Dec 1;109(12):3989-4006. doi: 10.3324/haematol.2023.284404.PMID: 38841800 Free PMC article.

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The eHealth-Hub welcomes new students and staff The eHealth-Hub for Cancer (www.ehealth4cancer.ie) is a HEA North-South Research Programme Emerging Hub of Excellence led by Prof Aedin Culhane, director of the Limerick Digital Cancer Research Centre, University of Limerick (UL) and Prof Mark Lawler, Associate Pro-Vice-Chancellor and Professor of Digital Health at the Patrick G Johnston Centre for Cancer Research, Queens University Belfast (QUB).

The eHealth-Hub led node at Limerick are delighted to welcome a senior administrator, research assistant and four PhD students who have recently joined us. They join PhD student team members, David Akwuru and Brendan Reardon.

Katie Cremin is the project senior administrator of the eHealth-Hub for Cancer.

Kemdil Anyaoku is a research assistant on the All-Island Characterization of Blood Cancers project, which supports implementation of clinical trials for Irish blood cancer patients. Kemdil is supervised by Prof. Aedin Culhane (UL) and Prof. Ruth Clifford (UHL).

Jeremiah Akintomide (PhD student) is working on harmonizing and connecting prostate cancer data at all-island clinical sites using the Observational Medical Outcomes Partnership Common Data Model. He is supervised by Prof. Katie Crowley (UL), Prof. Bill Watson (University College Dublin), Dr Amir Jalali (UL) and Dr. David Galvin (University College Dublin).

Arya Soman (PhD student) will undertake a study of Statistical Frameworks to Enable Federated Clinical Cancer Research, under the supervision of Dr. Shirin Moghaddam (UL), Dr. Amir Jalali (UL), and Dr. Claire Donohoe (Trinity College Dublin).

Abhishek (PhD student) supervised by Prof. Aedin Culhane (UL) and Prof. Asieh Golozar (Northeastern University) will focus on developing frameworks and standards for connecting and sharing genomics data to enable all-island clinical trials research.

Dibya Mohanty (PhD student) is researching The Role of Tissue Specificity in Immune Oncology: Phylogenetically and Tissue Informed Pharmacogenomics under guidance of Prof.

Aedin Culhane (UL) and Dr. Constantine Mitsiades (Dana-Farber Cancer Institute) to better match patients to precision oncology drug-repurposing clinical trials.

The arrival of these motivated and talented individuals marks an exciting milestone for the eHealth Hub project, as we continue our goal of leveraging technology to combat one of the most pressing healthcare challenges of our time. The team recently attending the OHDSI UK node meeting in London, and learned about the NHS Health Data Research UK plans to connect health data using Observational Medical Outcomes Partnership Common Data Model.

We are seeking two postdoctoral researchers, contact eHealth@ul.ie if you would like more information.

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On January 14th eHealth-Hub for Cancer will host an All Island Forum on Cancer Data at the University of Limerick. This conference will bring together international and all-island clinical, academic and industry leaders to discuss federated data infrastructure and requirements to connect, access and analyse clinical and genomics cancer data across institutes and hospitals.

Confirmed speakers include; Gianpiero Cavalleri, Professor of Human Genetics, RCSI Geoff Hall, Professor of Digital Health, Leeds University Paul Nagy, Assoc Professor at Bloomberg School of Public Health, Director Informatics and Data Science, Johns Hopkins University Xose Fernandez, Head Digital Oncology Network for Europe, IQVIA Lesley Anderson, Professor in Health Data Science, University of Aberdeen Martin Curley, Professor of Innovation, Maynooth University and Digital Health Leader Angela Clayton-Lea, Chief Operations Officer at Cancer Trials Ireland Giles Ducorroy, Head Global Real World Evidence Services at Novartis Forum themes include Case studies of successful federated cancer research Real-World Evidence in Cancer Research Data Innovation for All-Island Clinical Trials Leveraging electronic health records for cancer insights Cancer Genomics and Precision Medicine Data driven cancer policy

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Registration is free on Eventbrite here

eHealth Hub team members at the OHDSI UK meeting on September 25th 2024.

Back row, left to right: Kemdil Anyaoku (UL), Katie Cremin (UL), Jeremiah Akintomide (UL), Arya Soman (UL), Dibya Mohanty (UL), Prof Aedin Culhane (UL), Dr Shirin Moghaddam (UL), Dr Ethna McFerran (QUB), Dr Amir Jalali (UL). Front row, left to right: David Akwuru (UL) and Kluivert Boakye Duah (QUB).

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STUDENTS AT CONFERENCES ESMO 2024 Second year graduate student Brendan Reardon (from the Culhane lab) attended and presented a poster titled “Making the precision oncology landscape of Europe and the Republic of Ireland programmatically accessible” at this year’s European Society of Medical Oncology meeting in Barcelona, Spain in September 2024.

The Culhane lab generated a database cataloguing relationships between individual cancer drugs, mutations within a tumour’s DNA, and types of cancer. They did so by reading and synthesizing information from hundreds of documents from both the European Medicines Agency (EMA) and Health Service Executive (HSE). Using this database, they have been able to investigate potential disparities between what cancer treatments are authorized for use in the European Union, from the EMA, and which are approved for reimbursement in Ireland’s public health system, from the HSE.

Brendan Reardon with his poster at Emso in September 2024

They are also building a website so that anyone can access and use this database, currently available as an early version at https://ie.moalmanac.org. If you’re interested in learning more, he would be happy to chat and can be reached on brendan.reardon@ul.ie.

MAQC 2024 Ahmad Alkhan, a second-year PhD student in Professor Aedin Culhane’s lab, recently attended the 2024 MAQC conference, held in Jiashan, China, focused on the theme “Opportunities and Challenges: AI in Future Health.” This annual event gathered international experts to discuss advancements in quality control for high-throughput omics data, with a spotlight on integrating AI technologies in health and biomedical research. The program included keynote speeches on topics such as data-driven biomedical research, challenges in omics data integration, and the application of AI in health. Key sessions addressed single-cell and spatial omics, multi-omics data quality, and emerging trends in drug discovery.

The event featured workshops, scientific presentations, and discussions on the reproducibility and standardization of omics technologies, crucial for advancing personalized and precision medicine.

The LDCRC extends its heartfelt congratulations to Ahmad who won the prestigious Young Scientist Award at the MACQ Conference in China.

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EUROBIOC2024

In September, members of the Culhane Lab attended the EuroBioC2024 (European Bioconductor) conference in Oxford, UK. Bioconductor is an open-source software project which aims to develop and share open-source software for precise and repeatable analysis of biological data, and this annual event gathers computational biologists from various fields and backgrounds. Software users and developers presented their latest research on methods and their application to cutting-edge technologies such as bulk, single-cell, and spatial 'omics, helping to enhance our understanding of biology in health and disease.

The Culhane Lab actively contributes to the Bioconductor community. Prof. Aedin Culhane co-founded the Community Advisory Board, Dr. Maria Doyle was on the conference organising committee and is the Bioconductor Community Manager and Michael Lynch is both a user and developer with the project.

Dr Maria Doyle and Michael Lynch at EuroBioC2024

IMMUNOLOGY CONFERENCE 2024

Conference Report by Luisa Silva and Brian Gleeson On 1st September 2024, Dr Luisa Silva and Brian Gleeson attended the European Congress of Immunology Society for Immunotherapy of Cancer (ECI-SITC) satellite meeting in the Convention Centre in Dublin. The keynote speaker, Nobel Laureate Prof. James Allison of MD Anderson Cancer Centre, spoke about the history of immune checkpoint blockade, highlighted its clinical success in melanoma, and outlined key molecules that are targeted across a broad spectrum of solid cancers. These include programmed cell death 1 (PD-1) and PD-1 ligand (PD-L1), and cytotoxic T-lymphocyte associated protein 4 (CTLA-4). Prof.

Allison also spoke about novel immune checkpoints that may have clinical utility including lymphocyteactivating gene 3 (LAG3), V-type immunoglobulin domain-containing suppressor of T-cell activation (VISTA), and leukocyte immunoglobulin like receptor B2 (LILRB2).

His colleague at MD Anderson, Prof. Padmanee Sharma, expanded on the topic of immune checkpoint blockade using a tissue-agnostic approach based on tumour genomics. Prof. Sharma discussed novel findings from her group that explored immune checkpoints expressed by macrophage subsets and cancer-associated fibroblasts in pancreatic cancer. She also highlighted the importance of clinically relevant companion diagnostics, clinical trial equity and inclusion, and patient advocacy.

Prof. Jennifer Guerriero of Harvard Medical School discussed tumour associated macrophages in breast cancer, presenting new findings that identified diverse subsets of antigen-presenting CD163+ and VISTA+ macrophages using spatial biology and transcriptomics. Prof. Guerriero also described novel findings in macrophage reprogramming towards wound repair lipid metabolism suggesting that “M1-M2” dichotomy does not capture the full complexity of this innate cell type in patients with cancer.

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Prof. Alberto Mantovani of Humanitas University Milan described the complex crosstalk between tumourassociated macrophages and the complement system in patients with cancer. Prof. Mantovani highlighted several myeloid checkpoint molecules that have received less attention clinically including signal regulatory protein alpha (SIRPa), sialic acid binding Ig-like lectin 10 (SIGLEC-10), and butyrophilin subfamily 2 member A1 (BTN2A1). His group also identified that macrophages of large diameter become increasingly protumourigenic compared to small diameter anti-tumour macrophages.

Prof. Evelyn Ullrich of Goethe University Frankfurt discussed advances in natural killer (NK) cell immunotherapy for patients with acute myeloid leukaemia and acute lymphoblastic leukaemia. Prof. Ullrich presented novel methods for autologous chimeric antigen receptor (CAR)-NK cell production using the “Sleeping Beauty” transposon. She also highlighted how deleting killer cell lectin like receptor C1 (KLRC1, also called NKG2A) improves CAR-NK cell cytotoxicity and decreases cell exhaustion.

Prof. Thomas Marron of Mount Sinai Hospital discussed the relationship between type 2 immunity and the development of lung cancer. Prof. Marron reflected on the hygiene hypothesis, rising global allergy rates, and how the allergy-related cytokines interleukin-4 (IL-4) and IL-5 predict poor prognosis in patients with lung cancer. His group discovered that eosinophils and basophils are the source of these pro-tumourigenic cytokines in patients with lung cancer, and that blocking IL-4 receptor using dupilumab induces remission in patients with non-small cell lung cancer.

Overall, Luisa and Brian found this international satellite meeting to be well organised and highly informative. They will incorporate key methods and findings discussed at this meeting into their own experimental design to investigate the immune microenvironment of patients with chronic lymphocytic leukaemia.

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LDCRC OCTOBER EVENT On 8th October 2024, the LDCRC were delighted to host the meeting 'Cell Death, Data and AI in Cancer Research' in the Bernal Institute in UL. This was a multidisciplinary cross faculty event to facilitate discussions regarding the requirements of a data framework that could support AI and advancing cancer research within Limerick. The event was opened by Professor Norelee Kennedy, Vice President of the Research Office and was held across three sessions.

Session one covered Cancer Imaging with speakers Professor Jennifer Ní Mhuircheartaigh from the School of Medicine in UL discussing “Opportunities and Challenges for Machine Learning in Diagnostic Radiology”. Dr Emil Vassev and Dr Ciaran Eising from the Department of Computer Science and Information Systems in UL each discussed how AI maybe used for cancer research and Image Analysis Ahmad Alkhan a second year PhD student from Professor Aedin Culhane lab provided an overview of how “Using Deep learning to detect and segment perineural invasion in multiple cancers from H&E whole slide images” As part of the second session which covered Biology of Cancer, the LDCRC were delighted to host keynote speaker Professor Lisa Bouchier Hayes who is Associate Professor in the Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, on her visit to UL where she spoke about the "Apoptotic and non-apoptotic roles of caspases in health and disease" was discussed as part of the keynote speech.

The third session explored Electronic Patient Data, Digital Infrastructure, LLM and ChatGPT and updates were heard from students Kaushal Bhavsar and Gauri Vaidya from the BDS research group whose talks showed the significant implications of work that was ongoing with regards to personalised medicine and target therapies in relation to cancer research. Professor Culhane and Dara Walsh from University Hospital Limerick also provided an overview as to the requirements for an enhanced digital infrastructure to assist with cancer research in Limerick.

The LDCRC look forward to the next event which will be held in the CERC Building in University Hospital Limerick on 17th December and the agenda will follow in due course.

Professor Norelee Kennedy opening remarks

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Gauri Vaidya presenting

Irish Funding Opportunities Programme

Website

Closing Date

Disruptive Technologies Innovation Fund (DTIF) Call 7

https://enterprise.gov.ie/en/wha t-we-do/innovation-researchdevelopment/disruptivetechnologies-innovation-fund/

30 April 2025

Details: The Disruptive Technologies Innovation Fund (DTIF) Call 7 is now open for submissions.

This funding opportunity is designed for consortia involving SMEs, MNCs, and RPOs engaging in collaborative industrial research and/or experimental development projects. The goal is to address challenges associated with new disruptive technologies that will significantly transform the way we work and live. It encourages joint efforts among diverse enterprises in Ireland to develop technologies that can disrupt markets, redefine business operations, create new products, and foster new business models, and provides funding for projects that have the potential to alter existing markets and introduce innovative solutions.

European Funding Opportunities Programme

Website

Closing Date

EU4Health

EU4health

22 January 2025

Details: The EU4Health final of wave of calls has been launched (full work programme.) This includes a number of funding opportunities for health researchers, practitioners and SMEs seeking to improve healthcare systems and patient outcomes in cancer care: · CR-g-24-96 Call for proposals to support the establishment of new networks of expertise on cancer and cancer conditions (Work Programme pp. 80-81) · CR-g-24-41 Personalised cancer medicine (Work programme pp. 23-25 )

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US Funding Opportunities Programme

Website

Closing Date

National Cancer Institute Notice of Special Interest: Career Development Opportunities for Research on Cancer in Global Settings at the Center for Global Health at the National Cancer Institute

NOT-CA-24-098: Notice of Special Interest (NOSI): Career Development Opportunities for Research on Cancer in Global Settings at the Center for Global Health at the National Cancer Institute (nih.gov)

Multiple streams and dates, see call website for information

Details: The National Cancer Institute (NCI) Center for Global Health (CGH) is interested in applications from individuals committed to an independent career in global cancer research who propose mentored research projects in topics relevant to the LMIC where the research will be conducted. NCI is also interested in applications from established investigators committed to global cancer research education in LMICs. Topics of interest include but are not limited to, studies in cancer biology and genetics, cancer epidemiology, research in cancer primary and secondary prevention, clinical and translational research, implementation science and health systems research, health disparities, health surveillance, and cancer informatics research, studies in integrative oncology and cancer survivorship as well as investigations that employ technology (including mHealth and eHealth) to address cancer control. As relevant, the proposed career development, research education, and/or mentoring project must be aligned with cancer control priorities in the LMIC.

Programme

Website

Closing Date

National Cancer Institute Notice of Special Interest: Career Development Opportunities for Research on Cancer in Global Settings at the Center for Global Health at the National Cancer Institute

NOT-CA-24-098: Notice of Special Interest (NOSI): Career Development Opportunities for Research on Cancer in Global Settings at the Center for Global Health at the National Cancer Institute (nih.gov)

Multiple streams and dates, see call website for informati on

Details: The National Cancer Institute (NCI) Center for Global Health (CGH) is interested in applications from individuals committed to an independent career in global cancer research who propose mentored research projects in topics relevant to the LMIC where the research will be conducted. NCI is also interested in applications from established investigators committed to global cancer research education in LMICs. Topics of interest include but are not limited to, studies in cancer biology and genetics, cancer epidemiology, research in cancer primary and secondary prevention, clinical and translational research, implementation science and health systems research, health disparities, health surveillance, and cancer informatics research, studies in integrative oncology and cancer survivorship as well as investigations that employ technology (including mHealth and eHealth) to address cancer control. As relevant, the proposed career development, research education, and/or mentoring project must be aligned with cancer control priorities in the LMIC.

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UPCOMING EVENTS AND NEW STAFF

Date

Title and Details

Location

Tues Jan 14th

All Island Forum on Cancer Data

Bernal Institute, UL

5th-7th March

IACR 2025

Europe Hotel Belfast, Belfast, NI

13th July - 18th July 2025

39th International Workshop on Statistical Modelling (IWSM)

Limerick City

Cancer Research Survey Lero are conducting a study titled “Exploring the Potential for Digital Tools to Support Cancer Care” to better understand the needs of cancer patients and survivors in Ireland.

The insights gathered will guide the development of patient-centred digital tools to improve their care experience. Key details of the survey are as follows

Key Details: Who can participate: Cancer patients and survivors in Ireland.

Time required: Approximately 10 minutes.

Ethics approval: Approved by the University of Galway Ethics Committee (REF Number 2024.10.013).

Where: Click here or follow the link: https://forms.office.com/e/GpicH1tfeV Please support this survey so a diverse range of opinions can be heard

New Staff Member Tricia English joined the LDCRC in April 2024 as the new Senior Administrator. Tricia’s previous administration experience was within the finance and medical sector and spend 5.5 years working in various departments in Blackrock Clinic. Tricia can be contacted on ldcrc@ul.ie or tricia.english@ul.ie for any LDCRC queries.

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NOVEMBER IS LUNG AND PROSTATE CANCER AWARENESS MONTH On 30th October 2024, a €4.9 million partnership was announced between RCSI Cancer Centre and the Irish Cancer Society to tackle lung cancer. Further details on the pilot programme can be found here

There is almost 4000 cases of prostate cancer diagnosed in Ireland each year with one in six men diagnosed in their lifetime. A new treatment for prostate cancer was successfully performed in the Beacon last month by November 2024 by Mr Mohammud Shakeel Inder and further details can be found here

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MILLIN LECTURE 2024 On 8th November 2024, as part of the prestigious 47th Millin Lecture, Ms Christina Fleming FRCSI, Consultant General and Colorectal Surgeon at University of Limerick Hospital Group gave a lecture on the integration of new technologies in surgical training. The full lecture can be watched here

Professor Deborah McNamara RCSI President and Ms. Christina Fleming from UHL

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10X Genomics Spotlight

The 10x genomics portfolio is based on three synergistic technologies; 1) Chromium Single Cell 2) Visium Spatial 3) Xenium In-Situ.

Our single cell technologies support multiomic read outs from fresh, frozen and fixed sources and allow for both an RT and probe based read out that support different levels of scale, from a few hundred to several million cells. GEM-X is our newest single cell chemistry boasting the highest sensitivity and data quality on the market, that is fully multiomic enabled and compatible with cell fixation. Our single cell Flex probe-based approaches offer huge scale at low cost, is multiomic compatible and allows for chop fixed tissue, FFPE tissues and whole blood fixation solutions.

When it comes to 10x spatial offerings, we have taken complementary and parallel paths in the development of class leading spatial tools. Which tool to use is largely dependent on two factors - the type information you want to gain from the experiment and 2) your prior knowledge of their research/disease system.

- Visium HD (high definition) is class leading tool for unbiased discovery of whole tissue sections. It provides whole transcriptome data at single cell scale resolution that generates comprehensive gene expression insights and uncovers novel gene signatures.

- Xenium is a state of the art spatial imagining platform that provides targeted gene and protein expression with exquisite single cell resolution across whole tissue sections. The platform can assign individual transcripts to cells by leveraging inline cell segmentation with 10’s of nm precision. This provides true single cell spatial profiling with the highest per gene sensitivity.

At 10x we love to consult with our users on experimental design so please do not hesitate to reach out to our experts at marcus.levitt@10xgenomics.com 27

To avail of LDCRC benefits, including LDCRC funding, please join the LDCRC. LDCRC offers multiple membership levels including - Full or affiliate membership for academic and clinical cancer researchers Staff, students or postdocs who are members of LDCRC member labs Community PPI members industry To become a member, please fill in this application form or email us on ldcrc@ul.ie if you have any queries. Our website can be found if you scan the QR Code.

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Contributions are welcome for future newsletters and we will be aiming towards more frequent publications. If you wish to add your cancer research publication, event or research highlights in our newsletter please email ldcrc@ul.ie

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