Sequence and expression of complement factor H gene cluster variants and their roles in age-related macular degeneration risk

Purpose: To investigate how potentially functional genetic variants are coinherited on each of four common complement factor H (CFH) and CFH-related gene haplotypes and to measure expression of these genes in eye and liver tissues.

Methods: We sequenced the CFH region in four individuals (one homozygote for each of four common CFH region haplotypes) to identify all genetic variants. We studied associations between the haplotypes and AMD phenotypes in 2157 cases and 1150 controls. We examined RNA-seq profiles in macular and peripheral retina and retinal pigment epithelium/choroid/sclera (RCS) from eight eye donors and three liver samples.

Results: The haplotypic coinheritance of potentially functional variants (including missense variants, novel splice sites, and the CFHR3–CFHR1 deletion) was described for the four common haplotypes. Expression of the short and long CFH transcripts differed markedly between the retina and liver. We found no expression of any of the five CFH-related genes in the retina or RCS, in contrast to the liver, which is the main source of the circulating proteins.

Conclusions: We identified all genetic variants on common CFH region haplotypes and described their coinheritance. Understanding their functional effects will be key to developing and stratifying AMD therapies. The small scale of our expression study prevented us from investigating the relationships between CFH region haplotypes and their expression, and it will take time and collaboration to develop epidemiologic-scale studies. However, the striking difference between systemic and ocular expression of complement regulators shown in this study suggests important implications for the development of intraocular and systemic treatments.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.

Investigating Fractured Flow from Orthopaedics to Rehabilitation

Patients often spend time as inpatients in hospitals outside their home area because of the need to access specialist services. If there is a need for ongoing care after the need for specialist care has passed, patients are transferred (or ‘repatriated’) back to the inpatient care of a hospital in their local Health and Social Care Trust. The need for bed space in specialist units means that there is pressure for this transition to occur in a timely way. We investigated the flow of patients through a trauma and orthopaedics unit using the 6M Design® framework and Vitals Charts® in order to investigate concerns about delayed repatriation. We found that repatriation was part of a complex system that had interdependent components. There was considerable variation in the number of discharges (to any destination) by day of week, with a reduction on Saturdays and Sundays. Understanding that the pressure for quicker repatriation was really due to high work-in-progress led us to model the effects of strategies to address the high work-in-progress. We found that, because only a small proportion of patients require repatriation, expediting the repatriation process by one day for each patient would only reduce WIP by an average of 1.6 patients. Reducing the average length of stay for all trauma and orthopaedics inpatients by one day would reduce the WIP by 10 patients, which would make a much greater impact on the problem of high bed occupancy. Though the smooth and timely repatriation of patients to rehabilitation units is desirable, it is unlikely that efforts to achieve this will have a substantial impact on the problem of high WIP, so other strategies will be required. We will model the effects of strategies to reduce variation in daily discharges by the day of week in a future essay.