Rare Disease Research Partnership (RAinDRoP): a collaborative approach to identify research priorities for rare diseases in Ireland.

Background: The Rare Disease Research Partnership (RAinDRoP) was established in 2018 to bring together a wide variety of diverse voices in the rare disease community in Ireland and form a research partnership. This approach enabled clinicians, patients, carers and researchers to work together to identify top research priorities for rare diseases, which focused on a life-course perspective rather than a disease-specific need.                                                                                                           Methods: A participatory multiple phase approach was used to identify research priorities for rare diseases. The research process involved three main phases: Phase I, Public Consultation Survey on Research in Rare Diseases in Ireland (PCSRRDI); Phase II, Research Prioritisation Workshop (RPW); Phase III, Follow-up Public Consultation and Prioritisation Survey (FWPCPS). Results: In total, 240 individuals completed the phase I PCSRRDI, which comprised of a cross-section of health care professionals, researchers and people living with rare diseases. One thousand and fifteen statements were collected, reflecting issues and shared challenges in rare diseases. A shortlisting step by step was used to identify any statements that had received a total score of above 50% into 10-12 researchable questions or statements per the theme for the phase II workshop. Phase II was focused on three main themes: (1) Route to Diagnosis, (2) Living with Rare Disease, (3) Integrated and Palliative Care. In total, 62 individuals attended the overall workshop; 42 participated in the prioritisation sessions. A cross-section of health care professionals, researchers and people living with rare diseases were engaged at each workshop. Seventy-five individuals completed the final phase III public ranking by priority responses, and they ranked the top 15 research priorities defined by the multi-stakeholders at the phase II consensus meeting. Conclusions: This study identified priorities for rare diseases research aimed at improving the health and wellbeing of people living with rare diseases.

Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.

mRNA chimeras from chromosomal translocations often play a role as transforming oncogenes. However, cancer transcriptomes also contain mRNA chimeras that may play a role in tumor development, which arise as transcriptional or post-transcriptional events. To identify such chimeras, we developed a deterministic screening strategy for long-range sequence analysis. High-throughput, long-read sequencing was then performed on cDNA libraries from major tumor histotypes and corresponding normal tissues. These analyses led to the identification of 378 chimeras, with an unexpectedly high frequency of expression (≈2 x 10(-5) of all mRNA). Functional assays in breast and ovarian cancer cell lines showed that a large fraction of mRNA chimeras regulates cell replication. Strikingly, chimeras were shown to include both positive and negative regulators of cell growth, which functioned as such in a cell-type-specific manner. Replication-controlling chimeras were found to be expressed by most cancers from breast, ovary, colon, uterus, kidney, lung, and stomach, suggesting a widespread role in tumor development.

The colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information.

BACKGROUND: To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome. METHODS: DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information. RESULTS: The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance. CONCLUSIONS: Analysis from our in vitro and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including IGF2BP2, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.