Dr David Skerrett-Byrne
Postdoctoral Research Fellow
School of Environmental and Life Sciences
- Email:david.skerrett-byrne@newcastle.edu.au
- Phone:(02) 4921 6214
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)
Professional Experience
UON Appointment
| Title | Organisation / Department |
|---|
Teaching appointment
| Dates | Title | Organisation / Department |
|---|---|---|
| 24/7/2015 - 25/7/2019 | 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 |
Jennie Thomas Medical Research Travel Grant Hunter Medical Research Institute (HMRI) |
| 2017 |
Australian Society for Medical Research National Conference Student Travel Award Australian Society for Medical Research (ASMR) |
| 2017 |
Hunter Cancer Research Alliance Conference Student Sponsorship Hunter Cancer Research Alliance (HCRA) |
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 | 22/2/2016 - 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 | 9/5/2019 - 26/7/2019 |
| 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 | 20/7/2015 - 31/8/2017 |
Publications
For publications that are currently unpublished or in-press, details are shown in italics.
Journal article (13 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2020 |
Liu G, Baird AW, Parsons MJ, Fan K, Skerrett-Byrne DA, Nair PM, et al., 'Platelet activating factor receptor acts to limit colitis-induced liver inflammation', FASEB JOURNAL, 34 7718-7732 (2020) [C1]
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| 2020 |
Nixon B, Cafe SL, Eamens AL, De Iuliis GN, Bromfield EG, Martin JH, et al., 'Molecular insights into the divergence and diversity of post-testicular maturation strategies', Molecular and Cellular Endocrinology, 517 110955-110955 (2020) [C1]
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| 2020 |
Griffin RA, Swegen A, Baker M, Aitken RJ, Skerrett-Byrne DA, Rodriguez AS, et al., 'Mass spectrometry reveals distinct proteomic profiles in high- And low-quality stallion spermatozoa', Reproduction, 160 695-707 (2020) [C1] © 2020 Society for Reproduction and Fertility The horse breeding industry relies upon optimal stallion fertility. Conventional sperm assessments provide limited information regard... [more] © 2020 Society for Reproduction and Fertility The horse breeding industry relies upon optimal stallion fertility. Conventional sperm assessments provide limited information regarding ejaculate quality and are not individually predictive of fertilizing potential. The aim of this study was to harness mass spectrometry to compare the proteomic profiles of high- and low-quality stallion spermatozoa, with the ultimate goal of identifying fertility biomarker candidates. Extended stallion semen (n = 12) was fractionated using Percoll density gradients to isolate low-quality and high-quality sperm populations. Motility and morphological assessments were carried out, and proteomic analyses was conducted using UHPLC-MS/MS. High-quality spermatozoa recorded higher total (95.2 ± 0.52% vs 70.6 ± 4.20%; P = 0.001) and progressive motilities (43.4 ± 3.42% vs 27.3 ± 4.32%; P = 0.05), and a higher proportion of morphologically normal cells (50.2 ± 4.34% vs 38.8 ± 2.72%; P = 0.05). In total, 1069 proteins were quantified by UHPLC-MS/MS, of which 22 proteins were significantly more abundant in the high-quality sperm population (P = 0.05). A-kinase anchor protein 4 (AKAP4) and Hexokinase 1 (HK1) were considered possible biomarker candidates and their differential expression was confirmed by immunoblot. Protein expression was significantly correlated with total (AKAP4 R2 = 0.38, P = 0.01; HK1 R2 = 0.46, P = 0.001) and progressive motilities (AKAP4 R2 = 0.51, P = 0.001; HK1 R2 = 0.55, P = 0.01), percentage rapid (AKAP4 R2 = 0.29, P = 0.05; HK1 R2 = 0.58, P = 0.001), straight-line velocity (HK1 R2 = 0.50, P = 0.01) and straightness (HK1 R2 = 0.40, P = 0.01). Furthermore, AKAP4 was highly susceptible to adduction by 4-hydroxynonenal (4HNE), which resulted in a global reduction in the phosphorylation profiles following capacitation. In conclusion, the proteomic profiles of high- and low-quality stallion spermatozoa differ substantially, and proteins such as AKAP4 and HK1 could serve as biomarkers of ejaculate quality.
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| 2020 |
Tamessar CT, Trigg NA, Nixon B, Skerrett-Byrne DA, Sharkey DJ, Robertson SA, et al., 'Roles of male reproductive tract extracellular vesicles in reproduction', AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, (2020) [C1]
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| 2020 |
Murray HC, Enjeti AK, Kahl RGS, Flanagan HM, Sillar J, Skerrett-Byrne DA, et al., 'Quantitative phosphoproteomics uncovers synergy between DNA-PK and FLT3 inhibitors in acute myeloid leukaemia.', Leukemia, (2020)
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| 2020 |
Dun MD, Mannan A, Rigby CJ, Butler S, Toop HD, Beck D, et al., 'Shwachman Bodian Diamond syndrome (SBDS) protein is a direct inhibitor of protein phosphatase 2A (PP2A) activity and overexpressed in acute myeloid leukaemia', Leukemia, 34 3393-3397 (2020) [C1]
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| 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]
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| 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]
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| 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.', Mol Cell Proteomics, 18 Suppl 1 S58-S76 (2019)
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| 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.', Mol Cell Proteomics, 18 Suppl 1 S91-S108 (2019)
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| 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.
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| 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.
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Conference (6 outputs)
| Year | Citation | Altmetrics | Link | |||||
|---|---|---|---|---|---|---|---|---|
| 2020 |
Jackson ER, Duchatel RJ, Mannan A, Douglas A, Skerrett-Byrne DA, Smith N, et al., 'Panelist Invited Speakers', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2020)
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| 2020 |
Duchatel RJ, Jackson ER, Mannan A, Staudt D, Skerrett-Byrne DA, Nixon B, et al., 'Targeting phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) and protein kinase C (PKC) activation in diffuse midline glioma (DMG)', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2020)
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| 2020 |
Duchatel RJ, Mannan A, Jackson ER, Staudt D, Skerrett-Byrne DA, Jamaluddin MFB, et al., 'PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE (PI3K) INHIBITION DRIVES PROTEIN KINASE C ACTIVATION (PKC) IN DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)', NEURO-ONCOLOGY (2020)
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Grants and Funding
Summary
| Number of grants | 5 |
|---|---|
| Total funding | $22,982 |
Click on a grant title below to expand the full details for that specific grant.
20203 grants / $19,301
Mapping changes in cerebrospinal fluid composition after stroke to identify novel therapeutic targets for future drug discovery.$12,162
Funding body: John Hunter Hospital Charitable Trust
| Funding body | John Hunter Hospital Charitable Trust |
|---|---|
| Project Team | Doctor Kirsten Coupland, Professor Neil Spratt, Doctor David Skerrett-Byrne |
| Scheme | Research Grant |
| Role | Investigator |
| Funding Start | 2020 |
| Funding Finish | 2020 |
| GNo | G2000282 |
| Type Of Funding | C3112 - Aust Not for profit |
| Category | 3112 |
| UON | Y |
Priority Research Centre for Drug Development Equipment Grant$5,139
Funding body: Priority Research Centre for Drug Ddevelopment
| Funding body | Priority Research Centre for Drug Ddevelopment |
|---|---|
| Project Team | Dr David Skerrett-Byrne; CI: Dr Shaun Roman |
| Scheme | Equipment Grant |
| Role | Investigator |
| Funding Start | 2020 |
| Funding Finish | 2020 |
| GNo | |
| Type Of Funding | Internal |
| Category | INTE |
| UON | N |
Faculty Output Accelerator Initiative$2,000
Funding body: Faculty of Science | University of Newcastle
| Funding body | Faculty of Science | University of Newcastle |
|---|---|
| Project Team | Dr David Skerrett-Byrne ; Prof Brett Nixon |
| Scheme | Faculty Output Accelerator Initiative |
| Role | Lead |
| Funding Start | 2020 |
| Funding Finish | 2020 |
| GNo | |
| Type Of Funding | Internal |
| Category | INTE |
| UON | N |
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, Associate Professor 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 |
Research Supervision
Number of supervisions
Current Supervision
| Commenced | Level of Study | Research Title | Program | Supervisor Type |
|---|---|---|---|---|
| 2020 | PhD | Molecular Characterisation of Oncogenic Signalling Networks to Develop Treatment Strategies for Diffuse Intrinsic Pontine Glioma | PhD (Medical Biochemistry), College of Health, Medicine and Wellbeing, The University of Newcastle | Co-Supervisor |
| 2019 | Masters | Developing a Novel Diagnostic Test for Early Pregnancy of the Mare and Find out the Embryo Endometrial Interaction | M Philosophy (Biological Sc), College of Engineering, Science and Environment, The University of Newcastle | Co-Supervisor |
Past Supervision
| Year | Level of Study | Research Title | Program | Supervisor Type |
|---|---|---|---|---|
| 2020 | Honours | The Seminal Impact of Heat Stress in Reproduction | Biological Sciences, Priority Research Centre in Reproductive Science | Co-Supervisor |
Dr David Skerrett-Byrne
Position
Postdoctoral Research Fellow
School of Environmental and Life Sciences
College of Engineering, Science and Environment
Contact Details
| david.skerrett-byrne@newcastle.edu.au | |
| Phone | (02) 4921 6214 |
Office
| Room | LS4.39 |
|---|---|
| Building | Life Sciences |
| Location | Callaghan University Drive Callaghan, NSW 2308 Australia |
