Michael Mather

Minimal methylation classifier (MIMIC): A novel method for derivation and rapid diagnostic detection of disease-associated DNA methylation signatures

Rapid and reliable detection of disease-associated DNA methylation patterns has major potential to advance molecular diagnostics and underpin research investigations. We describe the development and validation of minimal methylation classifier (MIMIC), combining CpG signature design from genome-wide datasets, multiplex-PCR and detection by single-base extension and MALDI-TOF mass spectrometry, in a novel method to assess multi-locus DNA methylation profiles within routine clinically-applicable assays. We illustrate the application of MIMIC to successfully identify the methylation-dependent diagnostic molecular subgroups of medulloblastoma (the most common malignant childhood brain tumour), using scant/low-quality samples remaining from the most recently completed pan-European medulloblastoma clinical trial, refractory to analysis by conventional genome-wide DNA methylation analysis. Using this approach, we identify critical DNA methylation patterns from previously inaccessible cohorts, and reveal novel survival differences between the medulloblastoma disease subgroups with significant potential for clinical exploitation.

Gross Motor Function Measure-66 trajectories in children recovering after severe acquired brain injury

To explore the appropriateness of using the interval‐scale version of the Gross Motor Function Measure (GMFM‐66) in paediatric acquired brain injury (ABI), and to characterize GMFM‐66 recovery trajectories and factors that affect them.

Is anticoagulation beneficial in acute mastoiditis complicated by sigmoid sinus thrombosis?: Anticoagulation in Acute Mastoiditis

BACKGROUND Sigmoid sinus thrombosis (SST) remains a rare but serious intracranial complication of acute mastoiditis. Primary treatment includes surgical drainage by mastoidectomy and broad-spectrum antibiotic therapy. The role of anticoagulation remains controversial. Potential benefits include limiting thrombus propagation, improved sinus recanalization, and reduction in neurological sequelae. These benefits must be considered against potential risks, including intracranial hemorrhage, which is particularly significant in the context of patients who may require further staged surgical intervention. If a decision is made to anticoagulate, uncertainty exists regarding selection and duration of appropriate agents. Heparin has been the traditional mainstay. However, whereas newer direct oral anticoagulants (DOACs) have transformed the management of lower limb deepvenous thrombosis and pulmonary embolism, their role in SST remains unclear. Furthermore, although screening for thrombophilia may be helpful in guiding management, recommendations regarding testing in this cohort remain poorly defined. In this review, we aim to explore relevant literature defining the role of anticoagulation in acute mastoiditis complicated by SST.

Excess Mucin Impairs Subglottic Epithelial Host Defense in Mechanically Ventilated Patients

&NA; Rationale: Aspiration of infective subglottic secretions causes ventilator‐associated pneumonia (VAP) in mechanically ventilated patients. Mechanisms underlying subglottic colonization in critical illness have not been defined, limiting strategies for targeted prevention of VAP. Objectives: To characterize subglottic host defense dysfunction in mechanically ventilated patients in the ICU; to determine whether subglottic mucin contributes to neutrophil phagocytic impairment and bacterial growth. Methods: Prospective subglottic sampling in mechanically ventilated patients (intubated for four or more days), and newly intubated control patients (intubated for less than 30 min); isolation and culture of primary subglottic epithelial cells from control patients; laboratory analysis of host innate immune defenses. Measurements and Main Results: Twenty‐four patients in the ICU and 27 newly intubated control patients were studied. Subglottic ICU samples had significantly reduced microbiological diversity and contained potential respiratory pathogens. The subglottic microenvironment in the ICU was characterized by neutrophilic inflammation, significantly increased proinflammatory cytokines and neutrophil proteases, and altered physical properties of subglottic secretions, including accumulation of mucins. Subglottic mucin from ICU patients impaired the capacity of neutrophils to phagocytose and kill bacteria. Phagocytic impairment was reversible on treatment with a mucolytic agent. Subglottic mucus promoted growth and invasion of bacterial pathogens in a novel air‐liquid interface model of primary human subglottic epithelium. Conclusions: Mechanical ventilation in the ICU is characterized by substantial mucin secretion and neutrophilic inflammation. Mucin impairs neutrophil function and promotes bacterial growth. Mucolytic agents reverse mucin‐mediated neutrophil dysfunction. Enhanced mucus disruption and removal has potential to augment preventive benefits of subglottic drainage.

Bile acids: a potential role in the pathogenesis of pharyngeal malignancy

Gastro‐oesophageal reflux disease is thought to be a risk factor for head and neck malignancies. Bile acids are one of the principle components of gastric refluxate and have previously been implicated in the development of oesophageal and bowel malignancies. There is clear evidence that bile acids reflux into the laryngopharynx. Despite this, the carcinogenic properties of bile acids in this area are yet to be fully identified. We therefore investigated the potential role of bile acids in pharyngeal malignancy, through the highly conserved process of epithelial–mesenchymal transition (EMT). EMT occurs in invasion and metastasis and is a central process in the development of epithelial carcinoma.

A review of adenotonsillar hypertrophy and adenotonsillectomy in children after solid organ transplantation

OBJECTIVE Paediatric solid organ transplantation is an increasingly successful treatment. Improved survival is paralleled by increased secondary complications of immunosuppression, including post-transplant lymphoproliferative disease (PTLD). PTLD frequently presents in Waldeyers lymphatic ring. Adenotonsillar hypertrophy (ATH) is common in children, however in children after transplant, ATH may indicate PTLD. We review the literature on ATH and the role of adenotonsillectomy in children after transplantation. METHODS A comprehensive literature search was performed on the 26 th September 2017 of Ovid Medline (1996-September 2017), Embase (1996-2017) and EBM reviews (Cochrane database of systematic reviews 2005-September 20 th 2017). Results were limited to English language publications within the last 20 years. Abstracts were screened for relevance to PTLD and ATH in the paediatric solid organ transplantation population. Screening of the bibliographies identified further articles. RESULTS 85 unique articles were screened to yield 18 relevant publications. 10 were retrospective studies and 8 were prospective studies. CONCLUSION In children, we report a PTLD incidence of up to 15%, with up to 63% of cases presenting in the head and neck. Histological examination of adenotonsillectomy specimens found PTLD in a mean 5.7% (range 0-39%). We found a lack of prospective studies into this topic and further high quality research is needed. Clinical assessment of ATH in children after transplantation and when to perform a diagnostic adenotonsillectomy remains challenging. Children with ATH warrant prompt further investigation and support from colleagues in transplantation and oncology is required. .

Going where other methods cannot: A systematic mapping review of 25 years of qualitative research in Otolaryngology

To map the use of qualitative methods within otolaryngology, providing examples and identifying gaps in the literature.

Inconsistent availability of hearing aids during acute admission

Blustein and colleagues discuss the challenges faced by hearing impaired patients in busy acute healthcare settings.1 Receptive communication deficiency affects shared decision making, particularly in vulnerable patients. Hearing loss is independently associated with accelerated cognitive decline.2 As otolaryngology doctors, we were keen to clarify the current availability of assistive devices. A brief survey of 14 …

Development of a clinically applicable assay for medulloblastoma molecular subgroup classification

Abstract Background Medulloblastoma is the most common malignant tumour of childhood. Recent work shows that medulloblastoma comprises four molecular subgroups, which can be classified by a 450k DNA-methylation array. However, because this method is not practicable for routine clinical practice, there is a major unmet need for patient care and clinical trials. Work within our group suggests that a clinically applicable DNA-methylation-based, minimal-signature assay can rapidly identify these subgroups. We aimed to validate this new assay against the gold standard subgrouping by methylation array and apply it to tumour samples for which subgroup is unknown. Methods 100 ng of DNA from both fresh frozen and formalin-fixed paraffin-embedded (FFPE) biopsy samples were chemically treated to induce methylation-dependent single nucleotide polymorphisms. Subsequent amplification at specific loci via multiplex PCR permitted methylation status characterisation via mass spectrometry which enabled subgroup classification using in-house developed algorithms. We then challenged the assay by using scant and degraded DNA extracted from nuclear preparations originally intended for fluorescence in-situ hybridisation. Subgroup classification was correlated with clinical data. Findings 82·7% of fresh frozen, 62·9% of FFPE, and 73·3% of nuclear preparation samples could be amplified; 94 (91%) of 103 samples that passed quality control had a confidently assigned subgroup which, in every case, matched with the gold standard methylation array subgrouping call. Samples with as little as 50·4 ng of DNA were successfully subgrouped and some samples had been resected over 46 years ago (mean 12·7 years) with DNA quality (260 nm to 280 nm ratio) as low as 1·22 (mean 1·72). Interpretation We have shown that a low-cost minimal-methylation signature assay can reliably subgroup medulloblastoma, even with archival or degraded DNA, and could be used clinically for routine patient stratification. This assay uses only a tenth of the DNA amount that is typically used in methylation array subgrouping. Further work should investigate use of minimal-methylation signatures to identify methylation subgroups in other cancers. Funding North of England Childrens Cancer Research Fund, Northern Institute for Cancer Research.

Routine molecular subgrouping of medulloblastoma: Bridging the divide between research and the clinic using low-cost, mass spectrometry-based DNA methylomics

Schwalbe, E. C., Gohlke, H., Hicks, D., Rafiee, G., Enshaei, A., Potluri, S., Matthiesen, J., Mather, M., Chaston, R., Crosier, S., Smith, A. J., Williamson, D., Bailey, S., & Clifford, S. C. (2014). Routine molecular subgrouping of medulloblastoma: Bridging the divide between research and the clinic using low-cost, mass spectrometry-based DNA methylomics. National Cancer Research Institute (NCRI).