BSPR 2023 Bursaries and Fellowships

MJ Dunn Fellowships

##Sean Burnap (University of Oxford) I would first like to give a huge thank you to the British Society for Proteome Research for selecting me for the MJ Dunn Fellowship to attend the 2023 joint BSPR-EuPA meeting held in the beautiful and vibrant city of Newcastle upon Tyne. The organising committee put together an incredibly diverse and exciting programme of talks and posters, amplified by the bringing together of researchers not only from the UK and EU but also worldwide. A big thank you and congratulations must also be extended to Professor Matthias Trost and his lab for organising this wonderful meeting. It was an absolute pleasure to have the opportunity to discuss my own research over my poster focussing on the use of cross-linking mass spectrometry to determine lipoprotein-based interactors of the SARS-CoV-2 spike protein.

Professor Mike MacCoss kicked off the meeting with his plenary lecture exploring the use of next generation translational proteomics to determine protein drivers of Alzheimer’s Disease. Here Prof. MacCoss exemplified the power in using a cohort of very well-matched patients rather than attempting to obtain larger and larger cohorts that can introduce varying co-morbidities. A big take home here was the need to dig a little deeper into proteomic datasets and rather than just quantifying at a protein level, attention must be placed at a peptide level as peptides from differing regions of the same protein may be differentially changing, as beautifully shown in the case of amyloid and tau proteins. Prof. MacCoss ended by introducing the Mag-Net protocol which involves the use of hyper-porous strong-anion exchange magnetic microparticles, acting to enrich for membrane bound particles while also largely reducing the dynamic range of the plasma proteome, enabling greater depth of quantitation. The end of the opening plenary lecture gave way for the first night social event held in the Discovery Museum.

There were certainly too many illuminating and inspiring talks to list however I want to introduce a few that I particularly enjoyed. The first full day was opened by Professor Markus Ralser highlighting their work using high-throughput DIA-based methodologies to determine metabolic and proteomic landscapes after genetic perturbation at genome-scale. Professor Alexey Nesvizhskii discussed the ever-expanding toolbox of MSFragger with a particular focus on glycopeptide identification, a tool I have found incredibly useful in my own research of late. Professor Justin Benesch highlighted the complementarity of mass photometry alongside native mass spectrometry. Professor Tamar Geiger explored the power of single cell proteomics to probe tumour complexity. What was particularly evident at this meeting was the large strides being made in the single cell community, with a particular focus here on new instrumentation. Dr Nicola Ternette gave a fascinating and exciting talk exploring TCR-like antibody cancer therapeutics. Finally, the meeting was drawn to a close by Professor Sara Zanivan investigating the role of cancer-associated fibroblasts.

It was also incredible to see a large focus of the meeting given to support Early Career Researchers, not only through the selection of many to give talks but also through organised workshops and seminars, as well as with the wonderful presence of the Young Proteomics Investigators Club. A fantastic talk was given be Dr Alejandro Brenes, ultimately to be awarded best early career presentation, where he discussed the importance of data normalisation while also introducing the wonderful Immunological Proteome Resource. I must end by also mentioning what a fantastic choice for the conference dinner to be held at the Wylam Brewery, serving wonderful beer alongside delicious food, followed by a band giving the opportunity for everyone to let loose.

Once again thank you to the British Society for Proteome Research as well as everyone involved in organising this wonderful meeting. I met some incredible scientists who I very much look forward to seeing again at the next meeting.


##Charlotte Hutchings (Cambridge Centre for Proteomics) I would like to extend my thanks and gratitude to the British Society for Proteome Research for awarding me a travel grant to attend the BSPR - EuPA Annual Scientific Meeting 2023 in Newcastle upon Tyne.

Last year, I attended the BSPR Annual Scientific Meeting 2022 in Oxford as a first year PhD student who was new to the world of proteomics. Whilst I did not present, the conference left me excited about continuing my journey and delving deeper into the field. This year it felt completely different. I arrived in Newcastle (which, as a Northerner, I was thrilled about) feeling confident and ready to go. Luckily, BSPR – EuPA 2023 did not disappoint.

Not only was I reunited with familiar faces from the BSPR community, but the conference provided the opportunity to network with more distant colleagues from the European proteomics community. In particular, the Young Proteomics Investigators Club (YPIC as it is known) put on several great events ranging from pre-conference workshops to social activities in the evenings. They undoubtably contributed to the success of the meeting and made all early career researchers feel at home and comfortable. I met colleagues whom I know from all different contexts – a summer school in Italy, ex-lab members, HUPO ECR and BSPR committees, all in one place.

As for the science, BSRP – EuPA had put together a wonderfully varied programme of sessions. My favourite of these was most definitely the Bioinformatics and Data Processing session, particularly the discussion of a Bayesian framework for differential expression analyses as this has direct relevance to my work. It must be said that the early career researcher talks were very impressive, as were the 150+ posters. I also had the opportunity to present a poster of my own PhD research this year, gaining valuable insight and feedback from discussions with colleagues.

Finally, I would like to both thank and congratulate Prof. Matthias Trost and his team for organising such a smooth conference. Oh, and for throwing the best conference party that I have ever been to.

##Lilly Adair (University of Reading) I would like to express my utmost gratitude to the committee of the British Society of Proteome Research for awarding me with a student travel grant to attend the 71st American Society for Mass Spectrometry Conference 2023 in Houston, Texas. Attendance at this conference was especially significant to me as this was my first conference since beginning my PhD in September 2022, and what a way to begin! I was honoured to be provided with the opportunity to present my research in the form of a poster presentation at the conference, with Top-down proteomics being the main research focus of my presentation. Being able to discuss my work with other researchers and experts in the field was such an invaluable experience, providing me with feedback and further inspiration that I will carry forward throughout my PhD. A diverse and interesting range of topics were covered in the poster sessions and oral presentations over the five days that the conference took place. Sessions that were of particular interest included ‘Top-down Protein Analysis’, particularly the talk by Adrian Guthals discussing parameter-free deconvolution and ‘Instrumentation: detection of high-mass analytes’ where Martin Jarrold discussed the side-by-side comparison of Orbitrap Direct Mass Technology and Charge Detection Mass Spectrometry. The sessions on ‘ambient ionisation and applications’ and ‘microbes and the microbiome’ also had some fascinating talks. Watching such confident and passionate speakers was hugely exciting and motivating, further solidifying my interest in the field. It’s astonishing to see the vast number of developments and advancements in the technologies and their outstanding applications, such as the new Orbitrap Astral Mass Spectrometer unveiled by ThermoFisher at the beginning of the conference. Not only did the conference provide the opportunity to hear about current research in the field but also provided insight into the many career paths available for researchers, showed effective ways to improve accessibility for mass spectrometrists and celebrated the diversity seen in our community. Breakfast seminars and hospitality suites enabled casual discussion on projects and interests, leading to the formation of new friendships and potential collaborations.

The conference brought together people from all over the world with common interests and goals, making me feel proud to be part of this community. It was a perfect combination of learning and networking. I would like to give thanks again to BSPR for helping make this experience achievable, it was an excellent opportunity for my personal development as an independent researcher in the mass spectrometry community. Now I look forward to the BSPR-EuPA 2023 Conference in Newcastle!

##Ruth Walker (Newcastle University) Developing high throughput screening MALDI-TOF MS cellular assays for drug discovery in non-alcoholic fatty liver disease Ruth Walker1, José Luis Marín-Rubio1, Frank Büttner2, Matthias Trost1, Maria Emilia Dueñas1*

1Biosciences Institute Faculty of Medical Sciences, Newcastle University, UK, 2Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Germany, *Corresponding authors

Introduction Non-alcoholic fatty liver disease (NAFLD) is estimated to affect 25% of adults worldwide and is the leading cause of cirrhosis and hepatocellular carcinoma, having become the most common cause of chronic liver disease worldwide. Currently, pathophysiology between the different stages is not well understood and there are no drugs available to treat any stage. MALDI-TOF MS has become a highly versatile, cost-efficient, and powerful technique utilised in high-throughput screening (HTS) approaches in drug discovery, overcoming the shortcomings of conventional fluorescent label-based methods. Herein, we applied this technology to develop a novel phenotypic cellular assay, specifically to detect and characterise metabolites and lipids in a comprehensive, target agnostic, and unbiased HTS approach for drug discovery in NAFLD.

Methods Human hepatic stellate LX-2 cells (hHSCs) were used to develop an untargeted metabolic phenotypic cell based disease model using MALDI-TOF MS. TGF-β and PDGFββ, stimulating two complementary pathways, were employed since they are considered as the most potent cytokines inducing activation, fibrosis, and proliferation in hHSCs. First, ALK5i, imatinib, then lanifibranor, aramchol and pirfenidone were utilised to determine if pharmacological inhibition of these pathways could be monitored. After treatment, the cells were harvested, pellets snap-frozen and resuspended in 30% acetonitrile (0.1% TFA). Cells were then spotted, in triplicate, in their respective matrix and analysed at m/z 200-2000 and 2000-20000 using a rapifleX MALDI PharmaPulse mass spectrometer. Spectral profiles were inspected followed by statistical analyses to identify differences and determine significance.

Preliminary Data To establish whether metabolic changes in a biologically relevant disease model could be identified, optimal assay conditions with fibrosis stimuli TGF-β/PDGFββ and Alk5 (TGF-βR1 kinase inhibitor)/ imatinib (PDGF-βR inhibitor) were determined and validated using qPCR for key fibrosis markers, global proteomic analysis and MTT proliferation assays. Systematic screening of sample preparation conditions was optimised, employing automated liquid handling devices, including matrix, additives, extraction procedures, etc., to elucidate the most effective analysis parameters for metabolites and lipids. Furthermore, all protocols were simplified and adapted to HTS compatible platforms to ensure a smooth transition from an academic laboratory to industry. Preliminary testing using 2,5-dihydroxybenzoic acid and 2,5-dihydroxyacetophenon, showed spectral differences in both low (metabolite; m/z 200-2000) and high mass regions (protein; m/z 2000-20000) respectively, which could distinguish unstimulated, stimulated, and stimulated cells treated with inhibitors. Whilst there are currently no approved therapies to treat NAFLD, lanifibranor and aramchol are anti-fibrinogenic drugs currently in late-stage clinical testing to treat NAFLD, were utilized. Pirfenidone, which is currently approved to treat idiopathic pulmonary fibrosis, could be repurposed to treat NAFLD, and was included in a preliminary compound screen. Using principal component, hierarchical, multivariate analysis, and machine learning strategies, a unique subset of peaks for each condition tested were identified. The newly developed assay system employing MALDI-TOF MS identified lanifibranor, aramchol and pirfenidone as drugs, which blocked the fibrosis phenotype, indistinguishable to the unstimulated control cells. Ongoing work includes optimising analysis strategies to carry out larger screens in an industrial setting. Moreover, high-resolution mass spectrometry will be carried out to identify the different features and potentially elucidate novel biomarkers of NAFLD.

Novel Aspect A novel, unbiased and untargeted high-throughput MALDI-TOF MS phenotypic screening approach for identifying metabolites in NAFLD for drug discovery.

Conflict of Interest Disclosure All work was funded and completed as part of the scope of a PhD for Ruth Walker by Boehringer Ingelheim Pharma GmbH & Co. KG.

##Olga Tereszkowska-Kaminska (University of Liverpool) I am honoured to have received the Student and Support Staff Conference bursary and would like to thank the British Society for Proteome Research for the award. Being a first year PhD student at the University of Liverpool, it has been an amazing opportunity to attend the BSPR-EuPA conference in Newcastle and present my first poster. I was really happy to meet many people with different proteomics interests, introducing me to the wider research world of proteomics. I also got to meet other first year PhD students and compare experiences, some of whom were also attending their first conference which was nice to try and figure things out together.

The talks were diverse and very interesting, and I especially enjoyed the Post-Translational Modifications session with Tiziana Bonaldi’s talk on the role of protein methyltransferases in cancer plasticity and resistance. This session and talk related to my research and gave me new insights into where my PhD could take me. Attending the Thermo Fischer Scientific post-ASMS workshop also introduced me to new instruments and how they compare to the ones I am using now.

Exploring Newcastle was a highlight and an insight into living there for when I will be visiting my secondary supervisor’s lab. Therefore this funding is a great help with other parts of my PhD, as well as allowing me to attend my first conference and present my data so far to researchers in proteomics.

Thank you to the organisers of the conference and I hope to also attend next year. Again, I am grateful to the BSPR for awarding me this bursary.