Rev Med Suisse. 2024 Jan 31;20(859):255-258. doi: 10.53738/REVMED.2024.20.859.255.

ABSTRACT

The sequential effects of romosozumab and denosumab in osteoporosis are shown in real-life, while the mechanisms of post-denosumab rebound are reviewed extensively. A network meta-analysis confirms the superiority of anabolics vs anti-resorptives on fracture reduction, while the latter shown a reduction of mortality in a large population-based study. Fracture risk prediction by FRAXPlus is improved. New meta-analyses confirm the benefits of Vitamin D on fractures and falls. Finally, multiples trials with new molecules for the treatment of rare bone diseases, including osteogenesis imperfecta, fibrous dysplasia and hypoparathyroidism, shown promising results.

PMID:38299957 | DOI:10.53738/REVMED.2024.20.859.255

Med Sci (Paris). 2024 Jan;40(1):30-34. doi: 10.1051/medsci/2023192. Epub 2024 Feb 1.

ABSTRACT

TITLE: La Filière de Santé Maladies Rares TÊTECOU - Améliorer le parcours de soins, la formation et la recherche des malformations de la tête, du cou et des dents.

ABSTRACT: Les Filières de Santé Maladies Rares (FSMR) sont des structures nationales, labellisées par les ministères en charge de la Santé et de la Recherche, dans le cadre des Plans nationaux maladies rares (PNMR). Depuis 2004, les maladies rares sont en effet définies comme un enjeu de santé publique et bénéficient d’une organisation et de moyens spécifiques mis en œuvre dans les PNMR successifs.

PMID:38299900 | DOI:10.1051/medsci/2023192

HGG Adv. 2024 Jan 30:100273. doi: 10.1016/j.xhgg.2024.100273. Online ahead of print.

ABSTRACT

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.

PMID:38297832 | DOI:10.1016/j.xhgg.2024.100273

BMC Med Inform Decis Mak. 2024 Jan 31;24(1):30. doi: 10.1186/s12911-024-02439-w.

ABSTRACT

OBJECTIVE: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation.

MATERIALS AND METHODS: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations.

RESULTS: The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches.

CONCLUSION: Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

PMID:38297371 | PMC:PMC10829255 | DOI:10.1186/s12911-024-02439-w

J Am Heart Assoc. 2024 Feb 6;13(3):e031377. doi: 10.1161/JAHA.123.031377. Epub 2024 Jan 31.

ABSTRACT

BACKGROUND: Supravalvar aortic stenosis (SVAS) is a characteristic feature of Williams-Beuren syndrome (WBS). Its severity varies: ~20% of people with Williams-Beuren syndrome have SVAS requiring surgical intervention, whereas ~35% have no appreciable SVAS. The remaining individuals have SVAS of intermediate severity. Little is known about genetic modifiers that contribute to this variability.

METHODS AND RESULTS: We performed genome sequencing on 473 individuals with Williams-Beuren syndrome and developed strategies for modifier discovery in this rare disease population. Approaches include extreme phenotyping and nonsynonymous variant prioritization, followed by gene set enrichment and pathway-level association tests. We next used GTEx v8 and proteomic data sets to verify expression of candidate modifiers in relevant tissues. Finally, we evaluated overlap between the genes/pathways identified here and those ascertained through larger aortic disease/trait genome-wide association studies. We show that SVAS severity in Williams-Beuren syndrome is associated with increased frequency of common and rarer variants in matrisome and immune pathways. Two implicated matrisome genes (ACAN and LTBP4) were uniquely expressed in the aorta. Many genes in the identified pathways were previously reported in genome-wide association studies for aneurysm, bicuspid aortic valve, or aortic size.

CONCLUSIONS: Smaller sample sizes in rare disease studies necessitate new approaches to detect modifiers. Our strategies identified variation in matrisome and immune pathways that are associated with SVAS severity. These findings suggest that, like other aortopathies, SVAS may be influenced by the balance of synthesis and degradation of matrisome proteins. Leveraging multiomic data and results from larger aorta-focused genome-wide association studies may accelerate modifier discovery for rare aortopathies like SVAS.

PMID:38293922 | DOI:10.1161/JAHA.123.031377

Recenti Prog Med. 2024 Feb;115(2):67-75. doi: 10.1701/4197.41839.

ABSTRACT

INTRODUCTION: The text examines the impact of artificial intelligence (AI) in the context of rare diseases, exploring how patients turn to AI resources for health information, especially in situations where doctor-patient communication is limited. The article features the case of a doctor specializing in clinical psychology and psychotherapy, diagnosed with thymoma and Good's syndrome, who uses AI resources during his illness.

METHODS: The capabilities of five chatbots based on Large Language Models (LLMs), such as GPT-3.5, GPT-4, Bing Chat, Google Bard, and Anthropic Claude are explored. The AIs were queried on various aspects of the disease, from pre-diagnosis and diagnosis to therapeutic, psychological, and caregiver management issues. The responses were evaluated by five experts based on criteria such as: accuracy, relevance, coherence, clarity, practical utility, ethical considerations, empathy, and capacity to respond to questions and concerns.

RESULTS: The results indicate consistency in the evaluators' assessments, with generally high scores across all dimensions. Particularly, systems like Bard and GPT-4 received high ratings in terms of information accuracy and the ability to respond to questions and concerns. Bing and Claude were appreciated for their empathy and tone. Overall, the AI systems' responses were considered appropriate, respectful of ethics and privacy, and useful in the clinical context.

DISCUSSION: The article emphasizes the importance of understanding the reliability and precision of responses provided by AI systems in the clinical field. Although these systems offer high-quality responses, there is significant variability in their performance. Healthcare professionals must be aware of these differences and use such tools cautiously. AI can provide support in some aspects of care but cannot replace genuine human empathy and understanding. Integrating AI into clinical practice presents potential but also challenges, particularly the possibility of providing incorrect information.

CONCLUSIONS: The AI systems demonstrate the ability to provide useful advice on clinical and psychological issues, but their use requires caution. It is crucial to distinguish the benefits of AI for patients from the challenges it presents for healthcare professionals. As AI technology continues to evolve, it is essential that its integration into the clinical field is accompanied by continuous research and evaluations, to ensure safe and effective use in the healthcare sector.

PMID:38291931 | DOI:10.1701/4197.41839

Orphanet J Rare Dis. 2024 Jan 30;19(1):33. doi: 10.1186/s13023-024-03033-z.

ABSTRACT

BACKGROUND: Before COVID-19, people with rare diseases (RD) experienced numerous disparities in quality of life and healthcare access and quality, yet little is known about the experiences of this underserved group during the pandemic.

RESULTS: During the first wave of the COVID-19 pandemic in the United States, spring and summer of 2020, 759 participants representing 231 unique RDs responded to open-ended questions about the impact of the pandemic on life with a RD, healthcare access, and coping. Qualitative conventional content analysis was used to analyze responses. Identified themes represented positive and negative dimensions of change, including a shock to the (health) system, coping with uncertainty, and the value of social support while isolated.

CONCLUSIONS: Limitations in healthcare access and quality were the most frequently described as impacts of COVID-19. Other major negative impacts included exacerbation of symptoms, psychological distress, and a lack of usual social support and reliable information. However, participants also noted silver linings, especially in healthcare. For some, expanded telehealth enhanced their ability to access medical and mental health providers and RD specialists. Finally, many participants hoped that, by highlighting social and health inequities faced by people with RDs and other minorities, the pandemic would prompt greater understanding and policies that could improve the quality of life of the RD community.

PMID:38291466 | PMC:PMC10829377 | DOI:10.1186/s13023-024-03033-z

Commun Biol. 2024 Jan 30;7(1):140. doi: 10.1038/s42003-024-05820-7.

ABSTRACT

Plasma-derived therapeutic proteins are produced through an industrial fractionation process where proteins are purified from individual intermediates, some of which remain unused and are discarded. Relatively few plasma-derived proteins are exploited clinically, with most of available plasma being directed towards the manufacture of immunoglobulin and albumin. Although the plasma proteome provides opportunities to develop novel protein replacement therapies, particularly for rare diseases, the high cost of plasma together with small patient populations impact negatively on the development of plasma-derived orphan drugs. Enabling therapeutics development from unused plasma fractionation intermediates would therefore constitute a substantial innovation. To this objective, we characterized the proteome of unused plasma fractionation intermediates and prioritized proteins for their potential as new candidate therapies for human disease. We selected ceruloplasmin, a plasma ferroxidase, as a potential therapy for aceruloplasminemia, an adult-onset ultra-rare neurological disease caused by iron accumulation as a result of ceruloplasmin mutations. Intraperitoneally administered ceruloplasmin, purified from an unused plasma fractionation intermediate, was able to prevent neurological, hepatic and hematological phenotypes in ceruloplasmin-deficient mice. These data demonstrate the feasibility of transforming industrial waste plasma fraction into a raw material for manufacturing of new candidate proteins for replacement therapies, optimizing plasma use and reducing waste generation.

PMID:38291108 | PMC:PMC10828504 | DOI:10.1038/s42003-024-05820-7

JNMA J Nepal Med Assoc. 2023 Oct 1;61(266):819-821. doi: 10.31729/jnma.8303.

ABSTRACT

Klippel-Feil syndrome is a rare congenital bone disorder characterised by a triad of short neck, low posterior hairline and limited lateral bending of the neck with an annual incidence of 1 in 40,000 live births. It has remained an obscure term in the medical literature because of its variability in presentation and wide spectrum of anomalies involving multiple organ systems. It is unusual to find a case that has all three classical triad features. Here, we present a case of a 9-month-old infant who manifests not only all three classical triad features associated with Klippel-Feil syndrome but also demonstrates the presence of congenital heart disease, scoliosis, and renal ectopia. An early comprehensive evaluation of a suspected case is essential for diagnosis and counselling which impacts its prognosis, helps minimize social stigma and affords parents the opportunity to consider cosmetic surgery as an option, should they choose to pursue it.

KEYWORDS: case reports; congenital; heart diseases; Klippel-Feil syndrome; scoliosis.

PMID:38289771 | PMC:PMC10579768 | DOI:10.31729/jnma.8303

Int J Rheum Dis. 2024 Jan;27(1):e15051. doi: 10.1111/1756-185X.15051.

NO ABSTRACT

PMID:38287536 | DOI:10.1111/1756-185X.15051

J Invest Dermatol. 2024 Jan 27:S0022-202X(24)00079-4. doi: 10.1016/j.jid.2023.12.024. Online ahead of print.

ABSTRACT

Physical trauma disrupts skin barrier function. How the skin barrier recovers is not fully understood. We evaluated in mice the mechanism of skin barrier recovery following mechanical injury inflicted by tape stripping. Tape stripping disrupted skin barrier function as evidenced by increased trans epidermal water loss. We show that tape stripping induces IL-1, IL-23 and TCRγδ+ dependent upregulation of cutaneous Il17a and Il22 expression. We demonstrate that IL-17A and IL-22 induce epidermal hyperplasia, promote neutrophil recruitment, and delay skin barrier function recovery. Neutrophil depletion improved the recovery of skin barrier function and decreased epidermal hyperplasia. scRNAseq and flow cytometry analysis of skin cells revealed basophil infiltration into tape stripped skin. Basophil depletion upregulated Il17a expression, increased neutrophil infiltration, and delayed skin barrier recovery. Comparative analysis of genes differentially expressed in tape stripped skin of basophil depleted mice and Il17a-/- mice, indicated that basophils counteract the effects of IL-17A on the expression of epidermal and lipid metabolism genes important for skin barrier integrity. Our results demonstrate that basophils play a protective role by downregulating Il17a expression following mechanical skin injury, thereby counteracting the adverse effect of IL-17A on skin barrier function recovery and suggest novel interventions to accelerate this recovery.

PMID:38286187 | DOI:10.1016/j.jid.2023.12.024

Pediatr Dermatol. 2024 Jan-Feb;41(1):182-183. doi: 10.1111/pde.15465.

ABSTRACT

Incontinentia pigmenti (IP) is a rare X-linked dominant, male-lethal disorder characterized by pathognomic skin lesions. As described in the literature the typical cutaneous changes follow the pattern of Blaschko's lines and develop in four stages that usually start at birth. Stage 1 is called vesicular, bullous or inflammatory. The vesicles are rapidly filled with eosinophils and thus turn into pustules. Thus, the term "pustular" is relevant to the first phase of IP, and the stage can be considered as "vesiculopustular/inflammatory" to be more precise than "vesicular" or "bullous."

PMID:38284782 | DOI:10.1111/pde.15465

Front Immunol. 2024 Jan 12;14:1308305. doi: 10.3389/fimmu.2023.1308305. eCollection 2023.

ABSTRACT

BACKGROUND: Primary Immunodeficiency Disease (PID), also known as Inborn Errors of Immunity (IEI), comprises a group of rare genetic disorders that impair the body's immune responses. These conditions result from monogenic germline mutations that affect the function of genes governing the innate and adaptive immune system. Therefore, individuals with PID are more susceptible to infectious diseases, allergies, and autoimmune and autoinflammatory conditions. The prevalence of PID has been on the rise, with the number of classified diseases reaching 404, and 430 genetic defects reported to cause these conditions. However, in Malaysia, genetic testing for PID is currently limited and needs to be outsourced to overseas laboratories, posing financial challenges for families. Moreover, limited research has focused on the knowledge and awareness of genetic testing among parents of children with PID in Malaysia. This study aims to address this gap and provide valuable insights into the knowledge, awareness, and perception of genetic testing among this specific population.

METHOD: This qualitative cross-sectional study utilised online open-ended, semi-structured focus group interviews to explore the perceptions and experiences of parents of children with Primary Immunodeficiency (PID). Participants were recruited through convenience sampling from the Malaysian Patient Organisation for Primary Immunodeficiencies (MyPOPI), a non-governmental organisation dedicated to providing support and raising awareness about PID. The study spanned from May 2023 to July 2023 and included participants from diverse regions of Malaysia who had undergone different diagnostic journeys in various hospitals.

RESULT: The focus group discussions yielded 11 sub-themes that highlighted the experiences, understanding and challenges of the participants regarding genetic testing based on the semi-structured questions. These sub-themes were then grouped into four main themes that are awareness and understanding of genetic testing, the journey towards diagnosis and treatment, emotional impact and psychological factors, and the importance of medical experts in diagnosing and managing PID, as well as public perception and awareness.

CONCLUSION: In conclusion, this study highlights the diverse knowledge, awareness, and perception surrounding genetic testing for PID. Factors such as access to services, family history, and personal circumstances shape individuals' understanding of genetic testing. The importance of healthcare professionals, along with the need for improved accessibility and targeted communication strategies, is underscored to enhance understanding and reduce stigma surrounding genetic testing for rare diseases like PID.

PMID:38283358 | PMC:PMC10811462 | DOI:10.3389/fimmu.2023.1308305

Orphanet J Rare Dis. 2024 Jan 27;19(1):27. doi: 10.1186/s13023-024-03029-9.

ABSTRACT

BACKGROUND: Approximately 50% of rare diseases have symptom onset during childhood. A high level of nursing care and an often uncertain prognosis put caregivers of the affected children at high risk for psychological distress. At the same time, their caregivers have limited access to appropriate psychological care. The aim of this study was to evaluate a web-based psychological support program for caregivers of children with chronic rare diseases (WEP-CARE).

METHODS: German-speaking parents (recruited between May 2016 and March 2018) caring for children aged 0-25 years with a rare disease showing clinically relevant anxiety symptoms, were assigned to either the WEP-CARE (n = 38) or treatment as usual (n = 36) condition within a randomized controlled trial. The primary outcome measure was parental anxiety, assessed with the Generalized Anxiety Disorder Questionnaire (GAD-7). Secondary outcomes were fear of disease progression, depression, coping, quality of life and user satisfaction. The group differences were tested through repeated-measures analyses of variance. The WEP-CARE group was additionally followed up three months after the treatment.

RESULTS: A significant time-group interaction was found for anxiety (F (1,35) = 6.13, p = .016), fear of disease progression (F (1,331) = 18.23, p < .001), depression (F (1,74) = 10.79, p = .002) and coping (F (1,233) = 7.02, p = .010), suggesting superiority of the WEP-CARE group. Sustainability of the treatment gains regarding anxiety, fear of disease progression and coping was confirmed at the 6-month follow-up assessment (p < .01). A significant interaction effect could not be found for quality of life (F(1,2) = 0.016; p = .899). Both participating parents and therapists were satisfied with WEP-CARE.

CONCLUSIONS: Our results underline the efficacy and feasibility of WEP-CARE for parents of children with various rare diseases.

PMID:38281056 | PMC:PMC10821309 | DOI:10.1186/s13023-024-03029-9

Orphanet J Rare Dis. 2024 Jan 27;19(1):28. doi: 10.1186/s13023-024-03030-2.

ABSTRACT

BACKGROUND: In European Union countries, any disease affecting less than 5 people in 10,000 is considered rare. As expertise is scarce and rare diseases (RD) are complex, RD patients can remain undiagnosed for many years. The period of searching for a diagnosis, called diagnostic delay, sometimes leads to a diagnostic dead end when the patient's disease is impossible to diagnose after undergoing all available investigations. In recent years, extensive efforts have been made to support the implementation of ORPHA nomenclature in health information systems (HIS) so as to allow RD coding. Until recently, the nomenclature only encompassed codes for specific RD. Persons suffering from a suspected RD who could not be diagnosed even after full investigation, could not be coded with ORPHAcodes. The recognition of the RD status is necessary for patients, even if they do not have a precise diagnosis. It can facilitate reimbursement of care, be socially and psychologically empowering, and grant them access to scientific advances.

RESULTS: The RD-CODE project aimed at making those patients identifiable in HIS in order to produce crucial epidemiological data. Undiagnosed patients were defined as patients for whom no clinically-known disorder could be confirmed by an expert center after all reasonable efforts to obtain a diagnosis according to the state-of-the-art and diagnostic capabilities available. Three recommendations for the coding of undiagnosed RD patients were produced by a multi-stakeholder panel of experts: 1/ Capture the diagnostic ascertainment for all rare disease cases; 2/ Use the newly created ORPHAcode (ORPHA:616874 "Rare disorder without a determined diagnosis after full investigation"), available in the Orphanet nomenclature: as the code is new, guidelines are essential to ensure its correct and homogeneous use for undiagnosed patients' identification in Europe and beyond; 3/ Use additional descriptors in registries.

CONCLUSIONS: The recommendations can now be implemented in HIS (electronic health records and/or registries) and could be a game-changer for patients, clinicians and researchers in the field, enabling assessment of the RD population, including undiagnosed patients, adaptation of policy measures including financing for care and research programs, and to improved access of undiagnosed patients to research programs.

PMID:38280999 | PMC:PMC10822150 | DOI:10.1186/s13023-024-03030-2

Lancet. 2024 Feb 17;403(10427):592-593. doi: 10.1016/S0140-6736(23)02652-1. Epub 2024 Jan 23.

NO ABSTRACT

PMID:38278169 | DOI:10.1016/S0140-6736(23)02652-1

JCI Insight. 2024 Feb 22;9(4):e174097. doi: 10.1172/jci.insight.174097.

ABSTRACT

A distinct adipose tissue distribution pattern was observed in patients with methylmalonyl-CoA mutase deficiency, an inborn error of branched-chain amino acid (BCAA) metabolism, characterized by centripetal obesity with proximal upper and lower extremity fat deposition and paucity of visceral fat, that resembles familial multiple lipomatosis syndrome. To explore brown and white fat physiology in methylmalonic acidemia (MMA), body composition, adipokines, and inflammatory markers were assessed in 46 patients with MMA and 99 matched controls. Fibroblast growth factor 21 levels were associated with acyl-CoA accretion, aberrant methylmalonylation in adipose tissue, and an attenuated inflammatory cytokine profile. In parallel, brown and white fat were examined in a liver-specific transgenic MMA mouse model (Mmut-/- TgINS-Alb-Mmut). The MMA mice exhibited abnormal nonshivering thermogenesis with whitened brown fat and had an ineffective transcriptional response to cold stress. Treatment of the MMA mice with bezafibrates led to clinical improvement with beiging of subcutaneous fat depots, which resembled the distribution seen in the patients. These studies defined what we believe to be a novel lipodystrophy phenotype in patients with defects in the terminal steps of BCAA oxidation and demonstrated that beiging of subcutaneous adipose tissue in MMA could readily be induced with small molecules.

PMID:38271099 | DOI:10.1172/jci.insight.174097

Orphanet J Rare Dis. 2024 Jan 25;19(1):25. doi: 10.1186/s13023-024-03047-7.

ABSTRACT

BACKGROUND: The delay in diagnosis for rare disease (RD) patients is often longer than for patients with common diseases. Machine learning (ML) technologies have the potential to speed up and increase the precision of diagnosis in this population group. We aim to explore the expectations and experiences of the members of the European Reference Networks (ERNs) for RDs with those technologies and their potential for application.

METHODS: We used a mixed-methods approach with an online survey followed by a focus group discussion. Our study targeted primarily medical professionals but also other individuals affiliated with any of the 24 ERNs.

RESULTS: The online survey yielded 423 responses from ERN members. Participants reported a limited degree of knowledge of and experience with ML technologies. They considered improved diagnostic accuracy the most important potential benefit, closely followed by the synthesis of clinical information, and indicated the lack of training in these new technologies, which hinders adoption and implementation in routine care. Most respondents supported the option that ML should be an optional but recommended part of the diagnostic process for RDs. Most ERN members saw the use of ML limited to specialised units only in the next 5 years, where those technologies should be funded by public sources. Focus group discussions concluded that the potential of ML technologies is substantial and confirmed that the technologies will have an important impact on healthcare and RDs in particular. As ML technologies are not the core competency of health care professionals, participants deemed a close collaboration with developers necessary to ensure that results are valid and reliable. However, based on our results, we call for more research to understand other stakeholders' opinions and expectations, including the views of patient organisations.

CONCLUSIONS: We found enthusiasm to implement and apply ML technologies, especially diagnostic tools in the field of RDs, despite the perceived lack of experience. Early dialogue and collaboration between health care professionals, developers, industry, policymakers, and patient associations seem to be crucial to building trust, improving performance, and ultimately increasing the willingness to accept diagnostics based on ML technologies.

PMID:38273306 | PMC:PMC10809751 | DOI:10.1186/s13023-024-03047-7

Traffic. 2024 Jan;25(1):e12927. doi: 10.1111/tra.12927.

ABSTRACT

Endoplasmic reticulum (ER) retention of misfolded glycoproteins is mediated by the ER-localized eukaryotic glycoprotein secretion checkpoint, UDP-glucose glycoprotein glucosyl-transferase (UGGT). The enzyme recognizes a misfolded glycoprotein and flags it for ER retention by re-glucosylating one of its N-linked glycans. In the background of a congenital mutation in a secreted glycoprotein gene, UGGT-mediated ER retention can cause rare disease, even if the mutant glycoprotein retains activity ("responsive mutant"). Using confocal laser scanning microscopy, we investigated here the subcellular localization of the human Trop-2-Q118E, E227K and L186P mutants, which cause gelatinous drop-like corneal dystrophy (GDLD). Compared with the wild-type Trop-2, which is correctly localized at the plasma membrane, these Trop-2 mutants are retained in the ER. We studied fluorescent chimeras of the Trop-2 Q118E, E227K and L186P mutants in mammalian cells harboring CRISPR/Cas9-mediated inhibition of the UGGT1 and/or UGGT2 genes. The membrane localization of the Trop-2 Q118E, E227K and L186P mutants was successfully rescued in UGGT1-/- cells. UGGT1 also efficiently reglucosylated Trop-2-Q118E-EYFP in cellula. The study supports the hypothesis that UGGT1 modulation would constitute a novel therapeutic strategy for the treatment of pathological conditions associated to misfolded membrane glycoproteins (whenever the mutation impairs but does not abrogate function), and it encourages the testing of modulators of ER glycoprotein folding quality control as broad-spectrum rescue-of-secretion drugs in rare diseases caused by responsive secreted glycoprotein mutants.

PMID:38272446 | PMC:PMC10832616 | DOI:10.1111/tra.12927

Brief Bioinform. 2024 Jan 22;25(2):bbad508. doi: 10.1093/bib/bbad508.

ABSTRACT

Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.

PMID:38271481 | PMC:PMC10810331 | DOI:10.1093/bib/bbad508