Monogenic Etiology Research Articles

Searching for monogenic autoimmune etiology in patients with type 1 diabetes onset under 30 months of age.

The most frequent form of diabetes in pediatric patients is polygenic autoimmune diabetes (T1D), but single-gene variants responsible for autoimmune diabetes have also been described. Both disorders share clinical features, which can lead to monogenic forms being misdiagnosed as T1D. However, correct diagnosis is crucial for therapeutic choice, prognosis and genetic counseling. The aim of this study was to search for monogenic autoimmune diabetes in Spanish pediatric patients with early-onset T1D. Among 500 Spanish pediatric patients with T1D, those with disease onset between 9 and 30 months of age were selected for screening for monogenic autoimmune diabetes (n=44). Genetic testing was performed by NGS with a customized panel that included the major causative genes for monogenic autoimmune syndromes, including early-onset diabetes: AIRE, CTLA4, FOXP3, IL2RA, ITCH, LRBA, STAT1, STAT3, STAT5B. RT-PCR and cDNA sequencing of the RNA isolated from whole blood were used to analyze splicing variants. Genetic screening identified, in two patients with diabetes onset under one year of age, two likely pathogenic novel variants affecting canonical splicing sites: c.286-12_290del in STAT5B and c.-22-2delA in FOXP3. RNA analyses demonstrated that both variants modify mRNA splicing. The variant in STAT5B induced exon 4 skipping and the variant in FOXP3 caused a deletion of 16 nucleotides before the transcription start-site. T1D onset in the first year of life may indicate monogenic autoimmune diabetes and molecular testing may be recommended.

DOP127 A novel epithelial junction gene associated with very early onset IBD: a mechanistic study using patient organoids and transgenic mouse models

Abstract Background Very early onset inflammatory bowel disease (VEO-IBD) is often associated with a severe disease course and unique characteristics including underlying monogenic etiologies in some cases. In this study, we mechanistically defined the function of CGNL1, an epithelial junctional protein gene whose pathogenic variants may contribute to VEO-IBD. Methods Whole exome sequencing (WES) was performed on the affected patient and all first-degree relatives. Intestinal epithelial organoids (IEOs) were generated from the patient’s mucosal biopsies and were characterized by microscopy, whole-mount immunostaining, transcriptomics and transmission electron microscopy (TEM). In addition, we generated a new Cgnl1-/- mice for dextran-sodium sulfate (DSS)-induced colitis and infection by Citrobacter rodentium which directly compromises intestinal epithelium. Integrated analysis was performed to determine CGNL1 expression in single-cell datasets. Results In this patient with VEO-IBD who required early total colectomy with pouch formation, coexistent primary sclerosing cholangitis (PSC) and celiac disease, WES identified two rare, novel, pathogenic variants in the CGNL1 gene. Both pathogenic variants were also present in the patient’s younger sister, who has a similar history including fulminant UC and PSC-autoimmune hepatitis overlap syndrome. Furthermore, multiple relatives of the patient suffer from IBD and other inflammatory conditions including celiac disease, eosinophilic esophagitis, and type-1 diabetes. The RNA and protein levels of CGNL1 were diminished in the patient’s intestinal epithelium compared to that of healthy individuals and other IBD patients. The patient’s IEOs from pouch body and pre-pouch ileum formed smaller 3D spheroids with altered cell composition and significantly impaired barrier function compared to those from normal controls (Figure 1). TEM demonstrated disrupted tight junctions and adherens junctions in the patient’s IEOs. Similarly, impaired junctional complexes in intestinal epithelial cells and elevated intestinal permeability were present in Cgnl1-/- mice, which also showed increased susceptibility to DSS-induced colitis (Figure 2) and C. rodentium infection. Single-cell analysis revealed diminished expression of CGNL1 in intestinal and hepatic epithelial cells from patients with IBD or PSC, respectively. Conclusion The pathogenic CGNL1 variants may contribute to VEO-IBD and other inflammatory GI disease by disrupting gut barrier integrity. This study expands our understanding of epithelial barrier impairment in the pathogenesis of VEO-IBD and suggests the intestinal epithelium as a therapeutic target for some IBD patients.

Genetic Etiology Investigation in Treatment-Resistant Nocturnal Enuresis Children: A descriptive study.

Our study aimed to evaluate the genetic etiology of treatment-resistant nocturnal enuresis in children who have undergone at least 6 episodes of behavioral therapy, urotherapy, alarm therapy, and medical treatment. A total of 21 patients were included in the study. Inclusion criteria for the study comprised children aged 5-18 years diagnosed with treatment-resistant enuresis according to the International Children's Continence Society (ICCS) guidelines. The capture-based Sophia Hereditary Disease Panel by Sophia Genetics was used specifically for nocturnal enuresis, consisting of a panel of 19 genes (AGXT, AQP2, AVPR2, BNC2, CLCNKB, DLG3, ELN, FA2H, FAM20A, FOXP1, HPSE2, KCNJ10, MLXIPL, NPHP3, RNF168, SLC12A3, SLC25A13, SLC5A2, SMARCA2). Patients were analyzed for genetic variations in genes associated with nocturnal enuresis, including AGXT, AQP2, AVPR2, BNC2, CLCNKB, DLG3, ELN, FA2H, FAM20A, FOXP1, HPSE2, KCNJ10, MLXIPL, NPHP3, RNF168, SLC12A3, SLC25A13, SLC5A2, and SMARCA2. No pathogenic changes potentially explaining the etiology of the disease were detected in 20 patients. One patient exhibited a variant in the AQP2 gene at hg19:Chr12:50344908 exon 1, c.295G>A locus, classified as a Variant of Uncertain Significance (VUS) according to the American College of Medical Genetic and Genomics (ACMG) 2015 guidelines. The AQP2 gene is associated with autosomal dominant and autosomal recessive inherited nephrogenic diabetes insipidus (type 2) in the OMIM (Online Mendelian Inheritance in Man) database. Our study resembles studies indicating that nocturnal enuresis cases do not have a monogenic etiology but occur with multifactorial effects and have a weak correlation between genotype and phenotype.

Common variable immunodeficiency clinical manifestations are shaped by presence and type of heterozygous NFKB1 variants.

NFKB1 encodes p105, which is processed to p50 to mediate canonical NF-κB signaling. Though NF-κB is a central driver of inflammation and heterozygous NFKB1 variants are considered the most common monogenic etiologies of common variable immunodeficiency (CVID), few studies have explored how NFKB1 variants shape clinical course or inflammation in CVID. We leveraged a regional cohort of CVID patients with and without heterozygous NFKB1 variants to assess how clinical and inflammatory features of CVID are shaped by the presence of these variants. We compared clinical complications, immunological features, and plasma cytokine levels of 15 CVID patients with heterozygous NFKB1 variants with 77 genetically undefined CVID patients from the same referral base. We also assessed differences between CVID patients with frameshift or nonsense NFKB1 variants compared to those with missense NFKB1 variants. We found CVID patients with heterozygous NFKB1 variants to have increased autoimmune disease, bronchiectasis, gastrointestinal infections, inflammatory bowel disease (IBD), and plasma cytokines. These findings were more pronounced, and included elevation of monocytes, in CVID patients with frameshift or nonsense NFKB1 variants relative to those with missense NFKB1 variants. In a regional cohort, heterozygous NFKB1 variants were associated with worsened CVID clinical course and increased evidence of inflammation in the blood. CVID patients with frameshift or nonsense NFKB1 variants had more significant increases in non-infectious complications and peripheral monocytes than those with missense NFKB1 variants. Presence of pathogenic NFKB1 variants in CVID patients may worsen disease course and warrant closer monitoring.

Genetic Landscape of a Cohort of 120 Patients with Diminished Ovarian Reserve: Correlation with Infertility.

Diminished ovarian reserve (DOR) and primary ovarian insufficiency (POI) are major causes of female infertility. We recently found a monogenic etiology in 29.3% of POI, leading to personalized medicine. The genetic landscape of DOR is unknown. A prospective study (2018-2023) of an international cohort of 120 patients with unexplained DOR was performed using a large custom targeted next-generation sequencing panel including all known POI-causing genes. The diagnostic yield, based on the American College of Medical Genetics, was 24, 2%. Genes belong to different pathways: metabolism and mitochondria (29.7%), follicular growth (24.3%), DNA repair/meiosis (18.9%), aging (16.2%), ovarian development (8.1%), and autophagy (2.7%). Five genes were recurrently found: LMNA, ERCC6, SOX8, POLG, and BMPR1B. Six genes identified in single families with POI were involved in DOR, GNAS, TGFBR3, XPNPEP2, EXO1, BNC1, ATG, highlighting their role in maintaining ovarian reserve. In our cohort, 26 pregnancies were recorded, but no pregnancy was observed when meiosis/DNA repair genes were involved, suggesting severely impaired oocyte quality. Additional studies should confirm these preliminary results. This study with a large NGS panel defines the genetic landscape of a large cohort of DOR. It supports routine genetic diagnosis. Genetics could be a biomarker predicting infertility and progression to POI.

Defining ethical criteria to guide the expanded use of Noninvasive Prenatal Screening (NIPS): Lessons about severity from preimplantation genetic testing.

We hypothesized that ethical criteria that guide the use of preimplantation genetic testing (PGT) could be used to inform policies about expanded use of non-invasive prenatal screening (NIPS). We used a systematic review of reasons approach to assess ethical criteria used to justify using (or not using) PGT for genetic conditions. Out of 1135 identified documents, we retained and analyzed 216 relevant documents. Results show a clear distinction in acceptability of PGT for medical vs. non-medical conditions. Criteria to decide on use of PGT for medical conditions are largely based on their severity, but there is no clear definition of "severity". Instead, characteristics of the condition that relate to severity are used as sub-criteria to assess severity. We found that characteristics that are used as sub-criteria for assessing severity include monogenic etiology, high penetrance, absence of treatment, early age of onset, shortened lifespan, and reduced quality of life. Consensus about the use of PGT is highest for conditions that meet most of these criteria. There is no consensus around the acceptability of using PGT to detect non-medical conditions. We propose that the same severity criteria could be used by policymakers to assess the acceptability of using other genetic tests in screening and practice, including for the use of NIPS for additional conditions as indications broaden.

Monogenic obesity in a familial cluster: insights into laurence-moon-bardet-biedl syndrome and leptin deficiency associated with genetic variants in BBS12 and LEPR genes

Monogenic obesity is a rare but clinically significant condition characterized by excessive weight gain due to genetic mutations that affect appetite regulation and energy balance. This case series explores the clinical presentation and genetic underpinnings of monogenic obesity in a familial cluster, focusing on Laurence-Moon-Bardet-Biedl Syndrome (LMBBS) and leptin deficiency associated with genetic variants in the BBS1 and LEPR genes. The index patient, an 11-year-old female, presented with progressive weight gain since infancy, accompanied by acanthosis nigricans on the neck and axillary region. Genetic testing revealed mutations in both the BBS1 and LEPR genes, confirming a monogenic etiology of obesity. Remarkably, her two siblings and a cousin from the paternal side exhibited similar clinical profiles and shared the same genetic variants. This report shows the significance of genetic testing in diagnosing monogenic obesity disorders and highlights the familial clustering observed in such cases. The findings emphasize the need for heightened awareness and consideration of genetic factors in the evaluation of obesity, particularly in pediatric patients with a family history suggestive of monogenic obesity.

Steatotic liver disease associated with 2,4-dienoyl-CoA reductase 1 deficiency

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) is considered multifactorial with a number of predisposing gene polymorphisms known.MethodsThe occurrence of MASLD in 7 and 10 year old siblings, one without classical risk factors and one with type 2 diabetes suggested a monogenic etiology and prompted next-generation sequencing. Exome sequencing was performed in the proband, both parents and both siblings. The impact of a likely disease-causing DNA variant was assessed on the transcript and protein level.ResultsTwo siblings have hepatomegaly, elevated serum transaminase activity, and steatosis and harbor a homozygous DECR1 splice-site variant, c.330+3A>T. The variant caused DECR1 transcript decay. Immunostaining demonstrated lack of DECR1 in patient liver.ConclusionsThese patients may represent the first individuals with DECR1 deficiency, then defining within MASLD an autosomal-recessive entity, well corresponding to the reported steatotic liver disease in Decr1 knockout mice. DECR1 may need to be considered in the genetic work-up of MASLD.

Hematopoietic stem cell transplantation for primary immunodeficiency.

Primary immunodeficiencies, also commonly called inborn errors of immunity (IEI), are commonly due to developmental or functional defects in peripheral blood cells derived from hematopoietic stem cells. In light of this, for the past 50 years, hematopoietic stem cell transplantation (HSCT) has been used as a definitive therapy for IEI. The fields of both clinical immunology and transplantation medicine have had significant advances. This, in turn, has allowed for both an increasing ability to determine a monogenic etiology for many IEIs and an increasing ability to successfully treat these patients with HSCT. Therefore, it has become more common for the practicing allergist/immunologist to diagnose and manage a broad range of patients with IEI before and after HSCT. This review aims to provide practical guidance for the clinical allergist/immunologist on the basics of HSCT and known outcomes in selected forms of IEI, the importance of pre-HSCT supportive care, and the critical importance of and guidance for life-long immunologic and medical monitoring of these patients.

Polygenic Risk Score (PRS) Combined with NGS Panel Testing Increases Accuracy in Hereditary Breast Cancer Risk Estimation.

Breast cancer (BC) is the most prominent tumor type among women, accounting for 32% of newly diagnosed cancer cases. BC risk factors include inherited germline pathogenic gene variants and family history of disease. However, the etiology of the disease remains occult in most cases. Therefore, in the absence of high-risk factors, a polygenic basis has been suggested to contribute to susceptibility. This information is utilized to calculate the Polygenic Risk Score (PRS) which is indicative of BC risk. This study aimed to evaluate retrospectively the clinical usefulness of PRS integration in BC risk calculation, utilizing a group of patients who have already been diagnosed with BC. The study comprised 105 breast cancer patients with hereditary genetic analysis results obtained by NGS. The selection included all testing results: high-risk gene-positive, intermediate/low-risk gene-positive, and negative. PRS results were obtained from an external laboratory (Allelica). PRS-based BC risk was computed both with and without considering additional risk factors, including gene status and family history. A significantly different PRS percentile distribution consistent with higher BC risk was observed in our cohort compared to the general population. Higher PRS-based BC risks were detected in younger patients and in those with FH of cancers. Among patients with a pathogenic germline variant detected, reduced PRS values were observed, while the BC risk was mainly determined by a monogenic etiology. Upon comprehensive analysis encompassing FH, gene status, and PRS, it was determined that 41.90% (44/105) of the patients demonstrated an elevated susceptibility for BC. Moreover, 63.63% of the patients with FH of BC and without an inherited pathogenic genetic variant detected showed increased BC risk by incorporating the PRS result. Our results indicate a major utility of PRS calculation in women with FH in the absence of a monogenic etiology detected by NGS. By combining high-risk strategies, such as inherited disease analysis, with low-risk screening strategies, such as FH and PRS, breast cancer risk stratification can be improved. This would facilitate the development of more effective preventive measures and optimize the allocation of healthcare resources.

Homozygous TNNI3 frameshift variant in a consanguineous family with lethal infantile dilated cardiomyopathy.

Dilated cardiomyopathy (DCM) is characterized by dilatation of the left ventricle, systolic dysfunction, and normal or reduced thickness of the left ventricular wall. It is a leading cause of heart failure and cardiac death at a young age. Cases with neonatal onset DCM were correlated with severe clinical presentation and poor prognosis. A monogenic molecular etiology accounts for nearly half of cases. Here, we report a family with three deceased offspring at the age of 1 year old. The autopsy of the first deceased infant revealed a DCM. The second infant presented a DCM phenotype with a severely reduced Left Ventricular Ejection Fraction (LVEF) of 10%. Similarly, the third infant showed a severe DCM phenotype with LVEF of 30% as well, in addition to eccentric mitral insufficiency. Exome sequencing was performed for the trio (the second deceased infant and her parents). Data analysis following the autosomal dominant and recessive patterns of inheritance was carried out along with a mitochondrial pathways-based analysis. We identified a homozygous frameshift variant in the TNNI3 gene (c.204delG; p.(Arg69AlafsTer8)). This variant has been recently reported in the ClinVar database in association with cardiac phenotypes as pathogenic or likely pathogenic and classified as pathogenic according to ACMG. Genetic counseling was provided for the family and a prenatal diagnosis of choronic villus was proposed in the absence of pre-implantation genetic diagnosis possibilities. Our study expands the case series of early-onset DCM patients with a protein-truncating variant in the TNNI3 gene by reporting three affected infant siblings.

Fetal agenesis of the corpus callosum: Clinical and genetic analysis in a series of 40 patients

ObjectivesThis study aimed to explore the genetic causes of agenesis of the corpus callosum (ACC) and assess the utility of karyotype analysis, copy number variation sequencing (CNV-seq), and whole-exome sequencing (WES) to genetically diagnose fetal ACC. MethodsWe retrospectively examined 40 fetuses diagnosed with ACC who underwent prenatal ultrasonography or magnetic resonance imaging between January 2019 and October 2023. Genetic tests were conducted on the fetuses using karyotype analysis or CNV-seq as the first-line diagnosis. WES was performed if aneuploid and pathogenic CNVs were excluded. ResultsAmong the 40 fetuses, 29 (72 %) had non-isolated ACC and 11 (28 %) had isolated ACC. Cerebellar dysplasia and hydrocephalus were the most common abnormal developments in the central nervous system. Twenty-eight patients underwent karyotype analysis, with a detection rate of 14 % (4/28). Twenty-six patients underwent CNV-seq; three patients were found to have pathogenic CNVs, with a detection rate of 12 % (3/26). Thirty-three fetuses with no findings of karyotype analysis or CNV-seq were subsequently tested using WES, with a detection rate of 36 % (12/33). Overall, the total diagnostic yield was 48 % (19/40), and monogenic etiology accounted for 30 % (12/40). The genetic detection rate of fetal non-isolated ACC (62 %, 18/29) was higher than that of isolated ACC (9 %, 1/11). ConclusionPrenatal genetic analysis of fetuses with ACC is clinically significant, with monogenic disorders being the main cause. WES may enhance the detection rate of fetuses with ACC with negative karyotype analysis or CNV-seq results.

Genetic Testing of Children With Familial Tall Stature: Is it Worth Doing?

Familial tall stature (FTS) is considered to be a benign variant of growth with a presumed polygenic etiology. However, monogenic disorders with possible associated pathological features could also be hidden under the FTS phenotype. To elucidate the genetic etiology in families with FTS and to describe their phenotype in detail. Children with FTS (the life-maximum height in both the child and his/her taller parent > 2 SD for age and sex) referred to the Endocrinology center of Motol University Hospital were enrolled into the study. Their DNA was examined cytogenetically and via a next-generation sequencing panel of 786 genes associated with growth. The genetic results were evaluated by the American College of Molecular Genetics and Genomics guidelines. All of the participants underwent standard endocrinological examination followed by specialized anthropometric evaluation. In total, 34 children (19 girls) with FTS were enrolled in the study. Their median height and their taller parent's height were 3.1 SD and 2.5 SD, respectively. The genetic cause of FTS was elucidated in 11/34 (32.4%) children (47,XXX and 47,XYY karyotypes, SHOX duplication, and causative variants in NSD1 [in 2], SUZ12 [in 2], FGFR3, CHD8, GPC3, and PPP2R5D genes). Ten children had absent syndromic signs and 24 had dysmorphic features. Monogenic (and cytogenetic) etiology of FTS can be found among children with FTS. Genetic examination should be considered in all children with FTS regardless of the presence of dysmorphic features.

New insights from the genetic work-up in early onset nephrotic syndrome: report from a registry in western India.

Eighty-five percent of infants with congenital nephrotic syndrome (CNS) and 66% with infantile NS (INS) are likely to have a monogenic etiology. There exists a significant genetic variability between different regions and ethnic groups. This study aimed to determine the genetic defects in children with CNS and INS by establishing a registry in western India. In this cross-sectional study, pediatric nephrologists from 13 private and government institutions shared relevant clinical data and details of the genetic evaluation of children presenting with NS within the first year of life. The median age at presentation was 9months (range 1-23, IQR 3-13months), history of consanguinity between parents existed in 14 patients (34%), family history of similar illness in 6 (15%), and extra-renal manifestations in 17 (41%). Twenty-five (61%) were confirmed to have a monogenic etiology. NPHS1 gene was the most implicated (9/25) followed by PLCE1 (5/25). There were 12 variants of uncertain significance (VUS) involving 10 genes (10/25, 40%), and no definite genetic abnormality was found in 4 (25%). A re-analysis of these VUS attempted 2-3years later facilitated reclassification of 7/12 (58%); increasing the diagnostic yield from 61 to 68.2%. Consistent with worldwide data, variants in NPHS1 gene were the most common cause of NS in infancy; however, PLCE1 was implicated more frequently in our cohort. NUP93 and COL4A3 were reported in early onset NS for the first time. Reclassification of VUS should be attempted, if feasible, since it may lead to a useful revision of diagnosis.

Next-generation sequencing testing in children with epilepsy reveals novel clinical, diagnostic and therapeutic implications.

Introduction: Epilepsy is one of the commonest diseases in children, characterized by extensive phenotypic and genetic heterogeneity. This study was conducted to determine the diagnostic utility and to identify novel clinical and therapeutic implications of genetic testing in pediatric patients with epilepsy. Methods: Large multigene panel and/or exome sequencing was performed in 127 unrelated Polish and Ukrainian patients with suspected monogenic epilepsy. Diagnostic yields were presented for five phenotypic subgroups, distinguished by seizure type, electroencephalographic abnormalities, anti-seizure treatment response, and neurodevelopmental deficits. Results: A definite molecular diagnosis was established in 46 out of 127 cases (36%). Alterations in six genes were detected in more than one patient: SCN1A, MECP2, KCNT1, KCNA2, PCDH19, SLC6A1, STXBP1, and TPP1, accounting for 48% of positive cases. 4/46 cases (8.7%) were mosaic for the variant. Although the highest rates of positive diagnoses were identified in children with developmental delay and generalized seizures (17/41, 41%) and in developmental end epileptic encephalopathies (16/40, 40%), a monogenic etiology was also frequently detected in patients with solely focal seizures (10/28, 36%). Molecular diagnosis directly influenced anti-seizure management in 15/46 cases. Conclusion: This study demonstrates the high diagnostic and therapeutic utility of large panel testing in childhood epilepsies irrespective of seizure types. Copy number variations and somatic mosaic variants are important disease-causing factors, pointing the need for comprehensive genetic testing in all unexplained cases. Pleiotropy is a common phenomenon contributing to the growing phenotypic complexity of single-gene epilepsies.

Trio-based whole exome sequencing in patients with ectopic posterior pituitary.

Ectopic posterior pituitary (EPP) is a rare congenital abnormality, sometimes associated with other midline defects, such as pituitary stalk interruption syndrome (PSIS), in which thin or absent pituitary stalk and anterior pituitary hypoplasia are combined to EPP. Most cases are sporadic, with few reports of familial cases, and many congenital hypopituitarism (CH) cases remain unsolved. To search for candidate genes associated with this condition, we performed trio-based whole-exome sequencing (WES) on patients with EPP, including two familial cases. This study included subjects with EPP and PSIS diagnosed by a simple MRI protocol (FAST1.2). We performed two distinct analyses in the trio-based WES. We looked for previously described genes associated with pituitary development. Next, we investigated the whole exome for variants inherited in a pattern consistent with a monogenic etiology. Ten families were evaluated; eight were composed of a child with EPP and healthy parents, one has two affected siblings, and one family has a son and mother with EPP. When analyzing the previously described candidate variants associated with pituitary development, we found variants in GLI2 and FGFR1 in three families. We also found six other variants of interest in three patients: KMT2A, GALR3, RTN4R, SEMA3A, NIPBL, and DSCAML1. The analysis allowed us to find previously reported and not reported GLI2 variants, all inherited from healthy parents, which reinforces the incomplete penetrance pattern of GLI2 variants in the development of EPP and draws attention to possible future functional studies of those variants that have a recurrent expression in CH. We also found novel FGFR1 and SEMA3A variants that suggest an oligogenic mechanism in PSIS and EPP, as seen in patients with hypogonadotropic hypogonadism. We report the first case of a patient with Wiedemann-Steiner syndrome and PSIS, suggesting that the KMT2A gene may be related to pituitary development. Furthermore, the trios' analysis allowed us to find five other variants of interest. Future investigations may clarify the roles of these variants in the etiology of EPP and PSIS.

Genetics of Primary Hemophagocytic Lymphohistiocytosis.

Hemophagocytic lymphohistiocytosis (HLH) constitutes a rare, potentially life-threatening hyperinflammatory immune dysregulation syndrome that can present with a variety of clinical signs and symptoms, including fever, hepatosplenomegaly, and abnormal laboratory and immunological findings such as cytopenias, hyperferritinemia, hypofibrinogenemia, hypertriglyceridemia, elevated blood levels of soluble CD25 (interleukin (IL)-2 receptor α-chain), or diminished natural killer (NK)-cell cytotoxicity (reviewed in detail in Chapter 11 of this book). While HLH can be triggered by an inciting event (e.g., infections), certain monogenic causes have been associated with a significantly elevated risk of development of HLH, or recurrence of HLH in patients who have recovered from their disease episode. These monogenic predisposition syndromes are variably referred to as "familial" (FHL)or "primary" HLH (henceforth referred to as "pHLH") and are the focus of this chapter. Conversely, secondary HLH (sHLH) often occurs in the absence of monogenic etiologies that are commonly associated with pHLH and can be triggered by infections, malignancies, or rheumatological diseases; these triggers and the genetics associated with sHLH are discussed in more detail in other chapters in this book.

Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses

BackgroundNeuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes.MethodsWe analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis.ResultsInitially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21–0.82), while a positive family history (OR 5.46; 95%CI 2.60–11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11–7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies.ConclusionOur findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.

Prenatal dispositions and genetic analysis of monozygotic female twins with suprasellar cysts and hydrocephalus: A case report

IntroductionWe present a unique case of monozygotic female twins with virtually identical clinical and radiological presentations of supratentorial hydrocephalus and cystic formations from the suprasellar cistern.DiscussionEvaluating genetic predispositions and prenatal exposures is crucial for hydrocephalus in twins. Familial cases imply a genetic contribution to the development of these anomalies, including chromosomal abnormalities and specific variants linked to arachnoid cyst formation in various syndromes. Extensive genetic analyses found no pathogenic variants in the twins. Prenatal exposure to anti-epileptic medication was known during pregnancy and may be associated with fetal abnormalities, but not central nervous system (CNS) malformations, and was therefore not considered the cause of the condition in the twins. The twins presenting simultaneously with hydrocephalus caused by suprasellar cysts (SAC) underwent a two-step surgical management: initial ventriculoperitoneal shunt (VPS) placement followed by fenestration. Postoperative imaging showed cyst reduction, but a secondary VPS was necessary in both cases.ConclusionGenetic analysis is less likely to identify a monogenic etiology in non-syndromic cases of SACs, which are assumed to be multifactorial. There is no established evidence linking a teratogenic effect of anti-epileptic drugs to CNS malformations. Moreover, the surgical treatment of this complex condition constitutes a point of discussion.

Genetic risk factors for severe and fatigue dominant long COVID and commonalities with ME/CFS identified by combinatorial analysis

BackgroundLong COVID is a debilitating chronic condition that has affected over 100 million people globally. It is characterized by a diverse array of symptoms, including fatigue, cognitive dysfunction and respiratory problems. Studies have so far largely failed to identify genetic associations, the mechanisms behind the disease, or any common pathophysiology with other conditions such as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) that present with similar symptoms.MethodsWe used a combinatorial analysis approach to identify combinations of genetic variants significantly associated with the development of long COVID and to examine the biological mechanisms underpinning its various symptoms. We compared two subpopulations of long COVID patients from Sano Genetics’ Long COVID GOLD study cohort, focusing on patients with severe or fatigue dominant phenotypes. We evaluated the genetic signatures previously identified in an ME/CFS population against this long COVID population to understand similarities with other fatigue disorders that may be triggered by a prior viral infection. Finally, we also compared the output of this long COVID analysis against known genetic associations in other chronic diseases, including a range of metabolic and neurological disorders, to understand the overlap of pathophysiological mechanisms.ResultsCombinatorial analysis identified 73 genes that were highly associated with at least one of the long COVID populations included in this analysis. Of these, 9 genes have prior associations with acute COVID-19, and 14 were differentially expressed in a transcriptomic analysis of long COVID patients. A pathway enrichment analysis revealed that the biological pathways most significantly associated with the 73 long COVID genes were mainly aligned with neurological and cardiometabolic diseases.Expanded genotype analysis suggests that specific SNX9 genotypes are a significant contributor to the risk of or protection against severe long COVID infection, but that the gene-disease relationship is context dependent and mediated by interactions with KLF15 and RYR3.Comparison of the genes uniquely associated with the Severe and Fatigue Dominant long COVID patients revealed significant differences between the pathways enriched in each subgroup. The genes unique to Severe long COVID patients were associated with immune pathways such as myeloid differentiation and macrophage foam cells. Genes unique to the Fatigue Dominant subgroup were enriched in metabolic pathways such as MAPK/JNK signaling. We also identified overlap in the genes associated with Fatigue Dominant long COVID and ME/CFS, including several involved in circadian rhythm regulation and insulin regulation. Overall, 39 SNPs associated in this study with long COVID can be linked to 9 genes identified in a recent combinatorial analysis of ME/CFS patient from UK Biobank.Among the 73 genes associated with long COVID, 42 are potentially tractable for novel drug discovery approaches, with 13 of these already targeted by drugs in clinical development pipelines. From this analysis for example, we identified TLR4 antagonists as repurposing candidates with potential to protect against long term cognitive impairment pathology caused by SARS-CoV-2. We are currently evaluating the repurposing potential of these drug targets for use in treating long COVID and/or ME/CFS.ConclusionThis study demonstrates the power of combinatorial analytics for stratifying heterogeneous populations in complex diseases that do not have simple monogenic etiologies. These results build upon the genetic findings from combinatorial analyses of severe acute COVID-19 patients and an ME/CFS population and we expect that access to additional independent, larger patient datasets will further improve the disease insights and validate potential treatment options in long COVID.