Sharing is caring: a call for a new era of rare disease research and development

The state-of-the-art of N-of-1 therapies and the IRDiRC N-of-1 development roadmap

In recent years, a small number of people with rare diseases caused by unique genetic variants have been treated with therapies developed specifically for them. This pioneering field of genetic N-of-1 therapies is evolving rapidly, giving hope for the individualized treatment of people living with very rare diseases. In this Review, we outline the concept of N-of-1 individualized therapies, focusing on genetic therapies, and illustrate advances and challenges in the field using cases for which therapies have been successfully developed. We discuss why the traditional drug development and reimbursement pathway is not fit for purpose in this field, and outline the pragmatic, regulatory and ethical challenges this poses for future access to N-of-1 therapies. Finally, we provide a roadmap for N-of-1 individualized therapy development.

High-throughput assays to assess variant effects on disease

Interpreting the wealth of rare genetic variants discovered in population-scale sequencing efforts and deciphering their associations with human health and disease present a critical challenge due to the lack of sufficient clinical case reports. One promising avenue to overcome this problem is deep mutational scanning (DMS), a method of introducing and evaluating large-scale genetic variants in model cell lines. DMS allows unbiased investigation of variants, including those that are not found in clinical reports, thus improving rare disease diagnostics. Currently, the main obstacle limiting the full potential of DMS is the availability of functional assays that are specific to disease mechanisms. Thus, we explore high-throughput functional methodologies suitable to examine broad disease mechanisms. We specifically focus on methods that do not require robotics or automation but instead use well-designed molecular tools to transform biological mechanisms into easily detectable signals, such as cell survival rate, fluorescence or drug resistance. Here, we aim to bridge the gap between disease-relevant assays and their integration into the DMS framework.

Integrated Epigenetic and Transcriptomic Analysis Identifies Interleukin 17 DNA Methylation Signature of Malignant Peripheral Nerve Sheath Tumor Progression and Metastasis

PURPOSE

Sarcomas are a complex group of highly aggressive and metastatic tumors with over 100 distinct subtypes. Because of their diversity and rarity, it is challenging to generate multisarcoma signatures that are predictive of patient outcomes.

MATERIALS AND METHODS

Here, we identify a DNA methylation signature for progression and metastasis of numerous sarcoma subtypes using multiple epigenetic and genomic patient data sets. Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly metastatic sarcomas with frequent loss of the histone methyltransferase, PRC2. Loss of PRC2 is associated with MPNST metastasis and plays a critical noncanonical role in DNA methylation.

RESULTS

We found that over 900 5'-C-phosphate-G-3' (CpGs) were hypermethylated in MPNSTs with PRC2 loss. Furthermore, we identified eight differentially methylated CpGs in the IL17D/RD family that correlate with the progression and metastasis of MPNSTs in two independent patient data sets. Similar trends were identified in other sarcoma subtypes, including osteosarcoma, rhabdomyosarcoma, and synovial sarcoma. Analysis of scRNAseq data sets determined that IL17D/RD expression occurs in both the tumor cells and the surrounding stromal populations.

CONCLUSION

These results might have broad implications for the clinical management and surveillance of sarcoma.

Cancer researchers' experiences with and perceptions of research data sharing: Results of a cross-sectional survey

BACKGROUND

Despite wide recognition of the benefits of sharing research data, public availability rates have not increased substantially in oncology or medicine more broadly over the last decade.

METHODS

We surveyed 285 cancer researchers to determine their prior experience with sharing data and views on known drivers and inhibitors.

RESULTS

We found that 45% of respondents had shared some data from their most recent empirical publication, with respondents who typically studied non-human research participants, or routinely worked with human genomic data, more likely to share than those who did not. A third of respondents added that they had previously shared data privately, with 74% indicating that doing so had also led to authorship opportunities or future collaborations for them. Journal and funder policies were reported to be the biggest general drivers toward sharing, whereas commercial interests, agreements with industrial sponsors and institutional policies were the biggest prohibitors. We show that researchers' decisions about whether to share data are also likely to be influenced by participants' desires.

CONCLUSIONS

Our survey suggests that increased promotion and support by research institutions, alongside greater championing of data sharing by journals and funders, may motivate more researchers in oncology to share their data.

Determining Commonalities in the Experiences of Patients with Rare Diseases: A Qualitative Analysis of US Food and Drug Administration Patient Engagement Sessions

BACKGROUND

Rare diseases are estimated to affect more than one in ten Americans. However, most patients with a rare disease face significant emotional, physical, and social challenges. To better understand the burden of disease and unmet needs, the US Food and Drug Administration (FDA) conducts and supports multiple patient engagement platforms. We analyzed summaries from these discussions to identify commonalities among patients with disparate rare diseases, the results of which could inform priorities for cross-disease policies and medical product development.

METHODS

We conducted a qualitative analysis of patient engagement session summaries to investigate shared experiences across rare diseases. Cross-disease similarities were identified within four dimensions: product development/regulatory, clinical/physical, social/psychological, and economic/financial. Summaries from 29 rare diseases were included in our analyses.

RESULTS

Within the product development/regulatory dimension, we observed that patients and caregivers across rare diseases shared the desire for development of medical products that cured their disease or improved their overall quality of life. In the clinical/physical dimension, we found that patients had numerous common symptoms, including pain and fatigue. In the social/psychological dimension, we observed significant negative impact on mental health. Within the economic/financial dimension, patients and caregivers shared that disease burden caused significant financial hardships.

CONCLUSION

We found remarkable similarities among patients with rare diseases across all four dimensions. Our results indicate that, even among rare diseases with diverse etiologies, patients share numerous commonalties due to their diseases: a lack of effective treatment options, certain physical symptoms, mental health challenges, and financial concerns.

The value of using real-world evidence as a source of clinical evidence in the European medical device regulations: a mixed methods study

OBJECTIVES

This study investigates the benefits, limitations and awareness of using Real World Evidence and Real World Data for post-market clinical follow-up studies and clinical evaluation reports in the European Medical Device Regulations.

METHODOLOGY

A mixed methods study was utilized with qualitative interviews and a quantitative survey.

RESULTS

The findings from the study demonstrate that in the case of the Medical Device Regulations, opportunities exist for manufacturers of legacy devices to conduct Real World Evidence studies to bridge gaps in clinical evidence. The primary value of Real World Evidence lies in its ability to provide an accurate and, therefore, more reliable measure of device safety and performance. As a measure of safety and performance, it supplements clinical evidence generated from pre and post-market clinical investigations, reducing the costs associated with these studies and supporting the manufacturer's benefit: risk conclusion.

CONCLUSION

This study provides insight into how the medical device industry could utilize Real World Evidence and have an initiative in the EU similar to the FDA-sponsored NESTcc partnership. This would aid medical device manufacturers in transitioning to the MDR clinical evaluation requirements and mitigate the impact on medical device availability in the EU.

Characterizing a rare neurogenetic disease, SLC13A5 citrate transporter disorder, utilizing clinical data in a cloud-based medical record collection system

Introduction: SLC13A5 citrate transporter disorder is a rare autosomal recessive genetic disease that has a constellation of neurologic symptoms. To better characterize the neurologic and clinical laboratory phenotype, we utilized patient medical records collected by Ciitizen, an Invitae company, with support from the TESS Research Foundation. Methods: Medical records for 15 patients with a suspected genetic and clinical diagnosis of SLC13A5 citrate transporter disorder were collected by Ciitizen, an Invitae company. Genotype, clinical phenotypes, and laboratory data were extracted and analyzed. Results: The 15 patients reported all had epilepsy and global developmental delay. Patients continued to attain motor milestones, though much later than their typically developing peers. Clinical diagnoses support abnormalities in communication, and low or mixed tone with several movement disorders, including, ataxia and dystonia. Serum citrate was elevated in the 3 patients in whom it was measured; other routine laboratory studies assessing renal, liver and blood function had normal values or no consistent abnormalities. Many electroencephalograms (EEGs) were performed (1 to 35 per patient), and most but not all were abnormal, with slowing and/or epileptiform activity. Fourteen of the patients had one or more brain magnetic resonance imaging (MRI) reports: 7 patients had at least one normal brain MRI, but not with any consistent findings except white matter signal changes. Discussion: These results show that in addition to the epilepsy phenotype, SLC13A5 citrate transporter disorder impacts global development, with marked abnormalities in motor abilities, tone, coordination, and communication skills. Further, utilizing cloud-based medical records allows industry, academic, and patient advocacy group collaboration to provide preliminary characterization of a rare genetic disorder. Additional characterization of the neurologic phenotype will be critical to future study and developing treatment for this and related rare genetic disorders.