The role of multidisciplinary diagnostic and therapeutic model of care in Lamb-Shaffer syndrome - case report

This case study illustrates a multidisciplinary diagnostic and therapeutic model of care for a 7-year-old male with Lamb-Shaffer syndrome (LAMSHF). LAMSHF is an ultra-rare genetic neurodevelopmental disorder, caused by heterozygous alterations in the SOX5 gene. An integrative model of therapy of cognitive functions and speech is described. The presented approach allows the development of language competences through stimulation of basic cognitive functions, which allows the learning of the abstract rules of an inflected language. A surprising, unexpected improvement in the cognitive functioning of the child was observed (both in terms of reasoning and speech), as well as an increase in his independence. The clinically important problem of the need for continued stimulation of cognitive development, in spite of the unfavourable prognosis associated with LAMSHF, is highlighted.

The burden of disease and quality of life in patients with acute hepatic porphyria: COPHASE study

BACKGROUND

Acute hepatic porphyria (AHP) comprises a group of rare genetic diseases characterized by neurovisceral crises that are manifested by abdominal pain and neurological and/or psychological symptoms that interfere with the ability to lead a normal life. Our objective was to determine the burden of the disease in one year and the health-related quality of life (HRQoL) in patients with AHP.

RESULTS

28 patients were analyzed. The mean age was 36.6±10.2 years, 89.3% were women, and the average number of crises was 1.9±1.5. The average annual cost per patient was €38,255.40. 80.2% of the costs was direct medical costs, 17.5% was associated with loss of productivity and 2.3% was direct non-medical costs. 85.9% of the total cost corresponded to the crises. The intercrisis period accounted for the remaining 14.1%. The global index of the EQ-5D-5L (HRQoL) was 0.75±0.24. The dimensions of pain/discomfort, anxiety/depression and daily activities were the most affected. Leisure, travel/vacations and household activities were the most affected daily activities. 53.6% of patients required a caregiver due to AHP. 92.9% did not present overload and 7.1% presented extreme overload.

CONCLUSIONS

Patients with AHP are associated with a high economic impact and an affected HRQoL in the pain/discomfort dimension, with a negative impact on the performance of daily activities and a risk of psychiatric diseases.

Parental coping with uncertainties along the severe combined immunodeficiency journey

Background

Severe combined immunodeficiency (SCID) is a group of rare genetic disorders that cause disruption in immune system functioning. Parents of children with SCID experience many uncertainties related to their child’s diagnosis, treatment, recovery, and quality of life. To fully understand parents’ experiences throughout their SCID journey, it is important to explore the stressors generated by such uncertainties and how parents cope with these stressors.

Methods

We conducted 26 in-depth interviews with parents whose child was diagnosed with SCID or a SCID-like condition through newborn screening. The interviews explored uncertainties related to their child’s diagnosis and how parents coped with these uncertainties. Transcripts were generated from the interviews and analyzed using an inductive content analysis approach which included data immersion, generation and assignment of codes, and interpretation.

Results

Parents used a variety of behavioral, cognitive, and affective coping strategies which evolved throughout their SCID journeys. Some parents reported coping by playing an active role in their child’s treatment, which included reaching out to other SCID parents or seeking second medical opinions. Other types of coping included establishing house hygiene rules, thinking positively about the child’s treatment progress, and relying on family members for help. These coping strategies were both deliberate and intuitive. Participants also described their struggles in coping with stressors related to their child’s health and survival. They reported difficulty in processing their emotions and experiencing denial and guilt related to their child’s diagnosis. Some parents adapted to ongoing uncertainties through such strategies as positive thinking, self-reflection, and relying on family and community. With successful adaptation, parents emphasized that they continue to use these strategies today.

Conclusion

Our assessment revealed that parents of children diagnosed with SCID use a variety of behavioral, cognitive, and affective approaches to cope with SCID uncertainties. Although parents reported challenges in coping with SCID uncertainties, they also reported finding ways to overcome these stressors and establish patterns of effective coping. Findings from our study can serve as a guide for parents whose child was newly diagnosed with SCID and for providers such as social workers, genetic counselors, and psychologists.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02554-9.

Blindspot in the evidence base: A systematic review of psychological interventions for children and adolescents with intellectual disabilities and co-occurring obesity

BACKGROUND

Children and adolescents with intellectual disabilities (C&A-ID) face many disadvantages in healthcare research and service delivery. Intellectual disabilities have been found to precipitate weight-related problems, and together, they may be indicators of rare genetic diseases (RGDs). C&A-ID may require support for health problems exacerbated by primary diagnoses. While it is generally agreed that C&A-ID have more complex needs than typically developing individuals, psychological services to address these needs are under-explored.

AIMS

This systematic review aimed to identify psychological interventions for weight management in C&A-ID.

METHOD

MEDLINE, PsycINFO, CINAHL, The Cochrane Library and SCOPUS were systematically searched. Data extraction and quality appraisal were performed for all eligible studies RESULTS: The search strategy yielded seven studies published in English between 2010 and 2022. All interventions addressed obesity through multi-disciplinary programmes and resulted in weight reductions, with most interventions theoretically influenced by principles of behaviourism. Quality appraisal revealed methodological weaknesses in six of seven studies, such as heterogeneity in samples, interventions, and outcome measures, disallowing meta-analyses and weakening the generalisability of interventions to diverse contexts and groups CONCLUSIONS AND IMPLICATIONS: A genuine disconnect between empirical evidence and services for C&A with complex needs was observed. This emphasises an urgency for increased inclusion in clinical and behavioural research and for robust enquiries to test/adapt psychological interventions for weight management for C&A-ID. The findings of this review hold clinical utility for clinicians working with C&A-ID, and with RGDs such as Bardet-Biedl, Prader-Willi and Down syndromes. Recommendations and a conceptual framework are provided herein for enhanced efficacy of interventions.

Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: A Kleefstra syndrome case study

There are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance. Low throughput functional validation in specialist laboratories is the current ad hoc approach for functional validation of genetic variants, which creating major bottlenecks in patient diagnosis. This study investigates the application of CRISPR gene editing followed by genome wide transcriptomic profiling to facilitate patient diagnosis. As proof-of-concept, we introduced a variant in the Euchromatin histone methyl transferase (EHMT1) gene into HEK293T cells. We identified changes in the regulation of the cell cycle, neural gene expression and suppression of gene expression changes on chromosome 19 and chromosome X, that are in keeping with Kleefstra syndrome clinical phenotype and/or provide insight into disease mechanism. This study demonstrates the utility of genome editing followed by functional readouts to rapidly and systematically validating the function of variants of unknown significance in patients suffering from rare diseases.

CRISPR single base editing, neuronal disease modelling and functional genomics for genetic variant analysis: pipeline validation using Kleefstra syndrome EHMT1 haploinsufficiency

Background

Over 400 million people worldwide are living with a rare disease. Next Generation Sequencing (NGS) identifies potential disease causative genetic variants. However, many are identified as variants of uncertain significance (VUS) and require functional laboratory validation to determine pathogenicity, and this creates major diagnostic delays.

Methods

In this study we test a rapid genetic variant assessment pipeline using CRISPR homology directed repair to introduce single nucleotide variants into inducible pluripotent stem cells (iPSCs), followed by neuronal disease modelling, and functional genomics on amplicon and RNA sequencing, to determine cellular changes to support patient diagnosis and identify disease mechanism.

Results

As proof-of-principle, we investigated an EHMT1 (Euchromatin histone methyltransferase 1; EHMT1 c.3430C > T; p.Gln1144*) genetic variant pathogenic for Kleefstra syndrome and determined changes in gene expression during neuronal progenitor cell differentiation. This pipeline rapidly identified Kleefstra syndrome in genetic variant cells compared to healthy cells, and revealed novel findings potentially implicating the key transcription factors REST and SP1 in disease pathogenesis.

Conclusion

The study pipeline is a rapid, robust method for genetic variant assessment that will support rare diseases patient diagnosis. The results also provide valuable information on genome wide perturbations key to disease mechanism that can be targeted for drug treatments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-022-02740-3.

Two novel mutations of the LPL gene in two Chinese family cases with familial chylomicronemia syndrome

The aim of this study was to investigate the clinical features and genetic causes of two family cases with familial chylomicronemia syndrome (FCS). Clinical manifestations of proband 1 and her families, and also proband 2 showed severe hypertriglyceridemia, especially the triglycerides levels of two probands were extremely high. Gene sequencing results showed that the LPL genes in each of the two probands had a new mutation site. For the proband 1, a compound heterozygous mutation at c.429 (c.429 + 1G > T) was detected in the LPL gene, which was splicing mutation and inherited from her mother. Homozygous mutation was detected in the LPL gene of proband 2, the nucleotide mutation at c.802 (c.802C > T) exhibited missense mutation, his parents and brother had a heterozygous mutation at the same site. It was confirmed that the conservative lipoprotein lipase superfamily domain changed an amino acid from histidine to tyrosine at p. 268 (p. His268Tyr). Flow cytometry confirmed the deficient expression of LPL protein in two families. These results indicated that the mutation in LPL gene might be the cause of familial chylomicronemia syndrome.

TRIM E3 Ubiquitin Ligases in Rare Genetic Disorders

The TRIM family comprises proteins characterized by the presence of the tripartite motif composed of a RING domain, one or two B-box domains and a coiled-coil region. The TRIM shared domain structure underscores a common biochemical function as E3 ligase within the ubiquitination cascade. The TRIM proteins represent one of the largest E3 ligase families counting in human more than 70 members. These proteins are implicated in a plethora of cellular processes such as apoptosis, cell cycle regulation, muscular physiology, and innate immune response. Consistently, their alteration results in several pathological conditions emphasizing their medical relevance. Here, the genetic and pathogenetic mechanisms of rare disorders directly caused by mutations in TRIM genes will be reviewed. These diseases fall into different pathological areas, from malformation birth defects due to developmental abnormalities, to neurological disorders and progressive teenage neuromuscular disorders. In many instances, TRIM E3 ligases act on several substrates thus exerting pleiotropic activities: the need of unraveling disease-specific TRIM pathways for a precise targeting therapy avoiding dramatic side effects will be discussed.

Genome analysis and knowledge-driven variant interpretation with TGex

BACKGROUND

The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient's phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants.

RESULTS

We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex's main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex's broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. Examining use-cases from a variety of TGex users world-wide, we demonstrate its high diagnostic yields (42% for single exome and 50% for trios in 1500 rare genetic disease cases) and critical actionable genetic findings. The platform's support for integration with EHR and LIMS through dedicated APIs facilitates automated retrieval of patient data for TGex's customizable reporting engine, establishing a rapid and cost-effective workflow for an entire range of clinical genetic testing, including rare disorders, cancer predisposition, tumor biopsies and health screening.

CONCLUSIONS

TGex is an innovative tool for the annotation, analysis and prioritization of coding and non-coding genomic variants. It provides access to an extensive knowledgebase of genomic annotations, with intuitive and flexible configuration options, allows quick adaptation, and addresses various workflow requirements. It thus simplifies and accelerates variant interpretation in clinical genetics workflows, with remarkable diagnostic yield, as exemplified in the described use cases. TGex is available at http://tgex.genecards.org/.

Prevalence of fibrodysplasia ossificans progressiva (FOP) in France: an estimate based on a record linkage of two national databases

Background

Fibrodysplasia ossificans progressiva (FOP) is a rare, severely disabling, and life-shortening genetic disorder that causes the formation of heterotopic bone within soft connective tissue. Previous studies found that the FOP prevalence was about one in every two million lives. The aim of this study is to estimate the FOP prevalence in France by probabilistic record-linkage of 2 national databases: 1) the PMSI (Programme de médicalisation des systèmes d’information), an administrative database that records all hospitalization activities in France and 2) CEMARA, a registry database developed by the French Centres of Reference for Rare Diseases.

Results

Using a capture-recapture methodology to adjust the crude number of patients identified in both data sources, 89 FOP patients were identified, which results in a prevalence of 1.36 per million inhabitants (CI95% = [1.10; 1.68]). FOP patients’ mean age was 25 years, only 14.9% were above 40 years, and 53% of them were males. The first symptoms – beside toe malformations- occurred after birth for 97.3% of them. Mean age at identified symptoms was 7 years and above 18 years for only 6.9% of patients. Mean age at diagnosis was 10 years, and above 18 years for 14.9% of the patients. FOP patients were distributed across France.

Conclusions

Despite the challenge of ascertaining patients with rare diseases, we report a much higher prevalence of FOP in France than in previous studies elsewhere. We suggest that efforts to identify patients and confirm the diagnosis of FOP should be reinforced and extended at both national and European level.