Dr Mark Collins

Senior Lecturer
Deputy Director: Faculty of Science Mass Spectrometry Centre
Deputy Placements Lead

mark collins

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

CMIAD


Neuroscience


Cell Biology and Cancer

General

Brief career history

  • 2019-present: Senior Lecturer, University of Sheffield
  • 2013-2018: Lecturer, 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

Research themes

Neuroproteomics

We have a long standing interest in understanding how brain proteomes relate to fundamental aspects of learning and memory and how they are altered in disease. We have been at the forefront of proteomic studies of synapses from the interrogation of the composition of pre and post-synaptic fractions to the characterisation of postsynaptic glutamate receptor associated protein complexes and their regulation by post-translational modifications.

Synapse

We are currently investigating how the synapse proteome is regulated by palmitoylation and lysine acetylation; important PTMs that regulate association of proteins with pre and post synaptic membranes and protein stability, respectively.

We are together with our collaborators investigating the composition of synapse proteomes in several mouse models of disease and human iPS cell derived neuronal models of disease including Schizophrenia, Alzheimer's disease and ALS. Furthermore, we are currently conducting clinical proteomic studies of ALS patient cohorts to identify biomarkers of oxidative stress to enable the action of therapeutics to be assessed.

Regulation 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 3

Figure 1. Regulation of plasma membrane localisation of DHHC5 by Golga7b

 Woodley KT, Collins MO. S-acylated Golga7b stabilises DHHC5 at the plasma membrane to regulate cell adhesion. EMBO Reports. 2019 Oct 4;20(10):e47472.

Perturbed 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

Figure 2. 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.


Mass Spectrometry-based Proteomics

Figure 1

Figure 3. Proteome analysis using high-resolution tandem mass spectrometry.

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.

We 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.

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:

PhD Students

  • Keith Woodley
  • Maria Davies
  • Hatoon Alamri

Co-supervised PhD students

  • Tom Puttick  (with Prof. Dave Kelly, MBB)
  • Ashley Griffin (with Prof. Dave Kelly, MBB)
  • Ankur Patel (with Dr Stephane Mesnage, MBB)
  • Nick Verber (with Prof. Pamela Shaw, SITRaN)
  • Jorge Miguel Ferreira (with Dr Ana Valentim, University of Porto)

MSc Students

  • Luc Harris-Jukes

Summer Students

  • Nikolaos Stefanidis

Funding:

  • BBSRC
  • MRC
  • Weston Park Hospital Cancer Charity
  • Royal Society
Teaching

Undergraduate and postgraduate taught modules

Undergraduate:

  • BMS109 Cell & Molecular
  • BMS243 Advanced Concepts in Cell & Developmental Biology (Co-ordinator)
  • Level 3 Practical and Dissertation Modules

Masters (MSc):

  • BMS6007: Mass Spectrometry-based Proteomics and Metabolomics Course (Co-ordinator)
Opportunities

PhD studentship opportunities

I welcome applications from international students who are self-funded or have (or are applying for) a government scholarship.

We advertise PhD opportunities (Funded or Self-Funded) on FindAPhD.com

For further information and details of other projects on offer, please see the department PhD Opportunities page:

PhD Opportunities

Selected publications

Journal articles