Dr Mark Collins

Mark Collins

Lecturer
Deputy Director: biOMICS Mass Spectrometry Facility

Department of Biomedical Science
The University of Sheffield
Western Bank
Sheffield S10 2TN
United Kingdom

Room: E04 Florey building
Telephone: +44 (0) 114 222 2303
Email: mark.collins@sheffield.ac.uk

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General

Brief career history

  • 2013-present: Lecturer in Biological Mass Spectrometry, University of Sheffield
  • 2011-2013: Senior Staff Scientist, Wellcome Trust Sanger Institute
  • 2005-2011: Research Associate/Staff Scientist, Wellcome Trust Sanger Institute
  • 2001-2005: PhD, Division of Neuroscience, University of Edinburgh
  • 2000-2001: Research Assistant, Centre for Liver Disease, Mater Misericordiae University Hospital, Dublin.
  • 1996-2000: BSc, Department of Biochemistry, University College Dublin

Research interests

Cell Signalling & Proteome Dynamics
We are interested in how proteins are regulated by post-translational modifications and how cell signalling pathways are perturbed in disease. PTMs such as phosphorylation, ubiquitination, acetylation and palmitoylation regulate overlapping and distinct aspects of protein function, but the interplay of these modifications is not well understood.

We exploit biochemical and quantitative mass spectrometry-based approaches to understand how proteins are dynamically regulated by protein synthesis and degradation and an array of post-translational modifications.

Professional activities

  • Fellow of the Higher Education Academy (2016)
  • Peer reviewer for scientific journals and grant-awarding bodies

Full publications

Research

Cell Signalling and Proteome Dynamics

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Our lab is interested in the regulation of signalling pathways by post-translational modifications (PTMs). We use a combination of molecular, cell and mass spectrometry based approaches to study PTMs on a global scale and we are particularly interested in understanding the regulation and activity of enzymes that dynamically regulate PTMs such as protein kinases, palmitoyl-acyltransferases and lysine deacetylases.

The key enabling technology for our research is shotgun proteomics; in which protein samples (whole cell lysates, organelles, protein complexes etc.) are digested with into peptides, separated using nanoflow chromatography and analysed using high-resolution tandem mass spectrometry (biOMICS facility). This approach permits unbiased, quantitative analysis of protein levels and PTMs, with unrivalled accuracy and sensitivity.

Figure 1

Figure 1. Proteome analysis using high-resolution tandem mass spectrometry

Much of our knowledge of the biochemistry of signalling pathways is an aggregate of data from studies of individual PTM sites in single protein experiments. Whilst very useful, this fails to give an integrated and unbiased view of what happens to all relevant proteins for example, when a specific receptor is activated.

The crosstalk of PTMs is emerging as an important mechanism to confer higher order regulation of signalling pathways. We are developing approaches to assay many PTMs from the same sample on a proteome-scale in order to understand how for example, phosphorylation, acetylation and palmitoylation interact to regulate protein function.

We also exploit affinity purification and proximity labelling strategies to purify and characterise multiprotein complexes formed by protein kinases and palmitoyl-acyltransferases to identify their substrates as well as regulatory proteins that  determine substrate specificity or target these enzymes to different subcellular compartments or membrane microdomains.

Research themes

Figure 2Regulation of membrane protein function by S-acylation (Palmitoylation)

Palmitoylation, the only known reversible lipid modification of proteins, is a critical regulator of protein trafficking, stability and signalling and is important for all cell types, and organisms from yeast to humans.

Proteins can be palmitoylated by a family of 23 protein acyl transferases (PATs) in humans and many of these enzymes have been shown to regulate important aspects of cell biology and in particular in neuronal cells in the brain where palmitoylation of receptors and associated proteins are essential for communication between brain cells and therefore functions such as learning and memory.

Indeed, several PATs have been implicated in the pathophysiology of neurological disorders from Huntington’s disease to intellectual disability and schizophrenia and well as other diseases such as diabetes and cancer.

The identification of determinants of substrate specificity of palmitoyl acyltransferases is an important goal toward understanding how palmitoylation regulates cell function. Development of strategies to enrich, identify and quantify proteins and PTMs is also a major focus of research in our lab.

Figure 2. site-specific-Acyl-Biotin-Exchange (ssABE) for comprehensive identification and quantification of sites of S-acylation


Figure 3

Figure 3. Concurrent identification of palmitoylation and phosphorylation sites by mass spectrometry (click image for enlarged version)

Figure 4Perturbed signalling pathways in neurodegenerative diseases

Motor Neurone Disease or Amyotrophic lateral sclerosis (ALS) is a disorder that results in fatal paralysis within a few years of symptom onset. Defects in a growing list of genes are associated with the development of ALS/MND.

Many of these gene defects result in the accumulation of aggregates in cells of patients with ALS and these aggregates are believed to cause neurons to die, resulting in the symptoms of the disease.

Recently, a number of large exome sequencing studies of ALS patients have independently identified several loss of function mutations in protein kinases but it is not known how dysregulation of these kinases might contribute to development of disease.

We are using protein biochemistry, immunofluorescence microscopy and  phosphoproteomic approaches to understand how human mutations lead to molecular and cellular changes that contribute to to the pathogenesis of ALS.

Figure 4. Monitoring autophagy levels in NSC-34 cells using a tandem mRFP-EGFP-LC3 fluorescent reporter. Autophagosomes are visualised as yellow  labelled puncta whilst autolysosomes appear red due to loss of acid sensitive GFP signal.


Collaborations

Campylobacter jejuni is a food-borne pathogen of worldwide importance but little is known about how the pathogenicity of this bacteria is regulated by PTMs. We collaborate with Prof Dave Kelly at the Department of Molecular Biology and Biotechnology, University of Sheffield to develop and apply proteomic approaches to probe the function of acetylation and phosphorylation in C. jejuni though two BBSRC White Rose Mechanistic Biology DTP PhD studentships (2015-2019 & 2017-2021).

Histone deacetylase 1 and 2 (HDAC1/2) containing complexes have important roles in almost all cellular processes, including cell cycle, DNA synthesis, DNA repair and gene expression. In collaboration with Dr Shaun Cowley at the Department of Molecular and Cell Biology, University of Leicester we are developing and apply proteomic approaches  (acetylomics and BioID) to probe the function of acetylation in embryonic stem cells  (BBSRC-SFI project grant 2017-2020).

Constitutive secretion is required for many biologically important processes such as the secretion of antibodies and the extracellular matrix. In collaboration with Dr Andrew Peden at the Department of Biomedical Science, University of Sheffield, we are investigating the regulation of SNAREs by palmitoylation as well as using quantitative proteomics to characterise novel machinery required for post-Golgi trafficking and antibody secretion.

Peptidoglycan (PG) is an essential component of the bacterial cell envelope, made of glycan strands and peptide stems containing unusual amino acids. In collaboration with Dr Stéphane Mesnage at the Department of Molecular Biology and Biotechnology, University of Sheffield, we are developing an automated, high-resolution analysis pipeline for bacterial peptidoglycan structural analyses though a BBSRC White Rose Mechanistic Biology DTP iCASE PhD studentship (2017-2021).

Team members:

  • Keith Woodley (PhD student , Protein palmitoylation)
  • Maria Davies  (PhD student , ALS signalling pathways)
  • Tom Puttick  (PhD student , Campylobacter acetylation

Funding:

  • BBSRC
  • Royal Society
Teaching

Undergraduate and postgraduate taught modules

Level 1

  • BMS109/157 Principles of Molecular Biology

Level 3

  • BMS369 Laboratory Research Project
  • BMS349/BMS359 Extended Library Project

Postgraduate

  • Mass Spectrometry-based Proteomics & Metabolomics Course for postgraduate research students
Opportunities

PhD Studentship

Title: Molecular characterisation of the in vivo targets and mechanism of action of an acetylcholinesterase-derived peptide upregulated in Alzheimer’s disease

Supervisor: Dr Mark Collins

Funding status: Funded by a four-year White Rose DTP studentship from the BBSRC to start in October 2017.

Project Description

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that is characterised by the deposition and accumulation of amyloid beta plaques and phosphorylated tau filaments in the brain, the latter correlating with the onset of symptoms.

The vast majority of AD cases are sporadic and the basic mechanism driving the continuing process of neurodegeneration in selectively vulnerable cells, has not as yet been identified. However, our industrial partner, NeuroBio has recently determined that an AChE-derived 14-residue peptide (‘T14’) with a conspicuous sequence homology to amyloid beta, is upregulated in Alzheimer’s disease. T14 is present in all vulnerable cell populations irrespective of their neurotransmitter type and it drives the production of both amyloid and hyperphosphorylated tau.

These findings potentially place T14 upstream of amyloid and tau, however, a mechanistic understanding of the role of T14 in health and disease is lacking.

The aim of this project is to understand how T14 is involved in the pathogenesis of AD. We seek enthusiastic students who wish to gain expertise across disciplines including molecular neuroscience, protein biochemistry and mass spectrometry. The student will spend 6 months working in Neuro-Bio Ltd at their site in Abingdon, Oxfordshire.

For further information about projects within the department and how to apply, see our PhD Opportunities page:

PhD Opportunities

Selected publications

Journal articles