What happens when N = 1 and you want plus 1?

Comparative proteomics reveals elevated CCN2 in NGLY1-deficient cells

N-glycanase 1(NGLY1) catalyzes the removal of N-linked glycans from newly synthesized or misfolded protein. NGLY1 deficiency is a recently diagnosed rare genetic disorder. The affected individuals present a broad spectrum of clinical features. Recent studies explored several possible molecular mechanisms of NGLY1 deficiency including defects in proteostasis, mitochondrial homeostasis, innate immunity, and water/ion transport. We demonstrate abnormal accumulation of endoplasmic reticulum-associated degradation (ERAD) substrates in NGLY1-deficient cells. Global quantitative proteomics discovered elevated levels of endogenous proteins in NGLY1-defective human and mouse cells. Further biological validation assays confirmed the altered abundance of several key candidates that were subjected to isobarically labeled proteomic analysis. CCN2 was selected for further analysis due to its significant increase in different cell models of NGLY1 deficiency. Functional assays show elevated CCN2 and over-stimulated TGF-β signaling in NGLY1-deficient cells. Given the important role of CCN2 and TGF-β pathway in mediating systemic fibrosis, we propose a potential link of increased CCN2 and TGF-β signaling to microscopic liver fibrosis in NGLY1 patients.

Opportunities and pitfalls of social media research in rare genetic diseases: a systematic review

PURPOSE

Social media may be particularly valuable in research in rare genetic diseases because of the low numbers of patients and the rare disease community's robust online presence. The goal of this systematic review was to understand how social media is currently used in rare disease research and the characteristics of the participants in these studies.

METHODS

We conducted a systematic review of six databases to identify studies published in English between January 2004 and November 2020, of which 120 met inclusion criteria.

RESULTS

Most studies were observational (n = 114, 95.0%) and cross-sectional (n = 107, 89.2%), and more than half (n = 69, 57.5%) utilized only surveys. Only 101 rare diseases were included across all studies. Participant demographics, when reported, were predominantly female (70.1% ± 22.5%) and white (85.0% ± 11.0%) adult patients and caregivers.

CONCLUSION

Despite its potential benefits in rare disease research, the use of social media is still methodologically limited and the participants reached may not be representative of the rare disease population by gender, race, age, or rare disease type. As scholars explore using social media for rare disease research, careful attention should be paid to representativeness when studying this diverse patient community.

Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes

Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.

N-Glycanase 1 Transcriptionally Regulates Aquaporins Independent of Its Enzymatic Activity

Patients with pathogenic mutations in NGLY1 cannot make tears and have global developmental delay and liver dysfunction. Traditionally, NGLY1 cleaves intact N-glycans from misfolded, retrotranslocated glycoproteins before proteasomal degradation. We demonstrate that Ngly1-null mouse embryonic fibroblasts, NGLY1 knockout human cells, and patient fibroblasts are resistant to hypotonic lysis. Ngly1-deficient mouse embryonic fibroblasts swell slower and have reduced aquaporin1 mRNA and protein expression. Ngly1 knockdown and overexpression confirms that Ngly1 regulates aquaporin1 and hypotonic cell lysis. Patient fibroblasts and NGLY1 knockout cells show reduced aquaporin11 mRNA, supporting NGLY1 as regulating expression of multiple aquaporins across species. Complementing Ngly1-deficient cells with catalytically inactive NGLY1 (p.Cys309Ala) restores normal hypotonic lysis and aquaporin1 protein. We show that transcription factors Atf1/Creb1 regulate aquaporin1 and that the Atf1/Creb1 signaling pathway is disrupted in Ngly1-deficient mouse embryonic fibroblasts. These results identify a non-enzymatic, regulatory function of NGLY1 in aquaporin transcription, possibly related to alacrima and neurological symptoms.

The undiagnosed diseases program: Approach to diagnosis

Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.

Open Humans: A platform for participant-centered research and personal data exploration

BACKGROUND

Many aspects of our lives are now digitized and connected to the internet. As a result, individuals are now creating and collecting more personal data than ever before. This offers an unprecedented chance for human-participant research ranging from the social sciences to precision medicine. With this potential wealth of data comes practical problems (e.g., how to merge data streams from various sources), as well as ethical problems (e.g., how best to balance risks and benefits when enabling personal data sharing by individuals).

RESULTS

To begin to address these problems in real time, we present Open Humans, a community-based platform that enables personal data collections across data streams, giving individuals more personal data access and control of sharing authorizations, and enabling academic research as well as patient-led projects. We showcase data streams that Open Humans combines (e.g., personal genetic data, wearable activity monitors, GPS location records, and continuous glucose monitor data), along with use cases of how the data facilitate various projects.

CONCLUSIONS

Open Humans highlights how a community-centric ecosystem can be used to aggregate personal data from various sources, as well as how these data can be used by academic and citizen scientists through practical, iterative approaches to sharing that strive to balance considerations with participant autonomy, inclusion, and privacy.

Genetic disorders and mortality in infancy and early childhood: delayed diagnoses and missed opportunities

PURPOSE

Infants admitted to a level IV neonatal intensive care unit (NICU) who do not survive early childhood are a population that is probably enriched for rare genetic disease; we therefore characterized their genetic diagnostic evaluation.

METHODS

This is a retrospective analysis of infants admitted to our NICU between 1 January 2011 and 31 December 2015 who were deceased at the time of records review, with age at death less than 5 years.

RESULTS

A total of 2,670 infants were admitted; 170 later died. One hundred six of 170 (62%) had an evaluation for a genetic or metabolic disorder. Forty-seven of 170 (28%) had laboratory-confirmed genetic diagnoses, although 14/47 (30%) diagnoses were made postmortem. Infants evaluated for a genetic disorder spent more time in the NICU (median 13.5 vs. 5.0 days; p = 0.003), were older at death (median 92.0 vs. 17.5 days; p < 0.001), and had similarly high rates of redirection of care (86% vs. 79%; p = 0.28).

CONCLUSION

Genetic disorders were suspected in many infants but found in a minority. Approximately one-third of diagnosed infants died before a laboratory-confirmed genetic diagnosis was made. This highlights the need to improve genetic diagnostic evaluation in the NICU, particularly to support end-of-life decision making.

Evolving health care through personal genomics

With the rapid evolution of next-generation DNA sequencing technologies, the cost of sequencing a human genome has plummeted, and genomics has started to pervade health care across all stages of life - from preconception to adult medicine. Challenges to fully embracing genomics in a clinical setting remain, but some approaches are starting to overcome these barriers, such as community-driven data sharing to improve the accuracy and efficiency of applying genomics to patient care.