Thursday, 8 February 2018

Ken Baker - Thursday 1st March - 12.15pm - MED.L2.6

This should be interesting 😊





VIVA Seminar


Speaker: Ken Baker

Supervisors: Prof John Isaacs, Dr Arthur Pratt, Dr Ben Thompson


Predictors of Drug-Free Remission in Rheumatoid Arthritis


Background  Rheumatoid arthritis (RA) is a common autoimmune disease characterised by joint inflammation and systemic manifestations. Remission is achievable with disease- modifying anti-rheumatic drugs (DMARDs) prescribed in modern treat-to-target strategies, albeit with potential side effects, and inconvenient and expensive safety monitoring. Half of patients can maintain remission following DMARD cessation, though this cannot be reliably predicted. Clinicians and patients thus face a dilemma – when is it appropriate to stop DMARDs in RA remission?

Method Patients with established RA satisfying clinical and ultrasound remission criteria discontinued all DMARDs and were monitored for six months. The primary outcome was time-to-flare, defined as DAS28-CRP (disease activity score in 28 joints with C-reactive protein) ≥ 2.4. Baseline clinical and ultrasound measures, circulating cytokines, and peripheral CD4+ T cell gene expression were assessed for their ability to predict time-to- flare and flare/remission status by Cox regression and receiver-operating characteristic (ROC) analysis.

Results 23/44 (52%) eligible patients experienced an arthritis flare at a median (IQR) of 48 (31.5 – 86.5) days following DMARD cessation. A composite score incorporating five baseline variables (three genes, one cytokine and one clinical) differentiated future flare and drug- free remission with an area under the ROC curve of 0.96 (95% CI 0.92-1.00), sensitivity of

0.91 (0.78 – 1.00) and specificity of 0.95 (0.84 – 1.00). Longitudinal analysis identified increased concentrations of circulating pro-inflammatory cytokines, and upregulation of a

proliferative gene set by CD4+ T cells at the onset of flare.

Conclusions This study provides proof-of-concept evidence for the existence of biomarkers of drug-free remission in RA, and offers insights to the pathophysiology of arthritis flare. If validated, these biomarkers may help guide DMARD withdrawal, with consequent minimisation of medication side effects and healthcare costs.


Thursday 1st March, 12.15pm

Room L2.6, 2nd Floor William Leech Building

Monday, 29 January 2018

ICM Research Seminar - Wednesday 31st January - Dental Lecture Theatre F - 1pm

This could be interesting... 





ICM Research Seminar

Wednesday 31st January


Khalil Elgendy

(Prof John Mathers, Dr Fiona Malcomson)

DNA methylation as a biomarker of colorectal cancer risk: evaluation of surrogate tissues

This research project aims to investigate the relationship between DNA methylation in different tissues (longitudinal and cross-sectional approaches) in context of colorectal cancer (CRC) risk which may have an impact on development of more informative biomarkers for assessment of CRC risk and potential use as surrogate outcomes in studies of CRC prevention.


Dr Peter Vegh

(Prof Muzlifah Haniffa)

Application of single-cell RNA analysis in immunology

Modern sequencing technologies allow us to individually measure the transcriptomes of thousands of cells from the same sample. As the transcriptome is a good reflection of cell type and function, we employ this approach to examine the composition of human tissues, with a particular focus on the immune system. This presentation describes the workflow and illustrates its use in our study of healthy human skin. Our aim is to map and catalogue cell heterogeneity, an important step to understanding the immune system.


Chair: Carl Dale

Dental Lecture Theatre F, Medical School 1pm - 2pm




Monday, 15 January 2018

Mass spectrometry and proteomics: All you ever wanted to know but were afraid to ask.

Matthias Trost, the new Professor of Proteomics, would like to invite all institute PGR students, post-docs and PIs to attend a lecture series on the basics in mass spectrometry and proteomics that he is presenting as part of the Faculty's PGR Development Programme



The lectures cover what Matthias considers the absolute basics in mass spec and proteomics, including the newest methods developed in the last years. The aim would be that this basic knowledge will help you designing better experiments and understand possibilities as well as limitations of proteomics.


PGR students should register attendance in the usual manner ( so that the session appears in your eportfolio. Post-docs and PIs do not need to register.


Mon Jan 22nd 2018, 15:00               (Mass spec basics 1 – basic of mass measurement, ionisation techniques) Dental Lecture Theatre E

Mon Jan 29th 2018, 15:00                (Mass spec basics 2 – mass analysers, detectors, tandem mass spectrometry) RB Green Lecture Theatre, Dental School

Mon Feb 5th  2018, 15:00                (Mass spec basics 3 – fragmentation techniques, hybrid instruments) Dental Lecture Theatre E

Mon Feb 12th 2018, 15:00               (Proteomics basics 1 – what is proteomics?, sample preparation, experimental design) Dental Lecture Theatre F

Mon Feb 19th 2018, 15:00               (Proteomics basics 2 – search engines, databases, FDR, data analysis, data visualisation, quantification techniques) Dental Lecture Theatre C

Mon Feb 26th 2018, 15:00               (Proteomics basics 3 – fractionation techniques, phosphorylation and other PTMs) Dental Lecture Theatre E


Immunology North East Meeting

We are very excited to announce our first seminar of 2018 which will be on Thursday the 18th January at 4pm in the Research Beehive room 2.22 at Newcastle University. Tea and coffee will be provided from 3:30pm.


We are delighted to welcome:


Professor Adrian Hayday PhD FRS, F MedSci

Glendinning Professor of Immunobiology, King's College London & co-Lead, Clinical Academic Grouping, Genetics Rheumatology Infection Immunology & Dermatology King's Health Partners & Senior Group Leader, The Francis Crick Institute, London


Talk title:

In search of natural tissue-immunosurveillance: the roles of epithelial butyrophilins




Adrian Hayday trained as a biochemist, did his PhD studies in tumour virology, and pursued post-doctoral training at MIT where he characterised chromosome translocation breakpoints in human B cell lymphomas, and helped identify gamma delta (gd) T cells by being the first to describe gd TCR genes. On the Faculty at Yale University, he helped show that gd T cells occupy a distinct niche in lymphocyte biology, including disproportionate association with tissues rather than with lymphoid organs, and rapid responses to tissue-'stress'. At a time when tumour immune surveillance was not widely accepted, his lab showed that mice lacking gd T cells are more susceptible to carcinogens. His group returned to London in 1998 to establish the Peter Gorer Dept of Immunobiology at King's College London, then joined the Cancer Research UK London Research Institute (now part of the Francis Crick Institute) as a joint appointee in 2009. In recent years, his group has developed a strong programme in human immunology, including clinical trials applying gd T cells in immunotherapy. Amongst many honours, in 1997 he became the first biologist to win the William Clyde DeVane Medal, Yale College's prestigious prize for scholarship, and he was awarded a FRS in 2016.




Recent publications:

Wednesday, 15 November 2017

ICM Research Seminar - Wednesday 15th November - Dental Lecture Theatre F - 1pm to 2pm

Some interesting talks today.  Go Edith!




ICM Research Seminar

Wednesday 15th November

Rebecca Hanna

(Prof. M. Birch-Machin, Dr S. Amarnath)

Optimised detection of mitochondrial DNA strand breaks

Intrinsic and extrinsic factors that induce cellular oxidative stress will damage tissue integrity and promote ageing. At a sub- cellular level, this results in accumulative strand breaks to the mitochondrial DNA (mtDNA) genome. Limited repair mechanisms and close proximity of the genome to the site of superoxide generation, make mtDNA a prominent biomarker of oxidative damage. Using human DNA extracted by conventional methods, we describe a methodology that sensitively detects mtDNA strand breaks relative to a suite of short mitochondrial and nuclear DNA housekeeping amplicons which control for any variation in copy number. Some applications of this methodology will be discussed.


James Fletcher

(Prof. M. Haniffa, Prof. N. Reynolds)

Defining the landscape of human tissue mononuclear phagocytes using single cell RNA sequencing and mass cytometry

The mononuclear phagocyte system is a highly heterogeneous compartment of the immune system comprising many subsets of monocytes, macrophages and dendritic cells. As single cell analysis techniques increase in measurable parameters, this heterogeneity can be analysed in greater detail. Using human skin as a model organ for tissue immune cells, this project aims to utilise single cell RNA sequencing to dissect the human tissue mononuclear phagocyte compartment, and validate these findings using flow and mass cytometry.


Dr Edith Serrano Blesa

(Prof. J. Isaacs)

Use of Design of Experiments to optimize a SWATH-MS acquisition method for the discovery of protein biomarkers in serum

SWATH-MS is a recently described mass spectrometry technique that allows high coverage protein identification and accurate quantification. The parameters that impact detection by SWATH-MS are specially complex and so, optimization is sample and machine dependant. Design of experiments (DoE) uses statistical methodology for identifying the significant parameters and then optimising a response by fine-tuning them, thus improving the results in the analysis of complex protein samples.


Chair: Dr David Swan

Dental Lecture Theatre F,

Medical School 1pm - 2pm