Distal Deletion Research Articles

Late-onset tumors in rhabdoid tumor predisposition syndrome type-1 (RTPS1) and implications for surveillance.

Rhabdoid tumor predisposition syndrome type-1 (RTPS1) is characterized by germline pathogenic variants in SMARCB1 and development of INI1-deficient rhabdoid tumors in early childhood. Due to its poor prognosis, the risk of subsequent tumor development and the impact of surveillance at later ages are poorly understood. We retrospectively reviewed individuals referred to the Cancer Genetics Program at The Hospital for Sick Children for SMARCB1 genetic testing and/or surveillance for RTPS1. In addition, to explore characteristics of late-onset tumors in RTPS1, a literature review was conducted. Of eighty-three individuals (55 probands and 28 family members), 12 probands and 4 family members were genetically confirmed with RTPS1. Four pediatric probands with RTPS1 underwent surveillance. An additional three individuals, including one patient with 22q11.2 distal deletion without history of tumor, one patient with negative genetic testing results but clinically diagnosed with RTPS1, and one sibling identified through cascade testing, underwent surveillance. Three patients with RTPS1 developed tumors between the ages of 9 and 17, including malignant rhabdoid tumors (N = 3), schwannomas (N = 4), and epithelioid malignant peripheral nerve sheath tumor (N = 1). Three of these lesions were asymptomatically detected by surveillance. A literature review revealed 17 individuals with RTPS1 who developed INI1-deficient tumors after age five. Individuals with RTPS1 remain at elevated risk for developing INI1-deficient tumors after the peak age of rhabdoid tumor in early childhood. Extension of surveillance beyond 5 years of age could lead to improved survival and reduced morbidity for these patients, and prospective evaluation of revised approaches will be important.

Prenatal detection of distal 18p deletion by chromosomal microarray analysis: Three case reports and literature review.

Chromosome 18p deletion syndrome is caused by total or partial deletion of the short arm of chromosome 18 and associated with cognitive impairment, growth retardation and mild facial dysmorphism. However, most studies on the genotype-phenotype correlations in the 18p region are diagnosed postnatally. Prenatal reports involving 18p deletions are limited. Three pregnant women opted for invasive prenatal testing due to noninvasive prenatal testing indicating high risk for chromosome 18 abnormalities. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed simultaneously. The pregnancy outcomes for all cases were followed up. Meanwhile, we also made a literature review on prenatal phenotypes of 18p deletions. G-banding analysis showed that 2 fetuses presented abnormal karyotypes: 45,XN,der(18)t(18;21)(p11; q11),-21 (case 2) and 46,XN,18p- (case 3). The karyotype of case 1 was normal. Meanwhile, CMA detected 4.37 Mb (case 1), 7.26 Mb (case 2) and 14.97 Mb (case 3) deletions in chromosome 18p region. All 3 pregnancies were terminated finally according to genetic counseling based upon abnormal CMA results. Prenatal diagnosis of 18p deletion syndrome is full of challenges due to the phenotypic diversity, incomplete penetrance and lack of prenatal phenotypes. Increased nuchal translucency and holoprosencephaly are common prenatal phenotypes of distal 18p deletion. For fetuses carrying 18p deletions with atypical sonographic phenotypes, noninvasive prenatal testing could be adopted as an effective approach.

Title-molecular diagnostics of dystrophinopathies in Sri Lanka towards phenotype predictions: an insight from a South Asian resource limited setting

BackgroundThe phenotype of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) patients is determined by the type of DMD gene variation, its location, effect on reading frame, and its size. The primary objective of this investigation was to determine the frequency and distribution of DMD gene variants (deletions/duplications) in Sri Lanka through the utilization of a combined approach involving multiplex polymerase chain reaction (mPCR) followed by Multiplex Ligation Dependent Probe Amplification (MLPA) and compare to the international literature. The current consensus is that MLPA is a labor efficient yet expensive technique for identifying deletions and duplications in the DMD gene.MethodologyGenetic analysis was performed in a cohort of 236 clinically suspected pediatric and adult myopathy patients in Sri Lanka, using mPCR and MLPA. A comparative analysis was conducted between our findings and literature data.ResultsIn the entire patient cohort (n = 236), mPCR solely was able to identify deletions in the DMD gene in 131/236 patients (DMD-120, BMD-11). In the same cohort, MLPA confirmed deletions in 149/236 patients [DMD-138, BMD -11]. These findings suggest that mPCR has a detection rate of 95% (131/138) among all patients who received a diagnosis. The distal and proximal deletion hotspots for DMD were exons 45–55 and 6–15. Exon 45–60 identified as a novel in-frame variation hotspot. Exon 45–59 was a hotspot for BMD deletions. Comparisons with the international literature show significant variations observed in deletion and duplication frequencies in DMD gene across different populations.ConclusionDMD gene deletions and duplications are concentrated in exons 45–55 and 2–20 respectively, which match global variation hotspots. Disparities in deletion and duplication frequencies were observed when comparing our data to other Asian and Western populations. Identified a 95% deletion detection rate for mPCR, making it a viable initial molecular diagnostic approach for low-resource countries where MLPA could be used to evaluate negative mPCR cases and cases with ambiguous mutation borders. Our findings may have important implications in the early identification of DMD with limited resources in Sri Lanka and to develop tailored molecular diagnostic algorithms that are regional and population specific and easily implemented in resource limited settings.

Prenatal diagnosis of the recurrent 1q21.1 microdeletions in fetuses with ultrasound anomalies and review of the literature.

The recurrent 1q21.1 microdeletion syndrome is an autosomal dominant disorder and is characterized by dysmorphic facial features, microcephaly, developmental delay, and congenital defects. However, most studies on the distal deletions in the 1q21.1 region were diagnosed postnatally. This study aimed to provide a better understanding of the ultrasound and molecular findings of fetuses with recurrent 1q21.1 microdeletions in prenatal diagnosis. In this retrospective study, we reported 21 cases with the recurrent 1q21.1 microdeletion syndrome diagnosed at our prenatal diagnostic center from January 2016 to January 2023. The clinical data were reviewed for these cases, including the maternal demographics, indications for invasive testing, ultrasound findings, CMA results, and pregnancy outcomes. In the study, a total of 21 cases with recurrent 1q21.1 microdeletions were diagnosed prenatally by CMA. Fifteen cases were described with ultrasound indications, and the most common findings are as follows: increased nuchal translucency (NT) (26.7%), intrauterine growth retardation (IUGR) (26.7%), congenital heart defects (CHD) (20%), and congenital anomalies of the kidney and urinary tract (CAKUT) (13.3%). All the cases with the distal 1q21.1 deletions contain the common minimal region (located between BP3 and BP4) and eight OMIM genes. Parental studies to determine the inheritance of the deletion were performed for eight cases, and half of the cases were inherited from one of the parents. Pregnancy outcomes were available for nine cases; eight (88.9%) pregnancies were determined to be terminated and one (11.1%) was full-term delivery. To our knowledge, this is the largest study to find that fetuses with recurrent 1q21.1 microdeletions were closely associated with increased NT, CHD, IUGR, and CAKUT. In addition, ours is the first study to report that cerebral ventriculomegaly might be associated with recurrent 1q21.1 microdeletions. More comprehensive studies are needed for a better understanding of the prenatal phenotype-genotype relationship of the recurrent 1q21.1 microdeletion syndrome in future.

Beyond the Global Brain Differences: Intraindividual Variability Differences in 1q21.1 Distal and 15q11.2 BP1-BP2 Deletion Carriers

BackgroundCarriers of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants exhibit regional and global brain differences compared with noncarriers. However, interpreting regional differences is challenging if a global difference drives the regional brain differences. Intraindividual variability measures can be used to test for regional differences beyond global differences in brain structure. MethodsMagnetic resonance imaging data were used to obtain regional brain values for 1q21.1 distal deletion (n = 30) and duplication (n = 27) and 15q11.2 BP1-BP2 deletion (n = 170) and duplication (n = 243) carriers and matched noncarriers (n = 2350). Regional intra-deviation scores, i.e., the standardized difference between an individual’s regional difference and global difference, were used to test for regional differences that diverge from the global difference. ResultsFor the 1q21.1 distal deletion carriers, cortical surface area for regions in the medial visual cortex, posterior cingulate, and temporal pole differed less and regions in the prefrontal and superior temporal cortex differed more than the global difference in cortical surface area. For the 15q11.2 BP1-BP2 deletion carriers, cortical thickness in regions in the medial visual cortex, auditory cortex, and temporal pole differed less and the prefrontal and somatosensory cortex differed more than the global difference in cortical thickness. ConclusionsWe find evidence for regional effects beyond differences in global brain measures in 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants. The results provide new insight into brain profiling of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants, with the potential to increase understanding of the mechanisms involved in altered neurodevelopment.

The Phenotypic variability of 16p11.2 distal BP2–BP3 deletion in a transgenerational family and in neurodevelopmentally ascertained samples

BackgroundWe present genomic and phenotypic findings of a transgenerational family consisting of three male offspring, each with a maternally inherited distal 220 kb deletion at locus 16p11.2 (BP2–BP3). Genomic analysis...

Differentially expressed miRNAs may help explaining the pathogenesis of relevant 22q11.2 clinical manifestations

Background and aimsChromosome 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion syndrome with a widely variable clinical spectrum, with >200 features reported. Genetic alone cannot explain the variability of the phenotype. DiGeorge Critical Region Gene 8 (DGCR8) encoded in the deleted region is crucial for miRNA biogenesis and therefore, for gene regulation. Aim of this study is to evaluate the role of miRNA in the clinical variability observed in 22q11.2DS. MethodsWe characterized miRNA expression profile in the peripheral leucocytes of 14 patients with a typical 3Mb deletion and 3 patients with a distal deletion not including TBX1 and DGCR8 compared to 10 age-matched healthy controls. Nine out of 17 patients had a familial form and came from 4 different families. ResultsThe unbiased hierarchical cluster analysis revealed significant clustering of the 22q11.2DS samples compared to normal controls. Samples from patients with distal deletion, clustered with patients with typical deletion. Twenty-nine differentially expressed miRNAs (padj< 0.05) were identified. As expected, the expression of miR185, encoded in the proximal part of the deleted region, was comparable to controls in 3 patients with distal deletion. High similarity of miRNA expression among patients coming from the same family was observed in 3 out of 4 families. Collectively, the 29 differentially expressed miRNA were predicted to regulate the expression of 13063 target genes, linked to multiple function and pathways. Interestingly, some DE-miRNAs are involved in the development of relevant 22q11.2 clinical manifestations, such as schizophrenia and autism (miR-132, miR-185-5p, miR-486-3p and miR-148-3p), B- and T-cell immunodysregulation and autoimmunity (miR-185-5p, miR-21-3p and miR-148-3p) and megakaryocytic differentiation (miR-486-5p). ConclusionsPatients with 22q11.2DS display a different miRNA expression profile compared to healthy controls. Some of the DE-miRNAs are involved in the development of relevant 22q11.2DS clinical manifestations, such as schizophrenia and autism, B- and T-cell immunodysregulation and autoimmunity and megakaryocytic differentiation and may be helpful to better define the pathogenesis of 22q11.2DS.

A Comprehensive and Clinical Review of Distal Deletion Syndrome of Chromosome 5q14.3

Cardozo et al. (2009) reported 3 unrelated children, 2 boys and 1 girl, with severe mental retardation, epilepsy, and bilateral periventricular heterotopia limited to the subcutaneous region of the temporal bones and occipital lateral ventricles. Other features of this syndrome include hypotonia, delayed motor development, lack of speech, and minor facial deformities such as a prominent forehead, depressed nasal bridge, and high blood pressure

Molecular cytogenetic characterization of de novo concomitant proximal 21q deletion of 21q11.2q21.3 and distal Xp deletion of Xp22.33p22.2 due to an unbalanced X;21 translocation detected by amniocentesis

ObjectiveWe present molecular cytogenetic characterization of de novo concomitant proximal 21q deletion of 21q11.2q21.3 and distal Xp deletion of Xp22.33p22.2 due to an unbalanced X; 21 translocation detected by amniocentesis. Case reportA 35-year-old, primigravid woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 45,X,der(X)t(X; 21) (p22.2; q21.3),-21. Simultaneous array comparative genomic hybridization (aCGH) revealed the result of an 11.9-Mb Xp22.33p22.2 deletion encompassing HCCS, SHOX, AMELX and OFD1 and a 15.4-Mb 21q11.2q21.3 deletion encompassing NRIP1 and APP. The pregnancy was subsequently terminated, and a malformed fetus was delivered with craniofacial dysmorphism. The parental karyotypes were normal. Polymorphic DNA marker analysis by quantitative fluorescence polymerase chain reaction (QF-PCR) confirmed a paternal origin of the 21q proximal deletion. Cytogenetic analysis of cord blood confirmed the karyotype of 45,X,der(X)t(X; 21) (p22.2; q21.3),-21. aCGH analysis of the cord blood confirmed the prenatal diagnosis. ConclusionQF-PCR analysis is useful for determination of the parental origin of a de novo unbalanced X; autosome translocation detected by prenatal diagnosis. The information acquired is useful for genetic counseling under such a circumstance.

Molecular cytogenetic characterization of de novo concomitant distal 8p deletion of 8p23.3p23.1 and Xp and Xq deletion of Xp22.13q28 due to an unbalanced X;8 translocation detected by amniocentesis

ObjectiveWe present molecular cytogenetic characterization of de novo concomitant distal 8p deletion of 8p23.3p23.1 and Xp and Xq deletion of Xp22.13q28 due to an unbalanced X;8 translocation detected by amniocentesis. Case reportA 33-year-old primigravid woman underwent amniocentesis at 18 weeks of gestation because of a Down syndrome risk of 1/52 at the first-trimester maternal serum screening calculated from 0.29 multiples of the median (MoM) of pregnancy associated plasma protein-A (PAPP-A), 1.14 MoM of free β-hCG and 0.46 MoM of placental growth factor (PlGF). Amniocentesis revealed a karyotype of 45,X,add(8)(p23.1). The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) analysis on the DNA extracted from cultured amniocytes revealed a 137-Mb deletion of Xp22.13q28 and a 10.53-Mb deletion of 8p23.3p23.1. The karyotype thus was 45,X,der(8)t(X;8)(p22.13;p23.1). Prenatal ultrasound revealed pericardial effusion and skin edema. The pregnancy was subsequently terminated, and a 568-g malformed fetus was delivered with hypertelorism and low-set ears. The cord blood had a karyotype of 45,X,der(8)t(X;8)(p22.13;p23.1). aCGH analysis of the cord blood revealed the result of arr [GRCH37 (hg19)] 8p23.3p23.1 (191,530–10,724,642) × 1.0, arr Xp22.13q28 (18,194,098–155,232,907) × 1.0. ConclusionaCGH analysis is useful elucidating the genetic nature of an aberrant chromosome with an additional maternal of unknown origin attached to a chromosome terminal region.

Prenatal diagnosis of distal 13q deletion syndrome in a fetus with esophageal atresia: a case report and review of the literature

BackgroundChromosome 13q deletion syndrome shows variable clinical features related to the different potential breakpoints in chromosome 13q. The severely malformed phenotype is known to be associated with the deletion of a critical region in 13q32. However, esophageal atresia is a rare symptom and the relevant region is unknown. Thus, determining the association between accurate breakpoints and new clinical features is essential.Case presentationA 28-year-old Japanese primigravid woman was referred for fetal growth restriction, absence of a gastric bubble, cerebellar hypoplasia, overlapping fingers, and polyhydramnios at 31 weeks gestation. At 38 + 0 weeks, she delivered a 1774 g female infant. The infant presented with isolated esophageal atresia (Gross type A), Dandy–Walker malformation, right microphthalmia, left coloboma, overlapping fingers, pleurocentrum in the thoracic vertebrae, reduced anogenital distance, and hearing loss. Her karyotype was diagnosed as 46,XX,del(13)(q32.1–qter) by amniocentesis, but array comparative genomic hybridization after birth revealed the deletion of 13q31.3–qter. At 48 days after birth, the infant underwent surgery for esophageal atresia and was later discharged from the hospital at 7 months of age.ConclusionThis case report and the literature reviews supports the previous findings on the pathological roles of haploinsufficiency of the ZIC2/ZIC5 in Dandy–Walker malformation and the EFBN2 haploinsufficiency in eye malformation and hearing loss. Furthermore, the possible involvement of IRS2, COLA1, and COLA2 in eye malformation were identified. This is the first case of 13q deletion syndrome with esophageal atresia (Gross A), but it may be a symptom of VATER/VACTER association (vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects), as in the previous cases. These symptoms might also be associated with EFBN2 haploinsufficiency, although further research is required.

Rac1 deficiency impairs postnatal development of the renal papilla

Development of the renal medulla continues after birth to form mature renal papilla and obtain urine-concentrating ability. Here, we found that a small GTPase, Rac1, plays a critical role in the postnatal development of renal papilla. Mice with distal tubule-specific deletion of Rac1 reached adulthood but showed polydipsia and polyuria with an impaired ability to concentrate urine. The elongation of renal papilla that occurs in the first weeks after birth was impaired in the Rac1-deficient infants, resulting in shortening and damage of the renal papilla. Moreover, the osmoprotective signaling mediated by nuclear factor of activated T cells 5, which is a key molecule of osmotic response to osmotic stress in renal medulla, was significantly impaired in the kidneys of the Rac1-deficient infants. These results demonstrate that Rac1 plays an important role in the development of renal papilla in the postnatal period, and suggested a potential link between Rac1 and osmotic response.

1p36 deletion syndrome: Review and mapping with further characterization of the phenotype, a new cohort of 86 patients.

Chromosome 1p36 deletion syndrome (1p36DS) is one of the most common terminal deletion syndromes (incidence between 1/5000 and 1/10,000 live births in the American population), due to a heterozygous deletion of part of the short arm of chromosome 1. The 1p36DS is characterized by typical craniofacial features, developmental delay/intellectual disability, hypotonia, epilepsy, cardiomyopathy/congenital heart defect, brain abnormalities, hearing loss, eyes/vision problem, and short stature. The aim of our study was to (1) evaluate the incidence of the 1p36DS in the French population compared to 22q11.2 deletion syndrome and trisomy 21; (2) review the postnatal phenotype related to microarray data, compared to previously publish prenatal data. Thanks to a collaboration with the ACLF (Association des Cytogénéticiens de Langue Française), we have collected data of 86 patients constituting, to the best of our knowledge, the second-largest cohort of 1p36DS patients in the literature. We estimated an average of at least 10 cases per year in France. 1p36DS seems to be much less frequent than 22q11.2 deletion syndrome and trisomy 21. Patients presented mainly dysmorphism, microcephaly, developmental delay/intellectual disability, hypotonia, epilepsy, brain malformations, behavioral disorders, cardiomyopathy, or cardiovascular malformations and, pre and/or postnatal growth retardation. Cardiac abnormalities, brain malformations, and epilepsy were more frequent in distal deletions, whereas microcephaly was more common in proximal deletions. Mapping and genotype-phenotype correlation allowed us to identify four critical regions responsible for intellectual disability. This study highlights some phenotypic variability, according to the deletion position, and helps to refine the phenotype of 1p36DS, allowing improved management and follow-up of patients.

TOO NEAR, YET TOO FAR: 22Q DELETION AND VELOCARDIOFACIAL SYNDROME MIMIC

<h3>Introduction</h3> Chromosome 22q11.2 contains a cluster of low-copy repeats referred to as LCR22A-H. The deletion of LCR22A-D (proximal-nested) is the most common recurrent microdeletion, which leads to DiGeorge/Velocardiofacial Syndrome. In contrast, deletions in distal regions are less common but have been reported. We report a 36-year-old female with recurrent infections, ear abnormalities, facial asymmetry, and intellectual disability who was found to have deletion of LCR22D-E region. <h3>Case Description</h3> A 36-year-old female presented to our Immunodeficiency Clinic for a second opinion in the setting of recurrent infections and previous diagnosis of Velocardiofacial Syndrome. She was diagnosed with hemifacial microsomia (Goldenhar Syndrome) and ear abnormalities at birth. She was diagnosed with intellectual disability in childhood. At age 30, she developed recurrent infections. She was diagnosed with Velocardiofacial Syndrome at age 24 based on genetic testing. On review of her chromosomal microarray testing, the specific finding noted was a 1.2 mb deletion within the 22q11.21q11.22 at the distal interval, in the LCR22D-E region. <h3>Discussion</h3> Our patient had an outside diagnosis of Goldenhar Syndrome and Velocardiofacial Syndrome. Following re-review of her chromosomal microarray testing, neither of these two diagnoses were accurate. Rather, she had a deletion in the distal LCR22D-E region. Distal deletions are rarer than proximal deletions in the LCR22A-D region that lead to DiGeorge/Velocardiofacial Syndrome. Many patients with distal chromosome 22q11.2 deletions are suspicious for DiGeorge Syndrome due to phenotypic overlap. Reported features for individuals with distal deletions include abnormal ears, facial asymmetry, recurrent infections/immune deficiency, and intellectual disability, all of which our patient had.

RF24 | PSUN96 Setmelanotide in Patients With Heterozygous POMC, LEPR, SRC1, or SH2B1 Obesity: Design of EMANATE – A Placebo-Controlled Phase 3 Trial

Abstract Background The central hypothalamic melanocortin-4 receptor (MC4R) pathway is a key regulator of energy balance. Certain variants in genes upstream of MC4R, including those encoding the leptin receptor (LEPR), proopiomelanocortin (POMC), steroid receptor coactivator 1 (SRC1; also known as NCOA1), prohormone convertase (PC)1/3 (encoded by the gene PCSK1), and SH2B adaptor protein 1 (SH2B1) genes, lead to impaired MC4R pathway signaling and rare genetic diseases of obesity. While the deficiencies resulting from these genetic variants differ in some clinical features, they are all characterized by hyperphagia (pathologic insatiable hunger) and early-onset obesity during childhood. Setmelanotide, an MC4R agonist, reduced body weight and hyperphagia (assessed by hunger scores) after 3 months in patients with heterozygous POMC, including patients with the N221D variant in PCSK1; LEPR; SRC1; and SH2B1 (including a 220–kilobase pair distal deletion of chromosome 16p11.2) variants in an earlier Phase 2 trial. In the Phase 2 trial, 12 of 35 (34%) patients with heterozygous POMC, PCSK1, or LEPR variants; 9 of 30 patients (30%) with heterozygous SRC1 variants; and 13 of 35 (37%) patients with heterozygous SH2B1 variants achieved ≥5% weight loss after 3 months of setmelanotide treatment. Methods EMANATE is a randomized, double-blind, placebo-controlled Phase 3 trial (NCT05093634) comprising 5 similar independent sub-studies based on genetic variants. For eligibility, patients must be 6-65 years old, have history of hyperphagia and childhood obesity, current obesity defined as BMI ≥30 kg/m2 (in those ≥18 years old), and BMI ≥95th percentile (in those 6-17 years old). Patients must also have a heterozygous genetic variant in POMC or PCSK1; heterozygous genetic variant in LEPR; a homozygous, heterozygous, or compound heterozygous variant in SRC1 or SH2B1 (including a chromosomal deletion of 16p11.2 including SH2B1); or a heterozygous N221D variant in PCSK1. Patients with ≥2% weight loss in the prior 3 months, HbA1C &amp;gt;10%, clinically significant pulmonary, cardiac, or oncological disease, or history of significant liver or serious kidney disease are not eligible. Within each sub-study, patients will be randomized 1: 1 to receive daily subcutaneous injections of setmelanotide or placebo for 52 weeks. The primary outcome is the mean change in body weight in patients who receive setmelanotide compared with placebo. Safety will be assessed by frequency and severity of adverse events. Current Status: EMANATE is currently underway and began enrolling patients in early 2022. The planned enrollment is 560 patients. If successful, this placebo-controlled Phase 3 trial will support setmelanotide treatment for improvements in body weight–related measures and hunger in an expanded population of patients living with rare genetic diseases of obesity. Presentation: Sunday, June 12, 2022 12:30 p.m. - 2:30 p.m., Sunday, June 12, 2022 1:12 p.m. - 1:17 p.m.

RF24 | PSUN91 Body Mass Index and Weight Reduction in Patients With SH2B1 Genetic Variant Obesity After One Year of Setmelanotide

Abstract Background SH2B adaptor protein 1 (SH2B1) binds to Janus kinase 2 and enhances leptin signaling through the central melanocortin-4 receptor (MC4R) pathway, a key regulator of energy balance. Variants in SH2B1 or a 220–kilobase pair distal deletion of chromosome 16p11.2, including SH2B1, are associated with hyperphagia (pathologic insatiable hunger), severe early-onset obesity, reduced final height, and insulin resistance. Setmelanotide, an MC4R agonist, produced significant weight and hunger reduction after 3 months in patients with SH2B1 heterozygous variants or 16p11.2 deletion in a Phase 2 study. This analysis is the first to assess the continued efficacy of ∼1 year of setmelanotide treatment in patients with SH2B1 genetic obesity. Methods Patients aged ≥6 years with SH2B1 heterozygous variants or 16p11.2 deletion encompassing SH2B1 were eligible for this long-term extension (LTE) trial (NCT03651765) if they completed a prior (index) trial in which they received setmelanotide and demonstrated clinical benefit based on weight and hunger results, and acceptable safety as determined by the investigator. Patients received a minimum of 4 months of setmelanotide treatment as part of the index trial and began the LTE immediately following the completion of the index trial. Study visits occurred approximately every 3 months. Study objectives included evaluating changes in body weight measures and assessing tolerability. The current analysis reports outcomes after ∼1 year of setmelanotide treatment across the index and LTE trials relative to index trial baseline. Results As of October 29, 2021, 35 patients with obesity and SH2B1 heterozygous variants or 16p11.2 deletion had enrolled in the index trial. Of patients entering the LTE, 19, 15, and 14 had received at least 6, 9, and 12 months of treatment, respectively. At index trial baseline, mean (standard deviation [SD]) body mass index (BMI) for all patients was 47.2 (12.8) kg/m2, body weight in patients aged ≥18 years (n=22) was 139.7 (35.4) kg, and BMI Z-score in patients aged &amp;lt;18 years (n=13) was 3.56 (0.60). Mean (SD) percent change in BMI was −3.4% (8.1%; n=19), −5.9% (10.0%; n=15), and −9.7% (8.0%; n=14) after 6, 9, and 12 months of treatment. Mean (SD) percent change in body weight in patients aged ≥18 years was −4.4% (5.0%; n=9), −6.8% (5.0%; n=7), and −7.7% (10.0%; n=8) after 6, 9, and 12 months, respectively. Mean (SD) change in BMI Z-score was −0.55 (0.17; n=6) after 12 months. No patients discontinued due to adverse events during the LTE . No new safety concerns emerged during long-term treatment. Conclusions Setmelanotide treatment provided clinically meaningful reductions in weight-related measures in patients with SH2B1 heterozygous variants or 16p11.2 deletion up to ∼1 year. These data support the continued investigation of setmelanotide in this population, which is underway in the planned Phase 3 EMANATE trial (NCT05093634). Presentation: Sunday, June 12, 2022 12:30 p.m. - 2:30 p.m., Sunday, June 12, 2022 12:30 p.m. - 12:35 p.m.

Prenatally diagnosed 16p11.2 copy number variations by SNP Array: A retrospective case series

ObjectiveThe 16p11.2 copy number variations (CNVs) are increasingly recognized as one of the most frequent genomic disorders, with a broad spectrum of phenotypes. The fetal phenotype associated with 16p11.2 CNVs is poorly described. The current study presents prenatal series of 16p11.2 CNVs and provides a better understanding of this submicroscopic imbalance in prenatal diagnosis. MethodRetrospective case series were extracted from a single tertiary referral center performing prenatal single nucleotide polymorphism (SNP) array from April 2017 to December 2021. The maternal demographics, indication for amniocentesis, ultrasound findings, SNP array results, inheritance of the CNVs, and pregnancy outcomes were studied. ResultsWe indentified 30 fetuses carrying 16p11.2 CNVs, representing 0.35% (30/8578) of prenatal SNP array results. The series included 17 fetuses with a proximal deletion, 7 with a distal deletion, 4 with a proximal duplication, and 2 with a distal duplication. Prenatal ultrasound anomalies were reported in 80% of these cases. The most common presentation was vertebralanomalies (9/30). Other features noted in more than one fetus were increased nuchal translucency/nuchal fold (NT/NF) (5/30), absent/hypoplastic nasal bone (3/30), polyhydramnios (3/30), ventricular septal defect (VSD) (2/30), unilateral mild ventriculomegaly (2/30), fetal growth restriction (FGR) (2/30), right aortic arch (2/30). All the 9 vertebralanomalies were present in fetuses harboring proximal deletion (9/17). Familial transmission was confirmed in 44% of cases (11/25) and termination of pregnancy was requested in 62.1% (18/29) of cases. ConclusionThe 16p11.2 CNVs can have variable prenatal phenotypes and these CNVs are frequently inherited from parents with a milder or normal phenotype. Our results underline that vertebral deformities were frequent in cases of 16p11.2 proximal deletion, and further demonstrate the incomplete penetrance of the CNVs.

Low-level complex mosaic with multiple cell lines affecting the 18q21.31q21.32 region in a patient with de novo 18q terminal deletion

We describe a 5-year-old girl who was diagnosed at birth with 18q de novo homogeneous deletion at G-banding karyotype. Her clinical condition, characterized by hypotonia, psychomotor retardation, short stature, deafness secondary to bilateral atresia of the external auditory canals, was in agreement with the 18q deletion syndrome though presence of coloboma of a single eye only suggested a mosaic condition as an unusual sign. By combining multiple technologies including array-CGH, FISH, and WGS, we found that the terminal deletion 18q21.32q23 (21 Mb) was in segmental mosaicism of the proximal region 18q21.31q21.32 (2.7 Mb), which showed a variable number of copies: one, two, or three, in 7, 41 and 55% of the cells respectively. Breakpoint junction analysis demonstrated the presence of an inv-dup del (18q) with a disomic segment of 4.7 kb between the inverted and non-inverted copies of the duplicated region 18q21.31q21.32. From these results, we propose that all three types of abnormal chr18 (the inv-dup del and the two 18q terminal deletions of different sizes) arisen from breaks in a dicentric mirror chromosome 18q, either in more than one embryo cell or from subsequent breaking-fusion-bridge cycles. The duplication region was with identical polymorphisms as in all non-recurrent inv-dup del rearrangements though, in contrast with most of them, the 18q abnormality was of maternal origin. Taking into account that distal 18q deletions are not rarely associated with inv-dup del(18q) cell lines, and that the non-disjunction of chromosome 18 takes place especially at maternal meiosis II rather than meiosis I, multiple rescue events starting from trisomic zygotes could be considered alternative to the postmitotic ones. From the clinical point of view, our case, as well as those of del(18q) in mosaic with the dic(18q), shows that the final phenotype is the sum of the different cell lines that acted on embryonic development with signs typical of both the 18q deletion syndrome and trisomy 18. Asymmetrical malformations, such as coloboma of the iris only in the right eye, confirm the underlying mosaicism regardless of whether it is still detectable in the blood.

Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number.

Understanding meiotic crossover (CO) variation in crops like bread wheat (Triticum aestivum L.) is necessary as COs are essential to create new, original and powerful combinations of genes for traits of agronomical interest. We cytogenetically characterized a set of wheat aneuploid lines missing part or all of chromosome 3B to identify the most influential regions for chiasma formation located on this chromosome. We showed that deletion of the short arm did not change the total number of chiasmata genome-wide, whereas this latter was reduced by ~35% while deleting the long arm. Contrary to what was hypothesized in a previous study, deletion of the long arm does not disturb the initiation of the synaptonemal complex (SC) in early meiotic stages. However, progression of the SC is abnormal, and we never observed its completion when the long arm is deleted. By studying six different deletion lines (missing different parts of the long arm), we revealed that at least two genes located in both the proximal (C-3BL2-0.22) and distal (3BL7-0.63-1.00) deletion bins are involved in the control of chiasmata, each deletion reducing the number of chiasmata by ~15%. We combined sequence analyses of deletion bins with RNA-Seq data derived from meiotic tissues and identified a set of genes for which at least the homoeologous copy on chromosome 3B is expressed and which are involved in DNA processing. Among these genes, eight (CAP-E1/E2, DUO1, MLH1, MPK4, MUS81, RTEL1, SYN4, ZIP4) are known to be involved in the recombination pathway.

Genotype-Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature.

Background Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020. Results For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene PRKN and one distal critical region at 6q27 containing two haploinsufficient genes DLL1 and TBP . Deletions involving the PRKN gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the DLL1 gene correlate with the 6q terminal deletion syndrome. Conclusion The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.