Patient-derived explants (PDEs) as a powerful preclinical platform for anti-cancer drug and biomarker discovery.

Preclinical models that can accurately predict outcomes in the clinic are much sought after in the field of cancer drug discovery and development. Existing models such as organoids and patient-derived xenografts have many advantages, but they suffer from the drawback of not contextually preserving human tumour architecture. This is a particular problem for the preclinical testing of immunotherapies, as these agents require an intact tumour human-specific microenvironment for them to be effective. In this review, we explore the potential of patient-derived explants (PDEs) for fulfilling this need. PDEs involve the ex vivo culture of fragments of freshly resected human tumours that retain the histological features of original tumours. PDE methodology for anti-cancer drug testing has been in existence for many years, but the platform has not been widely adopted in translational research facilities, despite strong evidence for its clinical predictivity. By modifying PDE endpoint analysis to include the spatial profiling of key biomarkers by using multispectral imaging, we argue that PDEs offer many advantages, including the ability to correlate drug responses with tumour pathology, tumour heterogeneity and changes in the tumour microenvironment. As such, PDEs are a powerful model of choice for cancer drug and biomarker discovery programmes.

Novel plasma microRNA biomarkers for the identification of colitis-associated carcinoma.

BACKGROUND: Ulcerative colitis is an established risk factor for colorectal cancer, also known as colitis-associated cancer. Existing colonoscopic-based surveillance has many disadvantages, so a new accurate, efficient, cost-effective screening test is needed. MicroRNAs (miRNAs) regulate gene expression and are dysregulated in a range of diseases, including ulcerative colitis and colorectal cancer. This study aimed to establish the miRNAs associated with colitis-associated cancer. METHODS: Blood samples were collected from 45 adult patients undergoing colonoscopic screening for ulcerative colitis at the Leicester General Hospital, Leicester, UK. Pool A and B TaqMan Array 384-well cards were used to quantify the expression of 754 miRNAs in the circulating plasma. 28 high priority miRNA candidates showing abnormal expression were validated with real-time quantitative PCR. FINDINGS: Patients were allocated to three disease groups (ulcerative colitis, n=37; dysplasia, n=2; colitis-associated cancer, n=6). Analysis of variance was used to assess differences between the groups. miR-375 was significantly upregulated in the colitis-associated cancer cohort (p=0·0061) compared with active ulcerative colitis. Combining several miRNAs in a panel increased the capacity of the test to distinguish between colitis-associated cancer and different ulcerative colitis activity states. INTERPRETATION: Our study suggests that miRNAs have the potential to act as blood-based biomarkers to monitor the activity and progression of disease in patients with ulcerative colitis. FUNDING: Royal College of Surgeons of England.

Patient-Derived Tumor Explants As a "Live" Preclinical Platform for Predicting Drug Resistance in Patients.

An understanding of drug resistance and the development of novel strategies to sensitize highly resistant cancers rely on the availability of suitable preclinical models that can accurately predict patient responses. One of the disadvantages of existing preclinical models is the inability to contextually preserve the human tumor microenvironment (TME) and accurately represent intratumoral heterogeneity, thus limiting the clinical translation of data. By contrast, by representing the culture of live fragments of human tumors, the patient-derived explant (PDE) platform allows drug responses to be examined in a three-dimensional (3D) context that mirrors the pathological and architectural features of the original tumors as closely as possible. Previous reports with PDEs have documented the ability of the platform to distinguish chemosensitive from chemoresistant tumors, and it has been shown that this segregation is predictive of patient responses to the same chemotherapies. Simultaneously, PDEs allow the opportunity to interrogate molecular, genetic, and histological features of tumors that predict drug responses, thereby identifying biomarkers for patient stratification as well as novel interventional approaches to sensitize resistant tumors. This paper reports PDE methodology in detail, from collection of patient samples through to endpoint analysis. It provides a detailed description of explant derivation and culture methods, highlighting bespoke conditions for particular tumors, where appropriate. For endpoint analysis, there is a focus on multiplexed immunofluorescence and multispectral imaging for the spatial profiling of key biomarkers within both tumoral and stromal regions. By combining these methods, it is possible to generate quantitative and qualitative drug response data that can be related to various clinicopathological parameters and thus potentially be used for biomarker identification.

The Sensitivity and Specificity of Novel Primers for Detection of BRAFV600E Mutation.

OBJECTIVE: This study aimed to evaluate the sensitivity and specificity of a PCR-based novel technique for the detection of BRAF mutation in early stages of the cancer. METHODS: Different lengths of primer sets, ranging from 8 bp to 20 bp, were designed and used in this study. These primers were developed by applying on  cancer cell lines. After that, the sensitivity and specificity of the methodology  was evaluated by making serial dilutions. RESULTS: The quantitative allele specific discrimination PCR (QUASAqPCR) primer with 14 bp length was sensitive enough to detect significantly 1:1,000 ratio of BRAFV600E to wild-type background  (P = 0.011), when using 150 nanograms of DNA from cell lines in the reactions. CONCLUSION: High sensitivity and specificity levels of QUASA-qPCR method can improve diagnostic accuracy for BRAF mutation testing in patients at early stages of cancers and help stratify the appropriate choice of treatment.

Circulating tumor DNA in patients with colorectal adenomas: assessment of detectability and genetic heterogeneity.

Improving early detection of colorectal cancer (CRC) is a key public health priority as adenomas and stage I cancer can be treated with minimally invasive procedures. Population screening strategies based on detection of occult blood in the feces have contributed to enhance detection rates of localized disease, but new approaches based on genetic analyses able to increase specificity and sensitivity could provide additional advantages compared to current screening methodologies. Recently, circulating cell-free DNA (cfDNA) has received much attention as a cancer biomarker for its ability to monitor the progression of advanced disease, predict tumor recurrence and reflect the complex genetic heterogeneity of cancers. Here, we tested whether analysis of cfDNA is a viable tool to enhance detection of colon adenomas. To address this, we assessed a cohort of patients with adenomas and healthy controls using droplet digital PCR (ddPCR) and mutation-specific assays targeted to trunk mutations. Additionally, we performed multiregional, targeted next-generation sequencing (NGS) of adenomas and unmasked extensive heterogeneity, affecting known drivers such as APC, KRAS and mismatch repair (MMR) genes. However, tumor-related mutations were undetectable in patients' plasma. Finally, we employed a preclinical mouse model of Apc-driven intestinal adenomas and confirmed the inability to identify tumor-related alterations via cfDNA, despite the enhanced disease burden displayed by this experimental cancer model. Therefore, we conclude that benign colon lesions display extensive genetic heterogeneity, that they are not prone to release DNA into the circulation and are unlikely to be reliably detected with liquid biopsies, at least with the current technologies.

Expression of CTGF and Cyr61 in colorectal cancer.

BACKGROUND: The CCN genes encode secreted extracellular matrix proteins cysteine rich-61 (Cyr61), connective tissue growth factor (CTGF) and nephroblastoma overexpressed (Nov). They are involved in diverse cellular functions. Expression of these factors in tumours has produced conflicting results. More recently, research has focused on molecular biomarkers to indicate progression of a disease or the susceptibility of the disease to a given treatment. AIMS: The purpose of this study was to determine the expression of CTGF and Cyr61 genes and proteins in colorectal cancer. Expression was compared with various clinicopathological parameters including Dukes' stage and TNM stage. We determined the in vitro effects of hypoxia on Cyr61 and CTGF expression in colorectal cancer cell lines. RESULTS: Hypoxia significantly reduced CTGF mRNA expression (p<0.01) in HT29 and Caco-2 cell lines. Cyr61 was induced (p<0.01) in HT29 cell lines but significantly reduced (p<0.01) in Caco-2 cell lines under hypoxic conditions. High levels of CTGF and Cyr61 mRNA were found in colorectal cancer compared with normal colon (p<0.05). Expression was reduced in more advanced cancers (Dukes' C vs Dukes' A and B). There was a significant association between CTGF protein expression and advancing Dukes' stage (p<0.01), T stage (p<0.01) and lymph-node involvement (p<0.05), but there was no significant association between Cyr61 expression and clinicopathological parameters. CONCLUSION: Upregulation of Cyr61 and CTGF gene expression in colorectal cancer suggests they have a role in tumour initiation or development. However, the genes are not as highly expressed in advanced stages of colorectal cancer, suggesting their role may be important at an early stage of tumour development. These genes maybe used as early biomarkers to risk-stratify patients. Hypoxia alters the expression of these genes in colorectal cancer cell lines. Further studies are needed to determine whether targeting these genes would be useful in future therapy.

A ganglioneuroma of the sigmoid colon presenting as leading point of intussusception in a child: a case report.

We present a case of intestinal ganglioneuroma (GN) of the sigmoid colon in a 5-year-old girl, which caused intermittent colocolic intussusception. Ganglioneuromas are rare benign tumors of the autonomic nervous system composed of mature ganglion cells and satellite cells. Colonic GNs are uncommon. The unusual intramural proliferation of neural elements in this case resembled the diffuse intestinal ganglioneuromatosis, which is known to be associated with multiple endocrine neoplasia type 2B. However, the specific mutations of multiple endocrine neoplasia type 2B were not found by genetic sequencing. This is the first pediatric case described in the literature of a solitary polypoid GN presenting as a colocolic intussusception. We present a brief overview of intestinal ganglioneuromatous lesions and associated conditions.