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Dr. Mark Bates
Research Fellow, Histopathology

Biography

Dr Mark Bates graduated at the top of his class, with a first-class honours degree (BSc Ord) in Biosciences awarded by the Dublin Institute of technology (DIT). Dr Bates gained a further bachelor's degree (BSc Hons) in biomolecular science in 2012 from DIT and completed a PhD with the department of histopathology at Trinity College Dublin (TCD), awarded November 2016.

Since completing his PhD, Dr Bates continued working with TCD with the department of Obstetrics and Gynaecology as a Research Assistant and was involved in a study examining the role of Tissue Factor in the transition from endometriosis into clear cell ovarian cancer using Laser Capture Microdissection and has been involved in a number of collaborations with both the Royal College of Surgeons in Ireland and the Middlesex University of London. Dr Bates was extensively involved in management of the Discovary Biobank at TCD during this post.

Following completion of this post in February 2017, Dr Bates joined the Discipline of Radiation Therapy at TCD as a postdoctoral fellow as part of an SFI funded TIDA award under the direction of Dr Laure Marignol and Dr Adriele Prina Mello. Dr Bates project involved assessing the role of a novel protein biomarker as a companion diagnostic test for radiotherapy prostate cancer patients (CASPAR). A large component of this project also involved exploring the potential to patent and commercialise the CASPAR test, as a diagnostic test and included a 5-day intensive course in Entrepreneurship and Innovation; the SFI Spark Pre-Accelerator programme.

In 2018 Mark joined Dr Margaret Dunne's lab at the Department of Surgery at the Trinity Translational Medicine Institute (TTMI) as part of an 18-month Health Research Board-funded postdoctoral research position. The project involved a 12-month training secondment to Dr Peter Caie's Quantitative and Digital Pathology lab at the University of St Andrews, Scotland, and the remaining 6 months were spent in Dr Dunne's lab at the Trinity Translational Medicine Institute. The goal of this study was to investigate whether various tumour-scoring methods could predict patient clinical outcomes such as response to chemoradiotherapy regimens in oesophageal cancer. This project examined the prognostic value of various immune markers (CD3, CD8, FOXP3, HLA-DR, CD68, CD163, PD1, PDL1), vasculature markers (D240, CD105) and markers associated with inflammation, proliferation and metabolism (CRP, Ki67, ATP5B, PKM, 8OXODG) in combination with pathological indicators such as tumour budding, poorly differentiated clusters, percentage tumour stroma and lymphovascular invasion and density. These markers were assessed using state of the art digital and quantitative pathology. Circulating biomarkers in pre and post treatment serum samples from an overlapping cohort were assessed with the support of an IACR seed funding award in order to create a personalised multi-omics data set for each analysed patient.

Dr Mark Bates rejoined the department of Histopathology in August 2019 for and SFI Industry fellowship position in collaboration with industry partner Becton Dickinson (BD). The project entitled Characterising the proteogenome of Circulating Tumour Cells [CTCs] aims to utilised state of the art technologies including a BD Melody/FOCUS cell sorted, scRNAseq and Abseq technology to identify the unique molecular signature of CTCs and CTC clusters in breast cancer patients.

Publications and Further Research Outputs

Peer-Reviewed Publications

McShane R, Arya S, Stewart AJ, Caie P, Bates M., Prognostic features of the tumour microenvironment in oesophageal adenocarcinoma., Biochim Biophys Acta Rev Cancer, 2021, p188598 Journal Article, 2021 DOI

Ward, M.P., Kane, L.E., Norris, L.A et al. , Platelets, immune cells and the coagulation cascade; friend or foe of the circulating tumour cell?, Molecular Cancer, 20, 2021, p59- Journal Article, 2021 DOI

White, Christine M., Bakhiet, Salih, Bates, Mark, Ruttle, Carmel, Pilkington, Loretto J., Keegan, Helen, O"Toole, Sharon A., Sharp, Linda, O"Kelly, Ruth, Tewari, Prerna, Flannelly, Grainne, Martin, Cara M., O"Leary, John J., Exposure to tobacco smoke measured by urinary nicotine metabolites increases risk of p16/Ki-67 co-expression and high-grade cervical neoplasia in HPV positive women: A two year prospective study, Cancer Epidemiology, 68, 2020, p101793 Journal Article, 2020 DOI

Bates Mar, Furlong Fion, Gallagher Michael F, Spillane Cathy D, McCann Amand, O'Toole Sharo, O'Leary John J, Too MAD or not MAD enough: The duplicitous role of the spindle assembly checkpoint protein MAD2 in cancer, 469, 2020, p11 - 21 Journal Article, 2020 URL DOI

Bates M, Spillane CD, Gallagher MF, McCann A, Martin C, Blackshields G, Keegan H, Gubbins L, Brooks R, Brooks D, Selemidis S, O'Toole S, O'Leary JJ., The role of the MAD2-TLR4-MyD88 axis in paclitaxel resistance in ovarian cancer., PloS one, 15, (12), 2020, pe0243715 Journal Article, 2020 DOI

Kalachand RD, O'Riain C, Toomey S, Carr A, Timms KM, O'Toole S, Madden S, Bates M, O'Leary JJ, Gleeson N, O'Donnell D, Grogan L, Breathnach O, Farrelly A, Stordal B, Hennessy BT., Prevalence of tumor BRCA1 and BRCA2 dysfunction in unselected patients with ovarian cancer., Obstetrics & gynecology science, 63, (5), 2020, p643-654 Journal Article, 2020 DOI

Bates, Mark, Boland, Anna, McDermott, Niamh, Marignol, Laure, YB-1: The key to personalised prostate cancer management?, Cancer Letters, 2020 Journal Article, 2020 DOI

Annett Stephani, Moore Gillia, Short Am, Marshall Andre, McCrudden Cia, Yakkundi Anit, Das Sudipt, McCluggage W Glen, Nelson Laur, Harley Ia, Moustafa Nermee, Kennedy Catherine , deFazio Ann, Brand Aliso, Sharma Raghw, Brennan Dona, O†Toole Sharo, O†Leary Joh, Bates Mar, O†Riain Ciará, O†Connor Darra, Furlong Fion, McCarthy Hele, Kissenpfennig Adrie, McClements Lan, Robson Trac, FKBPL-based peptide, ALM201, targets angiogenesis and cancer stem cells in ovarian cancer, 2019 Journal Article, 2019 DOI URL

S Inder, M Bates, N Ni Labhrai, N McDermott, J Schneider, G Erdmann, T Jamerson, AN Flores, A Prina-Mello, P Thirion, PR Manecksha, D Cormican, S Finn, T Lynch, L Marignol, Multiplex profiling identifies clinically relevant signalling proteins in an isogenic prostate cancer model of radioresistance, Scientific Reports, 9, 2019, p1 - 12 Journal Article, 2019 DOI TARA - Full Text

Ffrench B, Gasch, Hokamp K, Spillane C, Blackshields G, Mahgoub TM, Bates M, Kehoe L, Mooney A, Doyle R, Doyle B, O'Donnell D, Gleeson N, Hennessy BT, Stordal B, O'Riain C, Lambkin H, O'Toole S, O'Leary JJ, and Gallagher MF., CD10-/ALDH- cells are the sole cisplatin-resistant component of a novel ovarian cancer stem cell network. Cell Death & Disease , Cell Death and Disease, 8, (10), 2017, e3128 Journal Article, 2017 TARA - Full Text

Sulaiman, G, Cooke A, Ffrench B, Gasch C, Abdullai OA, O'Connor K, Elbaruni S, Blacksheilds G, Spillane C, Keegan H, McEneaney V, Knittel R, Rogers A, Jeffery IB, Doyle B, Bates M, d'Adhemar C, Lee M, Campbell EL, Moynagh P, Higgins DG, O'Toole S, O'Neill L, O'Leary JJ and Gallagher MF. , MyD88 is an essential component of retinoic acid induced differentiation in human pluripotent embryonal carcinoma cells. , Cell Death & Differentiation , 24, (11), 2017, p1975 - 1986 Journal Article, 2017

White C, Bakhiet S, Bates M, Keegan H, Pilkington L, Ruttle C, Sharp L, O' Toole S, Fitzpatrick M, Flannelly G, O' Leary JJ, Martin CM. , Triage of LSIL/ASC-US with p16/Ki-67 dual staining and human papillomavirus testing: a 2-year prospective study. , Cytopathology, 27, (4), 2016, p269 - 276 Journal Article, 2016 DOI

d'Adhemar CJ, Spillane CD, Gallagher MF, Bates M, Costello KM, Barry-O'Crowley J, Haley K, Kernan N, Murphy C, Smyth PC, O'Byrne K, Pennington S, Cooke AA, Ffrench B, Martin CM, O'Donnell D, Hennessy B, Stordal B, Finn S, McCann A, Gleeson N, D'Arcy T, Flood B, O'Neill LA, Sheils O, O'Toole S, O'Leary JJ, The MyD88+ phenotype is an adverse prognostic factor in epithelial ovarian cancer., PloS one, 9, (6), 2014, pe100816 Journal Article, 2014 DOI TARA - Full Text

Non-Peer-Reviewed Publications

M Bates; D Costigan; C D Spillane; M F Gallagher; A McCann; J Barry-O'Crowley; C O'Riain; S O'Toole; J J O'Leary, The Role of the TLR4 Pathway and the Spindle Assembly Checkpoint in Ovarian Cancer Prognosis, Journal of Pathology, 237, 2015, ppS1-S52 Conference Paper, 2015

M Bates; D Costigan; C D Spillane; M F Gallagher; A McCann; J Barry-O'Crowley; C O'Riain; S O'Toole; J J O'Leary, The Role of MAD2 and MyD88 as Prognostic Indicators in Ovarian Cancer, Journal of Pathology, (237), 2015, ppS1-S52 Conference Paper, 2015

Research Expertise

Projects

  • Title
    • Development of a Companion diAgnostic teSt for radiotheraPy prostAte canceR patients (CASPAR)
  • Summary
    • There is an unmet need to develop companion diagnostic tests that can guide prostate cancer patients and their clinicians through the treatment decision process. This project is examining the role of a novel protein biomarker for its prognostic and therapeutic potential in high-risk radiotherapy prostate cancer patients. The long-term focus of CASPAR is to develop a novel companion diagnostic test and therapeutic combination that can allow personalized prescription of radiotherapy for these patients.
  • Funding Agency
    • SFI
  • Date From
    • March 2017
  • Date To
    • March 2018
  • Title
    • Assessment of the predictive value of immune and histological parameters in oesophageal adenocarcinoma using digital pathology
  • Summary
    • The goal of this study is to determine whether various tumour-scoring methods can predict patient clinical outcomes in OAC, such as response to neo-CRT treatment. The Immunoscore method involves measurement of immune markers (CD3, CD8, and CD45RO) in tumours and has shown superior predictive value to current UICC/TNM staging systems in colorectal cancer. We intend to assess the prognostic value of the traditional Immunoscore in OAC, and also in combination with expression of another immune marker, HLA-DR, which we have previously shown to have significant prognostic potential. Other tumour characteristics such as tumour budding, poorly differentiated clusters, percentage tumour stroma and lymphovascular invasion and density, which have shown promise as prognostic markers in other cancer types, will also be assessed in the novel context of OAC, for their ability to predict patient outcomes. Digital pathology methodology will be employed to standardise our measurements and minimise variability. Circulating markers of inflammation will also be measured in matched OAC patient serum, and levels will be correlated with tumour microenvironment scores. We aim to develop standardised methods of reliably measuring tumour and immune characteristics of potential prognostic value in OAC, which may be adopted for routine use in hospitals. As well as its timely clinical relevance, this project will yield plentiful data on the role of the immune system in cancer, and the factors required for successful tumour eradication
  • Funding Agency
    • Health Research Board
  • Date From
    • 01/03/18
  • Date To
    • 01/09/18
  • Title
    • Characterising the proteogenome of Circulating Tumour Cells [CTCs]
  • Summary
    • This project aims to utilise state of the art technologies including a BD Melody/FOCUS cell sorted, scRNAseq and Abseq technology to identify the unique molecular signature of CTCs and CTC clusters in both breast and ovarian cancer patients
  • Funding Agency
    • SFI
  • Date From
    • 01/08/2019
  • Date To
    • 01/08/2020

Keywords

Biomarkers; CANCER IMMUNOLOGY; CERVICAL CANCER; CHEMORESISTANCE; Circulating Tumour Cells; DIGITAL PATHOLOGY; EPIFLUORESCENCE MICROSCOPY; FLUORESCENCE; IMMUNOFLUORESCENCE; Liquid Biopsy; MULTIPLEX IMMUNOFLUORESCENCE; OESOPHAGEAL ADENOCARCINOMA; OESOPHAGEAL CANCER; ORGANISED CERVICAL CANCER SCREENING; Ovarian Cancer; Predictive Biomarkers; PROSTATE CANCER; radioresistance; SENESCENCE; WHOLE SLIDE SCANNING

Recognition

Awards and Honours

Characterising the proteogenome of Circulating Tumour Cells [CTCs] 2019-2020

DIT Lab Tech Supplies Prize 20/11/2011

IACR AOIFA seed funding award 26/2/2018

ICS Translational Summer Studentship 2021

Memberships

Member of INNOVATION- the Irish National Network for Ovarian Cancer Collaboration. 13/04/2015

TTMI Postdoctoral Representative for the Trinity St James's Cancer Institute Research Development Group 19/05/19

Member of the Irish Association for Cancer Research (IACR) 23/09/2018

Member of the European Association for Cancer Research (EACR) 04/10/2018

Member of the Trinity Research Staff Association committee 25/11/2019

TTMI social committee 21/10/2019