Dr David Skerrett-Byrne

Dr David Skerrett-Byrne

Postdoctoral Research Fellow

School of Environmental and Life Sciences

Career Summary

Biography

Research Focus

My research interests and expertise lie in the application of ever-evolving proteomic and phosphoproteomic technologies and bioinformatics to gain novel insights into complex diseases. My academic and research experience began with a Bachelor of Science (Hons) in Biochemistry and Molecular Biology at University College Dublin, Ireland with a strong focus on mass spectrometry, which sparked my fascination with these technologies and the dynamic diversity of proteomics. I continued my pursuit with a Master of Science in Biotechnology at Ulster University focusing on the role of epigenetics and downstream protein function. Ultimately, this led to a scholarship to undertake a PhD at The University of Newcastle, Australia, under the tutelage of Dr Matt Dun and Professor Phil Hansbro. This was a hugely formative experience and where my passion for mass spectrometry based proteomics exploded. Under the guidance of Dr. Dun, I was instrumental in establishing an advanced proteomics platform at The University of Newcastle, allowing us to apply our expertise to several Priority Research Centres at the University of Newcastle (e.g. Reproductive Science, Cancer Biology, Respiratory), evidenced in high impact publications in field-leading international journals including Molecular & Cellular Proteomics and Leukemia.

Currently I am a Postdoctoral Research Fellow in the Priority Research Centre for Reproductive Sciences under the supervision of Professor Brett Nixon. We are utilising the latest developments in proteomics and bioinformatics, predominately to dissect male gamete development and function, but also with our collaborators, to understand oocyte and ovarian biology. 

Research Esteem

Since starting my Postdoctoral position I have presented my research at two prestigious conferences, The 26th Society for Reproductive Biology Annual Scientific Meeting and The 18th Human Proteome Organization World Congress, receiving a Society for Reproductive Biology ‘Award for Excellence’ for best ECR poster presentation and aAustralasian Proteomics Society Early Career Researcher Travel Award, respectively.

During my PhD I have participated in twelve national and one international conference, including four oral presentations. I have presented my research at several prestigious international institutions including the University of Southern Denmark (Prof. Martin Larsen), Technische Universität München (Prof. Bernhard Kuster), Max Planck Institute für Biochemie (Prof. Matthias Mann), ETH Zürich (Dr. Ben Collins), and University College Dublin (Prof. Stephen Pennington), all made possible through a highly competitive travel grant.

Contribution to the field of research:

Closer to home, I have been able to make important contributions to the medical research community as convenor for the Australian Society for Medical Research Newcastle meeting in 2016-2017, raising >$35,000 to promote the research standing of the Hunter Region. Also, I acted as Sponsorship Liaison for ASMR in 2015-2016, raising >$15,000 in trade displays, and organised the first Newcastle ASMR Science in the Cinema, sparking a dialogue between experts in cancer biology and the general public.

Teaching, Supervision and Mentoring

To promote the use of proteomics at the university I founded the University of Newcastle Proteomics Journal Club. I successfully secured $2,000 of funding over two years for the club which gave us a platform to bring together researchers across faculties and schools at the university, to critically discuss recently published papers, keep up-to-date with the latest techniques and also host workshops on mass spectrometer technology and analysis software such as Proteome Discoverer, MaxQuant, and Perseus.

I have also been fortunate to contribute back to the young researchers of the future by supervising a number of third year and summer scholarship students to successful completion. In Prof Nixon’s research lab, I have been working closely along aside a number of PhD students to assist in developing and carrying out their projects. I have also developed and taught bioinformatical tutorials to undergraduate Biomedical Sciences students (HUBS3302), as well as teaching labs throughout the Biomedical Sciences undergraduate program.

Professional Memberships

  • 2019 – Present: Society for Reproductive Biology
  • 2019 – Present: The Australasian Proteomics Society
  • 2017 – Present: The Human Proteome Organization
  • 2017 – 2019: President of the UoN Proteomics Journal Club
  • 2014 – 2018: The Australian Society for Medical Research (ASMR)


Qualifications

  • Doctor of Philosophy, University of Newcastle
  • Bachelor of Science (Honours), University of Dublin - Ireland
  • Master of Science in Biotechnology, University of Ulster

Keywords

  • Biochemistry
  • COPD
  • Cancer
  • Mass Spectrometry
  • Phosphoproteomics
  • Proteomics
  • Reproductive Biology

Languages

  • German (Working)
  • English (Mother)

Fields of Research

Code Description Percentage
060102 Bioinformatics 20
110106 Medical Biochemistry: Proteins and Peptides (incl. Medical Proteomics) 30
111499 Paediatrics and Reproductive Medicine not elsewhere classified 50

Professional Experience

UON Appointment

Title Organisation / Department
Postdoctoral Research Fellow University of Newcastle
School of Environmental and Life Sciences
Australia

Teaching appointment

Dates Title Organisation / Department
24/07/2015 - 25/07/2019 Casual Academic School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle
Australia

Awards

Award

Year Award
2019 Australasian Proteomics Society ECR Travel Award
Australasian Proteomics Society
2017 Hunter Cancer Research Alliance Conference Student Sponsorship
Hunter Cancer Research Alliance (HCRA)
2017 Australian Society for Medical Research National Conference Student Travel Award
Australian Society for Medical Research (ASMR)
2017 Jennie Thomas Medical Research Travel Grant
Hunter Medical Research Institute (HMRI)

Research Award

Year Award
2019 Centre for Reproductive Health, Hudson Institute of Medical Research Award for Excellence for best ECR poster presentation
Society for Reproductive Biology

Teaching

Code Course Role Duration
HUBS2206 Human Biochemistry and Cell Biology
School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle
This course provides students with knowledge and understanding of the structure and function of the cells with an emphasis on molecular aspects. It involves integrated learning between the areas of Biochemistry and Molecular Biology. Practical sessions develop core skills that prepare students for a career in laboratory-based research in the biomedical sciences.
Casual Academic 22/02/2016 - 31/12/2017
HUBS3302 Bioinformatics and Functional genomics
School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle
The completion of the Human Genome project has resulted in an explosion of molecular information, with the corresponding development of high throughput techniques for sequencing DNA / proteins and looking at their expression profiles in different physiological and pathological situations. New computational tools for seeking, storing and analysing this information have also been developed. The challenge is to use the information stored in databases to solve biological problems and to inform hypothesis generation and future experiments. This course will focus on functional genomics and how to search and use the information using bioinformatics
Casual Lecturer 9/05/2019 - 26/07/2019
HUBS1202 Human Genomics and Biomolecular Analysis
School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle
This course represents a blend between fundamental concepts and current issues in molecular medicine. The course focuses on the relationships between structure, function and analysis of Proteins and Nucleic Acids as applied to human disease and provides an introduction to modern concepts of Genomic structure, function and analysis arising from the Human Genome project.
Casual Academic 20/07/2015 - 31/08/2017
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Journal article (5 outputs)

Year Citation Altmetrics Link
2019 Nixon B, De Iuliis GN, Hart HM, Zhou W, Mathe A, Bernstein IR, et al., 'Proteomic profiling of mouse epididymosomes reveals their contributions to post-testicular sperm maturation', Molecular and Cellular Proteomics, 18 S91-S108 (2019) [C1]
DOI 10.1074/mcp.RA118.000946
Citations Scopus - 7Web of Science - 11
Co-authors Brett Nixon, Muhammad Jamaluddin, David Skerrett-Byrne, Matt Dun, Geoffry DeiuliIs, Elizabeth Bromfield, Andrea Johns
2019 Nixon B, Johnston SD, Skerrett-Byrne DA, Anderson AL, Stanger SJ, Bromfield EG, et al., 'Modification of Crocodile Spermatozoa Refutes the Tenet That Post-testicular Sperm Maturation Is Restricted To Mammals', MOLECULAR & CELLULAR PROTEOMICS, 18 S59-S76 (2019) [C1]
DOI 10.1074/mcp.RA118.000904
Citations Scopus - 1Web of Science - 2
Co-authors Philip Hansbro, Jacinta Martin, Brett Nixon, Matt Dun, David Skerrett-Byrne, Elizabeth Bromfield
2018 Jamaluddin MFB, Ko YA, Kumar M, Brown Y, Bajwa P, Nagendra PB, et al., 'Proteomic profiling of human uterine fibroids reveals upregulation of the extracellular matrix protein periostin', Endocrinology, 159 1106-1118 (2018) [C1]

Copyright © 2018 Endocrine Society The central characteristic of uterine fibroids is excessive deposition of extracellular matrix (ECM), which contributes to fibroid growth and bu... [more]

Copyright © 2018 Endocrine Society The central characteristic of uterine fibroids is excessive deposition of extracellular matrix (ECM), which contributes to fibroid growth and bulk-type symptoms. Despite this, very little is known about patterns of ECM protein expression in fibroids and whether these are influenced by the most common genetic anomalies, which relate to MED12. We performed extensive genetic and proteomic analyses of clinically annotated fibroids and adjacent normal myometrium to identify the composition and expression patterns of ECM proteins in MED12 mutation-positive and mutation-negative uterine fibroids. Genetic sequencing of tissue samples revealed MED12 alterations in 39 of 65 fibroids (60%) from 14 patients. Using isobaric tagged-based quantitative mass spectrometry on three selected patients (n = 9 fibroids), we observed a common set of upregulated (.1.5-fold) and downregulated (,0.66-fold) proteins in small, medium, and large fibroid samples of annotated MED12 status. These two sets of upregulated and downregulated proteins were the same in all patients, regardless of variations in fibroid size and MED12 status. We then focused on one of the significant upregulated ECM proteins and confirmed the differential expression of periostin using western blotting and immunohistochemical analysis. Our study defined the proteome of uterine fibroids and identified that increased ECM protein expression, in particular periostin, is a hallmark of uterine fibroids regardless of MED12 mutation status. This study sets the foundation for further investigations to analyze the mechanisms regulating ECM overexpression and the functional role of upregulated ECM proteins in leiomyogenesis.

DOI 10.1210/en.2017-03018
Citations Scopus - 5Web of Science - 4
Co-authors Matt Dun, Muhammad Jamaluddin, Rodney Scott, Hubert Hondermarck, Mark Baker, Manishkumar Jhamb, Pradeep Tanwar, David Skerrett-Byrne
2018 Degryse S, de Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, et al., 'Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia (vol 32, pg 788, 2018)', LEUKEMIA, 32 2731-2731 (2018)
DOI 10.1038/s41375-018-0241-7
Co-authors Matt Dun, David Skerrett-Byrne, Nikki Verrills
2018 Degryse S, De Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, et al., 'Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia', Leukemia, 32 788-800 (2018) [C1]

© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Mutations in the interleukin-7 receptor (IL7R) or the Janus kinase 3 (JAK3) kinase occur frequen... [more]

© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Mutations in the interleukin-7 receptor (IL7R) or the Janus kinase 3 (JAK3) kinase occur frequently in T-cell acute lymphoblastic leukemia (T-ALL) and both are able to drive cellular transformation and the development of T-ALL in mouse models. However, the signal transduction pathways downstream of JAK3 mutations remain poorly characterized. Here we describe the phosphoproteome downstream of the JAK3(L857Q)/(M511I) activating mutations in transformed Ba/F3 lymphocyte cells. Signaling pathways regulated by JAK3 mutants were assessed following acute inhibition of JAK1/JAK3 using the JAK kinase inhibitors ruxolitinib or tofacitinib. Comprehensive network interrogation using the phosphoproteomic signatures identified significant changes in pathways regulating cell cycle, translation initiation, mitogen-activated protein kinase and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signaling, RNA metabolism, as well as epigenetic and apoptotic processes. Key regulatory proteins within pathways that showed altered phosphorylation following JAK inhibition were targeted using selumetinib and trametinib (MEK), buparlisib (PI3K) and ABT-199 (BCL2), and found to be synergistic in combination with JAK kinase inhibitors in primary T-ALL samples harboring JAK3 mutations. These data provide the first detailed molecular characterization of the downstream signaling pathways regulated by JAK3 mutations and provide further understanding into the oncogenic processes regulated by constitutive kinase activation aiding in the development of improved combinatorial treatment regimens.

DOI 10.1038/leu.2017.276
Citations Scopus - 17Web of Science - 12
Co-authors Nikki Verrills, David Skerrett-Byrne, Matt Dun
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Conference (3 outputs)

Year Citation Altmetrics Link
2019 Duchatel RJ, Jackson ER, Staudt D, Skerrett-Byrne DA, Jamaluddin MFB, Germon Z, et al., 'Keynote Speakers', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2019)
DOI 10.1111/ajco.13253
Co-authors David Skerrett-Byrne, Matt Dun
2018 Mclachlan T, Murray H, Skerrett-Byrne D, Dubois O, Withers K, Verrills N, Dun M, 'Molecular Characterization of Treatment Resistance in FLT3 Mutant Pediatric Acute Myeloid Leukemia', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2018)
Co-authors Nikki Verrills, Matt Dun, David Skerrett-Byrne
2016 Sillar J, Murray H, Al Mazi J, Skerrett-Byrne D, Kahl R, Flanagan H, et al., 'QUANTITATIVE, HIGH-RESOLUTION PROTEOMICS FOR A SYSTEMS BIOLOGICAL ANALYSIS OF ACUTE MYELOID LEUKEMIA', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2016)
Co-authors Matt Dun, David Skerrett-Byrne, Hubert Hondermarck
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Grants and Funding

Summary

Number of grants 2
Total funding $3,681

Click on a grant title below to expand the full details for that specific grant.


20191 grants / $300

Australasian Proteomics Society ECR Travel Award$300

Funding body: Australasian Proteomics Society

Funding body Australasian Proteomics Society
Project Team

Professor Brett Nixon

Scheme The Human Proteome Organisation Congress 2019 Awards
Role Lead
Funding Start 2019
Funding Finish 2019
GNo
Type Of Funding Not Known
Category UNKN
UON N

20171 grants / $3,381

Jennie Thomas Medical Research Travel Grant$3,381

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor David Skerrett-Byrne, Professor Phil Hansbro, Doctor Matt Dun
Scheme Jennie Thomas Medical Research Travel Grant
Role Lead
Funding Start 2017
Funding Finish 2017
GNo G1701070
Type Of Funding C3120 - Aust Philanthropy
Category 3120
UON Y
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Dr David Skerrett-Byrne

Position

Postdoctoral Research Fellow
School of Environmental and Life Sciences
Faculty of Science

Contact Details

Email david.skerrett-byrne@newcastle.edu.au
Phone (02) 4921 6267

Office

Room LS4.39
Building Life Sciences
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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