Respiratory Pathogens at Exacerbation in Chronic Bronchitis With Airway Bacterial Colonisation: A Cohort Study.

Background And Objective: COPD and bronchiectasis are common causes of morbidity, particularly around exacerbation. Colonisation with respiratory pathogens can increase the frequency and severity of exacerbations. However, bacterial and viral presence at exacerbation in people with airway colonisation has not been well studied.

Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust.

Throughout the COVID-19 pandemic, valuable datasets have been collected on the effects of the virus SARS-CoV-2. In this study, we combined whole genome sequencing data with clinical data (including clinical outcomes, demographics, comorbidity, treatment information) for 929 patient cases seen at a large UK hospital Trust between March 2020 and May 2021. We identified associations between acute physiological status and three measures of disease severity; admission to the intensive care unit (ICU), requirement for intubation, and mortality.

Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK.

Introduction: Throughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to spread, it is important to uncover the specific pathways by which nosocomial outbreaks occur to understand the most suitable transmission control strategies for the future.

Methods: In this investigation, SARS-CoV-2 genome sequences obtained from 694 healthcare workers and 1,181 patients were analyzed at a large acute NHS hospital in the UK between September 2020 and May 2021.

Management of a large outbreak of COVID-19 at a British Army training centre: lessons for the future.

Introduction: The COVID-19 pandemic has posed major challenges for infection control within training centres, both civilian and military. Here we present a narrative review of an outbreak that occurred at the Royal Military Academy Sandhurst (RMAS) in January-March 2021, in the context of the circulating, highly transmissible SARS-CoV-2 variant B.1.

Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward.

Background: COVID-19 has the potential to cause outbreaks in hospitals. Given the comorbid and elderly cohort of patients hospitalized, hospital-acquired COVID-19 infection is often fatal. Pathogen genome sequencing is becoming increasingly important in infection prevention and control (IPC).

Predicting survival in malignant pleural mesothelioma using routine clinical and laboratory characteristics.

Introduction: The prognosis of malignant pleural mesothelioma (MPM) is poor, with a median survival of 8-12 months. The ability to predict prognosis in MPM would help clinicians to make informed decisions regarding treatment and identify appropriate research opportunities for patients. The aims of this study were to examine associations between clinical and pathological information gathered during routine care, and prognosis of patients with MPM, and to develop a 6-month mortality risk prediction model.

Molecular pathology and thyroid FNA.

This review summarises molecular pathological techniques applicable to thyroid FNA. The molecular pathology of thyroid tumours is now fairly well understood. Molecular methods may be used as a rule-in test for diagnosis of malignancy in thyroid nodules, eg BRAF V600E point mutation, use of a seven-gene mutational panel (BRAF V600E, RAS genes, RET/PTC or PAX8/PPARG rearrangement), or as a comprehensive multigene next-generation sequencing panel, eg ThyroSeq v2.

The SENSOR Study: Protocol for a Mixed-Methods Study of Self-Management Checks to Predict Exacerbations of Pseudomonas Aeruginosa in Patients with Long-Term Respiratory Conditions.

Background: There are an estimated three million people in the United Kingdom with chronic obstructive pulmonary disease (COPD), and the incidence of bronchiectasis is estimated at around 0.1% but is more common in COPD and severe asthma. Both COPD and bronchiectasis are characterized by exacerbations in which bacteria play a central role.

Immunohistochemical expression of secreted frizzled receptor protein 1 in the invasive front of tongue squamous cell carcinoma.

The Wnt signalling pathway is involved in the development of oral cancer. When inactivated, secreted frizzled receptor protein 1 (SFRP1), a cellular Wnt-inhibitor protein, may enhance cancer development. The aim of this study was to assess the expression of SFRP1 in the invasive front of tongue squamous cell carcinoma (SCC).

Activity of EGFR, mTOR and PI3K inhibitors in an isogenic breast cell line model.

Background: The epidermal growth factor receptor family is expressed in breast cancer, and agents targeting this pathway have single agent effects (e.g. traztuzumab).

BRAF V600 co-testing in thyroid FNA cytology: short-term experience in a large cancer centre in the UK.

Aims: To ascertain whether BRAF V600 mutational analysis is useful for diagnosis of thyroid cancer in thyroid fine needle aspirate (FNA).

Methods: Over 8 months thyroid FNAs reported as Thy 3F (neoplasm possible/suggestive of follicular neoplasm), Thy4 (suspicious of malignancy) and Thy 5 (malignant) were tested for BRAF V600 mutation and managed as malignant if mutations were present.

Results: Of 207 FNAs from 176 patients, 5 were Thy 5, 19 Thy 4, 36 Thy 3f, 13 Thy 3a, 84 Thy 2 and 50 Thy 1.

BRAF V600 co-testing is technically feasible in conventional thyroid fine needle aspiration (FNA) cytology smears and can reduce the need for completion thyroidectomy.

Introduction: While fine needle aspiration cytology (FNAC) is the mainstay of diagnosis in thyroid nodules, molecular markers of thyroid cancer have recently been shown to be of value in improving the diagnosis and reducing the rates of unnecessary surgery.

Method: A technical method is presented for the assessment of the BRAF V600 gene mutation in thyroid cancer using a simple adaptation of a commercially available kit. After standard preparation and reporting of conventionally stained alcohol-fixed Papanicolaou or air-dried Giemsa-stained slides the coverslip is removed from one slide, the DNA is extracted and submitted for PCR analysis.

Targeting EGFR and PI3K pathways in ovarian cancer.

Background: The epidermal growth factor receptor (EGFR) is expressed in ovarian cancer, but agents targeting this pathway have shown little effect as single agents. This may be due to the presence of alternative pathways, particularly activation of the PI3K/Akt/MTOR pathway.

Methods: We have therefore examined the effect of inhibitors of this pathway (ZSTK474 and sirolimus) in combination with the EGFR inhibitors erlotinib and gefitinib in ovarian cancer primary cell cultures.

The effect of tricyclic antidepressants on cutaneous melanoma cell lines and primary cell cultures.

The tricyclic antidepressants have previously been shown to exert activity against glioma cells in vitro. Initial studies in cell lines suggested that this might extend to melanoma cells. We have therefore conducted a study in primary cell cultures from metastatic cutaneous melanoma deposits using a well established ATP-based tumour chemosensitivity assay to confirm and extend these findings.

Measuring gene expression from cell cultures by quantitative reverse-transcriptase polymerase chain reaction.

Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) offers a robust method for the measurement of RNA levels for any gene within cells harvested at any point before or during cell culture. The key elements of RNA extraction followed by a two-step qRT-PCR method (reverse transcription and PCR) are described, followed by a brief section on analysis of the results. There are a number of excellent kits available commercially for much of this work, but it is essential to ensure that the quality and quantity of cDNA produced is adequate for the standard PCR or array to be used.

Cell sensitivity assays: the ATP-based tumor chemosensitivity assay.

The ATP-based tumor chemosensitivity assay (ATP-TCA) is a standardised system which can be adapted to a variety of uses with both cell lines and primary cell cultures. It has a strong track record in drug development, mechanistic studies of chemoresistance and as an aid to clinical decision-making. The method starts with the extraction of cells in suspension from continuous cell culture (for cell lines), malignant effusions or biopsy material.

Isolation and culture of colon cancer cells and cell lines.

The preparation of cells from heavily contaminated tissue is challenging. It is usually best to avoid such specimens if possible, but for the study of colorectal and some other tumours, it is inevitable that this must be overcome. The best methods seem to use a combination of (1) debridement of necrotic or infected areas of the tumour, (2) enzymatic dissociation in the presence of antibiotics, (3) density centrifugation to remove debris, and (4) extensive washing of the tumour-derived cells prior to their use in cell culture methods.

The molecular basis of the chemosensitivity of metastatic cutaneous melanoma to chemotherapy.

Background: Chemotherapy benefits relatively few patients with cutaneous melanoma. The assessment of tumour chemosensitivity by the ATP-based tumour chemosensitivity assay (ATP-TCA) has shown strong correlation with outcome in cutaneous melanoma, but requires fresh tissue and dedicated laboratory facilities.

Aim: To examine whether the results of the ATP-TCA correlate with the expression of genes known to be involved in resistance to chemotherapy, based on the hypothesis that the molecular basis of chemosensitivity lies within known drug resistance mechanisms.

Molecular basis of chemosensitivity of platinum pre-treated ovarian cancer to chemotherapy.

Background: Ovarian cancer shows considerable heterogeneity in its sensitivity to chemotherapy both clinically and in vitro. This study tested the hypothesis that the molecular basis of this difference lies within the known resistance mechanisms inherent to these patients' tumours.

Methods: The chemosensitivity of a series of 31 ovarian tumours, all previously treated with platinum-based chemotherapy, was assessed using the ATP-based tumour chemosensitivity assay (ATP-TCA) and correlated with resistance gene expression measured by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) in a TaqMan Array following extraction of mRNA from formalin-fixed paraffin-embedded tissue.

Efficacy of anti-cancer agents in cell lines versus human primary tumour tissue.

The discovery of anti-cancer drugs has become dependent on cell lines, which are used to screen potential compounds for activity as well as to explore cancer biology. Cell lines produce rapid results, but their relevance to patient outcomes is questionable as they undergo selection over many passages to a point where they are no longer representative of their originating tumour. This has led to the increasing use of primary cell cultures, primary tumour cell explants, early passage cell lines, and xenografts to improve the accuracy of results during drug development.

The effect of pentamidine on melanoma ex vivo.

Pentamidine is a small molecule inhibitor of the Ca(+)-binding protein S100B and disrupts the S100B-p53 protein-protein interaction; this is thought to restore wild-type p53 tumour suppressor function in melanoma. Additional anticancer effects may be the result of inhibition of regenerating liver family phosphatases. In this study, we have used a standardized ATP-tumour chemosensitivity assay to investigate the effect of pentamidine on cells derived from 18 skin melanoma samples and one uveal melanoma sample.

Resistance gene expression determines the in vitro chemosensitivity of non-small cell lung cancer (NSCLC).

Background: NSCLC exhibits considerable heterogeneity in its sensitivity to chemotherapy and similar heterogeneity is noted in vitro in a variety of model systems. This study has tested the hypothesis that the molecular basis of the observed in vitro chemosensitivity of NSCLC lies within the known resistance mechanisms inherent to these patients' tumors.

Methods: The chemosensitivity of a series of 49 NSCLC tumors was assessed using the ATP-based tumor chemosensitivity assay (ATP-TCA) and compared with quantitative expression of resistance genes measured by RT-PCR in a Taqman Array following extraction of RNA from formalin-fixed paraffin-embedded (FFPE) tissue.