Cancer biomarker development from basic science to clinical practice

The amount of published literature on biomarkers has exponentially increased over the last two decades. Cancer biomarkers are molecules that are either part of tumour cells or secreted by tumour cells. Biomarkers can be used for diagnosing cancer (tumour versus normal and differentiation of subtypes), prognosticating patients (progression free survival and overall survival) and predicting response to therapy. However, very few biomarkers are currently used in clinical practice compared to the unprecedented discovery rate. Some of the examples are: carcino-embryonic antigen (CEA) for colon cancer; prostate specific antigen (PSA) for prostate; and estrogen receptor (ER), progesterone receptor (PR) and HER2 for breast cancer. Cancer biomarkers passes through a series of phases before they are used in clinical practice. First phase in biomarker development is identification of biomarkers which involve discovery, demonstration and qualification. This is followed by validation phase, which includes verification, prioritisation and initial validation. More large-scale and outcome-oriented validation studies expedite the clinical translation of biomarkers by providing a strong ‘evidence base’. The final phase in biomarker development is the routine clinical use of biomarker. In summary, careful identification of biomarkers and then validation in well-designed retrospective and prospective studies is a systematic strategy for developing clinically useful biomarkers

Cancers of unknown primary diagnosed during hospitalization: a population-based study

Background: Cancers of Unknown Primary (CUP) are the 3-4th most common causes of cancer death and recent clinical guidelines recommend that patients should be directed to a team dedicated to their care. Our aim was to inform the care of patients diagnosed with CUP during hospital admission. Methods: Descriptive study using hospital admissions (Scottish Morbidity Record 01) linked to cancer registrations (ICD-10 C77-80) and death records from 1998 to 2011 in West of Scotland, UK (population 2.4 m). Cox proportional hazards models were used to assess effects of baseline variables on survival. Results: Seven thousand five hundred ninety nine patients were diagnosed with CUP over the study period, 54.4% female, 67.4% aged ≥ 70 years, 36.7% from the most deprived socio-economic quintile. 71% of all diagnoses were made during a hospital admission, among which 88.6% were emergency presentations and the majority (56.3%) were admitted to general medicine. Median length of stay was 15 days and median survival after admission 33 days. Non-specific morphology, emergency admission, age over 60 years, male sex and admission to geriatric medicine were all associated with poorer survival in adjusted analysis. Conclusions: Patients with a diagnosis of CUP are usually diagnosed during unplanned hospital admissions and have very poor survival. To ensure that patients with CUP are quickly identified and directed to optimal care, increased surveillance and rapid referral pathways will be required

Profiling, Comparison and Validation of Gene Expression in Gastric Carcinoma and Normal Stomach

Gastric carcinoma is the second most common cause of cancer death world-wide but its molecular biology is not well understood. My aims were to catalogue the genes expressed in gastric carcinoma and normal stomach and to identify differentially expressed and gastric-specific transcripts. Serial analysis of gene expression (SAGE) produces comprehensive, quantitative and reproducible expression profiles. The method of SAGE was established in this laboratory then used to study normal gastric antral mucosa and two gastric adenocarcinomas of distal, intestinal type. The libraries were compared on-line with other glandular epithelial tissues. Selected genes were validated in a panel of 19 normal and tumour gastro-intestinal tissues and cell lines by Northern blotting and immunohistochemistry. 29,480 transcripts, derived from 10,866 genes, were identified. The validation studies corroborated the SAGE profiles although tumour heterogeneity was noted. 1% of genes were differentially expressed (by over five-fold and with a p-value below 0.01) between the pooled gastric carcinomas and normal stomach. The most abundant transcripts included ribosomal and mitochondrial proteins, of which most were up- regulated in the tumours, as were other widely expressed genes including transcription factors (Id1), signalling molecules (fibroblast growth factor receptor and serine/threonine protein kinases), coatomer and proteasome components, thymosin beta 10 and collagenase I. In contrast, cytoskeletal proteins (alpha actinin and profilin) were down-regulated in the tumours. Many genes which were more highly expressed in normal stomach are important in normal gastric function, including gastrin, immunoglobulin alpha, lysozyme, mucin (MUC5), trefoil peptides (pS2 and spasmolytic polypeptide) and pepsinogens, which were amongst 55 gastric-specific transcripts. Some transcripts had previously been characterised only minimally (prostate stem cell antigen) or not at all (aquaporin 5) in the stomach. Some genes (intestinal trefoil factor) which were up-regulated in gastric carcinoma reflect the intestinal-type histology. Some genes abundant in normal gastric antrum had previously been regarded as markers of pancreatic carcinoma. Many differentially expressed species, some tumour-associated, were novel and await investigation. One new gene which was identified was highly expressed in normal stomach but absent from gastric carcinomas. This new gene was selected for further investigation. The SAGE expression profile was confirmed by Northern blotting and in situ hybridisation by which the mRNA was located in the superficial/foveolar (pit) epithelium of the gastric mucosa, so the gene was termed foveolin. The transcript was expressed outwith the stomach only in metaplastic gastric epithelium, in Barrett's oesophagus or the ulcer-associated cell lineage in the gut, and outwith the gut only in ovarian mucinous tumours. The mRNA was present in the stomach of mouse, rat and cow in the same location as in humans. The 5' and 3' ends of the mRNA were characterised by Rapid Amplification of cDNA Ends (RACE). Homologous mouse and cow mRNAs were identified, characterised and compared. The full-length genomic sequences for the human and mouse were obtained using on-line databases, characterised and compared. A partial human genomic clone was obtained from a PAC library, and used to map the gene by fluorescent in situ hybridisation (FISH) to human chromosome 2. The predicted protein product, like the mRNA and DNA sequences, is highly conserved between the human, mouse and cow species. The protein shows no homology to any known protein sequences or motifs, but bears an initial signal peptide and is therefore predicted to have an extracellular location, being either retained on the outer cell surface or secreted into the gastric lumen, much like gastric mucin (MUC5) and the trefoil peptide pS2 (TFF1), with which foveolin shares a similar location in the superficial and foveolar gastric epithelium. These are the first global profiles of gene expression in the stomach. The molecular anatomy correlated with the morphology. The gastric carcinoma profiles resembled other tumours, which supports the existence of common cancer-associated molecular targets. The normal gastric profile differed from other normal glandular tissues but agreed with existing literature. Many new transcripts were identified, of which one has been further characterised here in its first detailed description. These data increase our knowledge about the genes involved in normal gastric function and in malignant change in the stomach, and provide a catalogue of candidates from which to develop markers for better diagnosis and therapy of gastric carcinoma

Prevalent low-grade dysplasia: the strongest predictor of malignant progression in Barrett's columnar-lined oesophagus

No abstract

A33 shows similar sensitivity to but is more specific than CDX2 as an immunomarker of colorectal carcinoma

Aims: CDX2 is widely used as a sensitive and specific immunomarker for colorectal carcinoma (CRC) but neither this sensitivity nor specificity is absolute. This study is the first known comparison of CDX1 and A33 against CDX2 as immunomarkers for CRC. Methods and Results: As a pilot study, whole sections of 51 cases of liver metastatic carcinoma of different origins - colorectum (n=32), breast (n=3), oesophagogastric tract (n=4), lung (n=3), pancreas (n=8), and prostate (n=1) - were immunostained with CDX1, CDX2 and A33. Compared with CDX1, A33 showed higher sensitivity as a CRC immunomarker, greater interobserver reproducibility for assessment of expression, and less background cross-reactivity. Therefore, only A33 was compared with CDX2 for a tissue microarray-based study of primary adenocarcinomas of different origin: CRC (n=55), liver deposits of metastatic CRC (n=60), breast (n=101), lung (n=40), oesophagogastric tract (n=134), ovary (n= 67), pancreas (n= 77), and prostate (n= 56). Combining the whole section and TMA cases of CRC, A33 had a sensitivity of 95.9% and CDX2 a sensitivity of 97.2%. Combining all the whole section and TMA cases of non-colorectal carcinomas, A33 showed 85.4% specificity as a marker of CRC compared to CDX2 which showed a specificity of 64.3%. The higher specificity of A33 as a colorectal carcinoma immunomarker compared with CDX2 was particularly seen amongst pancreatic and ovarian carcinomas. Further, unlike with CDX2, none of the prostatic and lung carcinomas studied showed A33 positivity. Conclusions: A33 shows similar sensitivity to but is more specific than CDX2 as an immunomarker of CRC

Digital pathology access and usage in the UK: results from a national survey on behalf of the National Cancer Research Institute's CM-Path initiative.

Aim To canvass the UK pathology community to ascertain current levels of digital pathology usage in clinical and academic histopathology departments, and prevalent attitudes to digital pathology. Methods A 15-item survey was circulated to National Health Service and academic pathology departments across the UK using the SurveyMonkey online survey tool. Responses were sought at a departmental or institutional level. Where possible, departmental heads were approached and asked to complete the survey, or forward it to the most relevant individual in their department. Data were collected over a 6-month period from February to July 2017. Results 41 institutes from across the UK responded to the survey. 60% (23/39) of institutions had access to a digital pathology scanner, and 60% (24/40) had access to a digital pathology workstation. The most popular applications of digital pathology in current use were undergraduate and postgraduate teaching, research and quality assurance. Investigating the deployment of digital pathology in their department was identified as a high or highest priority by 58.5% of institutions, with improvements in efficiency, turnaround times, reporting times and collaboration in their institution anticipated by the respondents. Access to funding for initial hardware, software and staff outlay, pathologist training and guidance from the Royal College of Pathologists were identified as factors that could enable respondent institutions to increase their digital pathology usage. Conclusion Interest in digital pathology adoption in the UK is high, with usage likely to increase in the coming years. In light of this, pathologists are seeking more guidance on safe usage

Time for change: a new training programme for morpho-molecular pathologists?

The evolution of cellular pathology as a specialty has always been driven by technological developments and the clinical relevance of incorporating novel investigations into diagnostic practice. In recent years, the molecular characterisation of cancer has become of crucial relevance in patient treatment both for predictive testing and subclassification of certain tumours. Much of this has become possible due to the availability of next-generation sequencing technologies and the whole-genome sequencing of tumours is now being rolled out into clinical practice in England via the 100 000 Genome Project. The effective integration of cellular pathology reporting and genomic characterisation is crucial to ensure the morphological and genomic data are interpreted in the relevant context, though despite this, in many UK centres molecular testing is entirely detached from cellular pathology departments. The CM-Path initiative recognises there is a genomics knowledge and skills gap within cellular pathology that needs to be bridged through an upskilling of the current workforce and a redesign of pathology training. Bridging this gap will allow the development of an integrated 'morphomolecular pathology' specialty, which can maintain the relevance of cellular pathology at the centre of cancer patient management and allow the pathology community to continue to be a major influence in cancer discovery as well as playing a driving role in the delivery of precision medicine approaches. Here, several alternative models of pathology training, designed to address this challenge, are presented and appraised

Increased prevalence of precancerous changes in relatives of gastric cancer patients: critical role of H. pylori

Background & Aims:Helicobacter pylori is believed to predispose to gastric cancer by inducing gastric atrophy and hypochlorhydria. First-degree relatives of patients with gastric cancer have an increased risk of developing gastric cancer. The aim of this study was to determine the prevalence of atrophy and hypochlorhydria and their association with H. pylori infection in first-degree relatives of patients with gastric cancer. Methods:H. pylori status, gastric secretory function, and gastric histology were studied in 100 first-degree relatives of patients with noncardia gastric cancer and compared with those of controls with no family history of this cancer. Results: Compared with healthy controls, relatives of patients with gastric cancer had a higher prevalence of hypochlorhydria (27% vs. 3%) but a similar prevalence of H. pylori infection (63% vs. 64%). Relatives of cancer patients also had a higher prevalence of atrophy (34%) than patients with nonulcer dyspepsia (5%) matched for H. pylori prevalence. Among the relatives of cancer patients, the prevalence of atrophy and hypochlorhydria was increased only in those with evidence of H. pylori infection, was greater in relatives of patients with familial cancer than in relatives of sporadic cancer index patients, and increased with age. Eradication of H. pylori infection produced resolution of the gastric inflammation in each subject and resolution of hypochlorhydria and atrophy in 50% of the subjects. Conclusions: Relatives of patients with gastric cancer have an increased prevalence of precancerous gastric abnormalities, but this increase is confined to those with H. pylori infection. Consequently, prophylactic eradication of the infection should be offered to such subjects

The CM-Path Biobanking Sample Quality Improvement Tool : A Guide for Improving the Quality of Tissue Collections for Biomedical Research and Clinical Trials in Cancer

Funding: The NCRI's CM-Path initiative was established in 2016 with the aim of re-invigorating academic pathology. It is funded as a collaborative venture between ten of the NCRI partner organisations: Bloodwise, Breast Cancer Now, Cancer Research UK, the Chief Scientist Office (Scotland), the Department of Health and Social Care (England), Health and Care Research Wales, Health and Social Care (Northern Ireland), the Medical Research Council, Prostate Cancer UK and Tenovus Cancer Care. These organisations did not participate in study design; collection, analysis and interpretation of data; writing the report or the decision to submit the paper for publication. Acknowledgments Thanks to the following for assisting in the scoping exercise: Joanna Baxter, Cambridge Blood and Stem Cell Bank; Chris Birkett, Human Tissue Authority; Tim Brend, Breast Cancer Now Tissue Bank, University of Leeds; Brian Clark, Novo Nordisk; Emma Lawrence, UKCRC Tissue Directory and Coordination Centre; Alex MacLellan, CRUK Tissue Group, Edinburgh; Balwir Matharoo-Ball, Nottingham Health Sciences Biobank; Bill Mathieson, NHS Grampian Biorepository; Gita Mistry Children’s Cancer and Leukaemia Group Tissue Bank; Will Navaie, Health Research Authority; Rob Oliver, Salford Royal NHS Foundation Trust; Kathleen Potter, Cancer Sciences Tissue Bank, University of Southampton; Doris Rassl, Papworth Hospital NHS Foundation Trust; Jane Steele, Human Biomaterials Resource Centre, University of Birmingham; Sarah Yeats, WISH Lab, University of Southampton. Special thanks Anne Carter for her tireless work with CCB and to staff at the following biobanks who piloted the Sample Quality Improvement Tool: Greater Glasgow & Clyde Biorepository, Leeds Breast Cancer Now Tissue Bank, Leeds Multidisciplinary Research Tissue Bank and Southampton Tissue Bank.Peer reviewedPostprin

Pathology and regulation for research in the UK: An overview [version 2; peer review: 3 approved]

The input of pathologists is essential for the conduct of many forms of research, including clinical trials. As the custodians of patient samples, pathology departments have a duty to ensure compliance with the relevant regulations, standards and guidelines to ensure the ethical and effective use for their intended investigational analysis, including when patients are participating in a research study. The results of research studies have impacts beyond the research study itself as they may inform changes in policy and practice or support the licensing of medicines and devices. Compliance with regulations and standards provides public assurance that the rights, safety and wellbeing of research participants are protected, that the data have been collected and processed to ensure their integrity and that the research will achieve its purpose. The requirements of the regulatory environment should not be seen as a barrier to research and should not significantly impact on the work of the laboratory once established and integrated into practice. This paper highlights important regulations, policy, standards and available guidance documents that apply to research involving NHS pathology departments and academic laboratories that are contributing to research involving human subjects