Unknown Clinical Significance Research Articles

Analysis of BRCA1 germline variants (exons 5, 11 and 20) in breast cancer families from Libya

ABSTRACT Breast cancer (BC) is a leading cause of cancer deaths in Libyan women. BRCA1 variants differ globally due to the diversity of genetic makeup and populations history. Their distribution, prevalence, and significance in Libyans remain largely unexplored. This study investigated the characteristics and distribution of BRCA1 variants in exons 5, 11, and 20 in Libyan families with BC. Thirty-six BC patients at ≤ 45 years, between 46–50 years and with a family history of breast, ovarian, pancreatic or prostate cancer in close relatives, or with triple-negative BC, were selected from 33 unrelated families during 2018–2020 at the National Cancer Institute, Sabratha, Libya. From these 33 families, 20 women (18 BC patients and two unaffected) were screened for BRCA1 exons 5, 11 and 20 using Sanger sequencing. All families completed an epidemiology and family history questionnaire. Twenty-seven variants (26 in exon 11 and 1 in exon 20, minor allele frequency of < 0.01) were detected in 10 of 18 unrelated families (55.6%.) Among the 27 variants, 26 (96%) were heterozygous. A frameshift pathogenic variant, c.2643del, and one novel variant c.1366A>G were identified. Furthermore, seven variants with unknown clinical significance were detected: c.1158T>A, c.1346C>G, c.1174C>G, c.3630 G>T, c.3599A>T, and c.3400 G>C in exon 11, and c.5244T>A in exon 20. Six variants with conflicting pathogenicity interpretations, c. 3460T>A, c. 3572 G>A, c. 3700 G>C, c. 1246C>G, c. 1344C>G, and c. 1054 G>A, were also identified. Twelve benign/likely benign variants were identified. Rare BRCA1 variants that have not been reported in North Africa were found in Libyan patients. These findings provide preliminary insights into the BRCA1 variants that could contribute to hereditary BC risk in Libyans. Further functional, computational, and population analyses are essential to determine their significance and potential impact on BC risk, which could ultimately lead to more personalized management strategies.

The detection of a strong episignature for Chung-Jansen syndrome, partially overlapping with Börjeson-Forssman-Lehmann and White-Kernohan syndromes.

Chung-Jansen syndrome is a neurodevelopmental disorder characterized by intellectual disability, behavioral problems, obesity and dysmorphic features. It is caused by pathogenic variants in the PHIP gene that encodes for the Pleckstrin homology domain-interacting protein, which is part of an epigenetic modifier protein complex. Therefore, we hypothesized that PHIP haploinsufficiency may impact genome-wide DNA methylation (DNAm). We assessed the DNAm profiles of affected individuals with pathogenic and likely pathogenic PHIP variants with Infinium Methylation EPIC arrays and report a specific and sensitive DNAm episignature biomarker for Chung-Jansen syndrome. In addition, we observed similarities between the methylation profile of Chung-Jansen syndrome and that of functionally related and clinically partially overlapping genetic disorders, White-Kernohan syndrome (caused by variants in DDB1 gene) and Börjeson-Forssman-Lehmann syndrome (caused by variants in PHF6 gene). Based on these observations we also proceeded to develop a common episignature biomarker for these disorders. These newly defined episignatures can be used as part of a multiclass episignature classifier for screening of affected individuals with rare disorders and interpretation of genetic variants of unknown clinical significance, and provide further insights into the common molecular pathophysiology of the clinically-related Chung-Jansen, Börjeson-Forssman-Lehmann and White-Kernohan syndromes.

The genetics and clinical outcomes in 151 cases of fetal growth restriction: A Chinese single-center study

ObjectiveTo determine the detection rate of chromosomal abnormalities and pregnancy outcomes in fetuses with intrauterine growth restriction.Study designA total of 151 fetal samples with intrauterine growth restriction were were divided into the isolated fetal growth restriction (FGR) group, FGR group with structural malformation, and FGR group with non-structural malformation, according to ultrasound abnormalities. The enrolled patients were divided into an early onset FGR group (<32 weeks) and a late-onset FGR group (≥32 weeks). Chromosomal karyotype and microarray analyses were performed and pregnancy outcomes were monitored.ResultsThe karyotypes of 122 patients were analyzed. Four patients exhibited abnormal chromosome numbers or structures. Variations in copy number were detected in 151 cases; 19 cases were found to have chromosomal abnormalities, with a positivity rate of 12.6 %. There was one trisomy in 18 cases, one trisomy in 21 cases, eight pathogenic copy number variations (CNVs), and nine CNVs of unknown clinical significance. The detection rate of FGR combined with structural malformation was significantly higher than that of isolated FGR group. The detection rate of FGR with structural malformations was significantly higher than that with non-structural malformations. The positive detection rate in the FGR group was similar to that in the FGR group with non-structural malformations, with no statistical significance. Chromosomal abnormalities were detected in 17 patients with early onset FGR, with a positivity rate of 13.8 %. Two cases of chromosomal abnormalities were detected in the late-onset FGR group, with a positive rate of 7.1 %, with no statistical significance. A total of 151 fetuses with FGR were followed up for pregnancy outcomes, resulting in 36 cases of pregnancy termination and 13 cases of loss to follow-up. Among the 102 delivered fetuses, six exhibited delayed growth and development, one presented with hypospadias, and another failed the hearing screening. The remaining 94 fetuses demonstrated normal growth and development.ConclusionsThis study confirms the value of CNV detection in fetuses and dynamic ultrasound monitoring for fetuses with intrauterine growth restriction.

Clinical characteristics and genetic analysis of six children with carnitine palmitoyltransferase 2 deficiency.

To investigate the clinical characteristic and genetic variants of children with carnitine palmitoyltransferase 2 (CPT2) deficiency. The clinical and genetic data of 6 children with CPT2 deficiency were retrospectively analyzed. The blood acylcarnitines and genetic variants were detected with tandem mass spectrometry and whole-exon gene sequencing, respectively. There were 4 males and 2 females with a mean age of 32 months (15 d-9 years) at diagnosis. One case was asymptomatic and with normal laboratory test results, 2 had delayed onset, and 3 were of infantile type. Three cases were diagnosed at neonatal screening, and 3 cases presented with clinical manifestations of fever, muscle weakness, and increased muscle enzymes. Five children presented with decreased free carnitine and elevated levels of palmitoyl and octadecenoyl carnitines. CPT2 gene variants were detected at 8 loci in 6 children (4 harboring biallelic mutations and 2 harboring single locus mutations), including 3 known variants (p.R631C, p.T589M, and p.D255G) and 5 newly reported variants (p.F352L, p.R498L, p.F434S, p.A515P, and c.153-2A>G). It was predicted by PolyPhen2 and SIFT software that c.153-2A>G and p.F352L were suspected pathogenic variants, while p.R498L, p.F434S and p.A515P were variants of unknown clinical significance. The clinical phenotypes of CPT2 deficiency are diverse. An early diagnosis can be facilitated by neonatal blood tandem mass spectrometry screening and genetic testing, and most patients have good prognosis after a timely diagnosis and treatment.

Germline mutations in BRCA1 and BRCA2 among Brazilian women with ovarian cancer treated in the Public Health System

BackgroundGermline mutations in BRCA1 and BRCA2 genes are among the main causes of hereditary ovarian cancer. Identifying these mutations may reduce cancer risk, facilitate early detection, and enable personalized treatment. However, genetic testing is limited in the Brazilian Public Health System, and data regarding germline mutations in many regions are scarce. Therefore, the study aimed to investigate the prevalence of germline mutations in BRCA1 and BRCA2 in women with ovarian cancer treated in the Public Health System in Pernambuco, Brazil.MethodsA cross-sectional study was conducted in the Hereditary Cancer Program from two reference oncological centers in Pernambuco. Women (n = 45) with high-grade serous ovarian cancer underwent genetic counseling and DNA sequencing for BRCA1 and BRCA2 genes.ResultsThe prevalence of deleterious mutations in the BRCA1 and BRCA2 genes was 33%. Of the 15 germline mutations found, 13 were in BRCA1 and 2 in BRCA2; two mutations of unknown clinical significance were also found in BRCA2. Mutations c.5266dupC and c.2215 A > T were the most frequent; each was mutation observed in three patients. Additionally, the mutations c.7645dupT and c.921dupT were reported for the first time.ConclusionOne in three women showed a pathogenic mutation, demonstrating a significant prevalence of germline mutations in this sample. Additionally, the small sample revealed an interesting number of mutations, indicating the need to explore more regions of the country.

Diagnostic Approaches to Investigate JAK2-Unmutated Erythrocytosis Based on a Single Tertiary Center Experience.

Erythrocytosis is attributed to various clinical and molecular factors. Many cases of JAK2-unmutated erythrocytosis remain undiagnosed. We investigated the characteristics and causes of JAK2-unmutated erythrocytosis. We assessed the clinical and laboratory results of patients with erythrocytosis without JAK2 mutations and performed targeted next-generation sequencing (NGS) panels for somatic and germline mutations. In total, 117 patients with JAK2-unmutated erythrocytosis were included. The median hemoglobin and hematocrit levels were 17.9 g/dL and 53.4%, respectively. Erythropoietin levels were not below the reference range. Thrombotic events were reported in 17 patients (14.5%). Among JAK2-unmutated patients, 44 had undergone targeted panel sequencing consisting of myeloid neoplasm-related genes, and 16 had one or more reportable variants in ASXL1 (5/44), TET2, CALR, FLT3, and SH2B3 (2/44). Additional testing for germline causes revealed eight variants in seven genes in eight patients, including NF1, BPGM, EPAS1, PIEZO1, RHAG, SH2B3, and VHL genes. One NF1 pathogenic, one BPGM likely pathogenic, and six variants of undetermined significance were detected. Somatic and germline mutations were identified in 36.4% and 33.3 % of the JAK2-unmutated group; most variants had unknown clinical significance. Not all genetic causes have been identified; comprehensive diagnostic approaches are crucial for identifying the cause of erythrocytosis.

Abstract 1735: DNA demethylating agents have cell type-specific effects on viability and BRCA2 alternative splicing

Abstract Introduction: BRCA2 is one of two principal tumor suppressors responsible for hereditary breast/ovarian cancer syndrome (HBOC). Patients with strong family histories of breast/ovarian cancer may carry BRCA2 DNA sequence variants of unknown clinical significance (VUSs). To evaluate which of these VUSs may contribute to cancer risk by altering splicing patterns, naturally occurring BRCA2 mRNA alternate splicing events have been extensively characterized, but it is not yet known which if any of these alternate splicing events plays a role in BRCA2 function. One variant lacking exon 3 (∆3), which maintains the full length translational reading frame, lacks sequence encoding EMSY and PALB binding domains as well as transactivation function. Previous work has shown that, while some VUSs associated with increased levels of ∆3 in lymphoblastoid cell lines are not pathogenic, germline deletions that eliminate BRCA2 exon 3 are associated with increased breast cancer risk. It is therefore of interest to characterize the factors that influence the frequency of naturally occurring BRCA2 exon 3-skipping, including cell types and therapies. DNA demethylating agents are used as cancer therapy to promote expression of tumor suppressor genes that may be epigenetically silenced in tumors. However, DNA methylation has been shown to be more frequent in exonic than intronic regions of protein-coding genes, suggesting that methylation may play a role in recruiting spliceosomal components to nascent pre-mRNA. It is therefore of interest to determine whether genomic demethylation affects alternative splicing patterns. Here, we explore whether BRCA2 exon 3 alternative splicing patterns are altered by demethylating agents. Methods: To determine whether DNA demethylating agents can alter the levels of ∆3, MCF7 and/or the non-cancer breast cell line MCF 10A was treated with 5-aza 2’-deoxycytidine (5-AzadC) or 5-Azacytidine (5-AzaC), and isoform-specific RT-PCR was used to compare relative levels of splice junctions containing or skipping exon 3. Results and Conclusions: 1) While the IC50 for both 5-AzadC and 5-AzaC in MCF 10A was similar (less than 1 μM), MCF7 showed considerably more resistance to 5-AzaC than 5-AzadC (IC50 of ≥ 5 μM vs ≤ 0.2 μM). 2) 5-AzaC treatment reduces the proportion of MCF 10A cultures in apoptosis but does not increase the proportion of viable cells, indicating it causes cell death by some other means. 3) While both 5-AzaC and 5-AzadC reduce relative levels of ∆3 in MCF7, 5-azadC does not reduce relative levels of ∆3 in MCF 10A, suggesting there may be a cell type-specific splicing response to genomic demethylation therapies. Citation Format: Jordan Werner, Hiba Siddiqui, Samiha Syed, Osman Khan, Servando Casillas Garabito, James D. Fackenthal. DNA demethylating agents have cell type-specific effects on viability and BRCA2 alternative splicing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1735.

14 and 6 Hz like spike wave activity is a common finding in in young patients with Prader-Willi syndrome.

Our aim was to characterize the 14 and 6 like spike wave activity seen on electroencephalogram (EEG) in children with Prader-Willi syndrome (PWS) undergoing polysomnogram (PSG). We performed a retrospective review of children with PWS and healthy controls who underwent diagnostic PSGs between January 1, 2007 to December 31, 2020 at SickKids, Toronto, Canada. EEGs from the PSGs were reviewed for the presence of the 14 and 6 like spike wave activity and its characteristics. Clinical correlation of the EEG variant with sleep disordered breathing indices from the PSG was also evaluated. 94 children with PWS and 50 healthy controls were included. The age, median (IQR) for the cohort was 1.42 (0.6, 4.2) years. There were 50 (53.2%) males in the PWS cohort. The EEG variant prevalence in this cohort was 51.0% (n=48) in children with PWS and 0% for the healthy controls. 14 and 6 Hz like spike wave activity was bilateral in 52% (25/48) children with PWS. The waves had a negative deflection in almost all patients 44/48 (92%) with PWS. It was predominantly located in the frontal leads for children with PWS, 23/48 (47.9%). It most frequently occurred during NREM stage 2 sleep for children with PWS, 25/48 (52.0%). The mean (SD) frequency was 6.8 (0.97) Hz. The median (IQR) length of the waves was 1.1 (0.8, 1.4) seconds in children with PWS. There was no correlation between the presence of the EEG variant and sleep disordered breathing indices in children with PWS. 14 and 6 Hz like spike wave activity EEG variant was present in more than 50% of a pediatric cohort of PWS as compared to 0% in healthy children. This EEG variant did not appear to be associated with sleep disordered breathing indices in children with PWS and is of unknown clinical significance.

Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy

Objective The primary objective of this study is to address the challenge posed by the increasing number of variants of unknown clinical significance within the GABRD gene, which encodes the δ subunit of γ-Aminobutyric acid type A receptors. The focus is on predicting the most pathogenic GABRD VUS to enhance precision medicine and improve our understanding of relevant pathophysiology. Methods The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. Initially, separate algorithms based on sequence homology are utilized to assess this variant set. Subsequently, consensus variants predicted as pathogenic undergo further evaluation through a web server employing an algorithm based on structural homology. The resulting 11 variants are then validated using in silico tools that assess variant effects based on genetic and molecular data. The evaluation includes consideration of disease association and protein stability due to amino acid substitutions. Results The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. These variants are evolutionarily conserved, mapped onto the extracellular domain of the δ subunit, and associated with idiopathic generalized epilepsy. Conclusions The findings suggest structural or functional consequences that lead to pathogenicity, offering valuable insights for wet-lab experimentation. Besides, the findings contribute to the validation of clinically significant genetic variants in the GABRD gene, which is critical for epilepsy precision medicine.

Challenges in Genetic Diagnosis of Mitochondrial Diseases: What Can Functional Genomics' Studies Do?

Mitochondrial oxidative phosphorylation (OXPHOS) diseases are challenging both from clinical and therapeutic perspectives. The advent of next-generation sequencing (NGS) boosted the discovery of new genetic defects affecting OXPHOS, with pathogenic variants identified in >350 genes to date [1]. However, in many patients, novel variants of unknown clinical significance are found. Subsequent functional studies may clarify its pathogenic consequences and modify the variant's classification, establishing a genetic diagnosis [2, 3]. Analysis of data obtained from patients (P1-P5) with novel genetic causes and functional genomics' studies performed, namely OXPHOS respiratory/glycolytic rates (Seahorse XF), enzymatic activity and assembly (BN-page), protein levels (SDS-WB), single muscle fiber assay, NGS and bioinformatics. P1-Leigh syndrome (40y, male); Complex IV activity deficiency (full assembly absent), homozygous deletion (c.-11_13del, SURF1), not detected by NGS[2]. P2- Epileptic encephalopathy (8y, male); homozygous c.882-1G>A, FASTKD2; OXPHOS decrease; reduced FASTKD2 expression and abnormal respiratory/glycolytic rates. P3-Cardiomyopathy/ nephropathy (39y, male); c.29G>C, FASTKD2; OXPHOS decrease; reduced FASTKD2 levels. P4-CPEO (62y, female); multiple OXPHOS deficiency; mtDNA alterations (m.7486G>A, MTTS1; 4,977bp del); higher levels of mutant mtDNA alterations in COX-deficient fibers [3]. P5- Polyneuropathy (15y, female); heterozygous c.1437C>A, POLG; combined def. or normal OXPHOS activity/respiratory capacity (tissue variable), raised CI assembly; normal POLG levels. Also, proteins' expression levels were reduced (P1-4), confirming pathogenicity. In P5, data do not support pathogenicity. If specific functional results are similar to controls, one might inquire about the pathogenicity of the studied variant and more genetic or bioinformatics analyses and family investigations are needed. There are also limitations of NGS in mutation detection that Sanger sequencing can overcome (P1). When performed first, the OXPHOS activity may guide to genetic screening or interpretation, concordant to later assembly results. All cases were solved and data may be crucial for genetic counseling.

In silico analysis of TRPM4 variants of unknown clinical significance

Background TRPM4 is a calcium-activated channel that selectively permeates monovalent cations. Genetic variants of the channel in cardiomyocytes are associated with various heart disorders, such as progressive familial heart block and Brugada syndrome. About97% of all known TRPM4 missense variants are classified as variants of unknown clinical significance (VUSs). The very large number of VUSs is a serious problem in diagnostics and treatment of inherited heart diseases. Methods and results We collected 233 benign or pathogenic missense variants in the superfamily of TRP channels from databases ClinVar, Humsavar and Ensembl Variation to compare performance of 22 algorithms that predict damaging variants. We found that ClinPred is the best-performing tool for TRP channels. We also used the paralogue annotation method to identify disease variants across the TRP family. In the set of 565 VUSs of hTRPM4, ClinPred predicted pathogenicity of 299 variants. Among these, 12 variants are also categorized as LP/P variants in at least one paralogue of hTRPM4. We further used the cryo-EM structure of hTRPM4 to find scores of contact pairs between parental (wild type) residues of VUSs for which ClinPred predicts a high probability of pathogenicity of variants for both contact partners. We propose that 68 respective missense VUSs are also likely pathogenic variants. Conclusions ClinPred outperformed other in-silico tools in predicting damaging variants of TRP channels. ClinPred, the paralogue annotation method, and analysis of residue contacts the hTRPM4 cryo-EM structure collectively suggest pathogenicity of 80 TRPM4 VUSs.

Whole exome sequencing identifies novel pathogenic variants in TGM1 and ALOX12B in patients with hereditary ichthyosis.

Hereditary ichthyosis is a clinically and genetically heterogeneous disorder associated with more than 50 genes with TGM1, ALOX12B, and ALOXE3 being the most prevalent. Establishing an accurate diagnosis is important for effective genetic counseling and optimal patient management. We studied the diagnostic value of whole exome sequencing (WES) in a small case series with hereditary ichthyosis. During a 1-year period, index cases of 5 unrelated families clinically diagnosed with hereditary ichthyosis went through WES, followed by extensive segregation analysis. Prenatal diagnosis (PND) was conducted where indicated. We identified 4 homozygous variants-2 in TGM1 (c.655A>G and c.797A>G) and 2 in ALOX12B (c.527+2T>G and c.1654G>T)-alongside a heterozygous variant in TGM1 (c.428G>A) in 5 families. The variants were all pathogenic/likely pathogenic according to the ACMG classification and segregation analysis, except for c.797A>G in TGM1 which remained a variant of unknown clinical significance. Four variants were novel. All families were referred either during pregnancy or before reproductive planning; 4 benefited from WES as it identified the mutation in the probands and enabled carrier detection in at-risk relatives; PND was conducted in 2 families. Our findings further support WES is a powerful tool for the comprehensive, accurate, and rapid molecular diagnosis of hereditary ichthyosis and can offer opportunities for reproductive planning, carrier screening and prenatal diagnosis to at-risk families.

Genomic characterization of an esthesioneuroblastoma with spinal metastases: illustrative case.

Esthesioneuroblastoma (ENB) is a rare neoplasm of the sinonasal tract. Currently, the optimal treatment includes maximal resection combined with radiotherapy and/or chemotherapy. Although ENBs often recur and have an aggressive clinical course, spinal metastases are extremely rare and the underlying molecular mechanisms are poorly understood. Here, the authors describe a 50-year-old male with an aggressive ENB, initially treated with resection and chemotherapy/radiation, who developed multiple thoracic and lumbar spinal metastases. The authors performed targeted exome sequencing on both the resected primary tumor and biopsied spinal metastases, which revealed 12 total variants of unknown clinical significance in genes associated with the PI3K/AKT/mTOR pathway, chromatin remodeling, DNA repair, and cell proliferation. Six of these variants were restricted to the metastatic lesion and included missense mutations with predicted functional effects in GRM3, DNMT3B, PLCG2, and SPEN. This report discusses the potential impact of these variants on tumor progression and metastasis, as well as the implications for identifying potential new biomarkers and therapies.

Rapid Progression of Myelodysplastic/Myeloproliferative Neoplasm with Neutrophilia to Acute Myeloid Leukemia: A Case Report

Abstract Introduction/Objective Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) with neutrophilia, formerly atypical chronic myeloid leukemia, is a subtype of MDS/MPN that is characterized by peripheral blood neutrophilia with frequent left-shifted myeloid cells, dysplastic granulocytes, and an absence of the Philadelphia chromosome or BCR- ABL1 fusion gene. Its clinical course is variable, ranging from a chronic indolent disease to an aggressive leukemia. Herein, we report a case of who was diagnosed with MDS/MPN with neutrophilia and had rapid progression to acute myeloid leukemia. Methods/Case Report A 63-year-old male patient with no significant medical history presented with incidental findings of abnormal peripheral blood counts: leukocytosis of 153 × 109/L, platelets of 82 × 109/L, and Hb of 6.7g/dl. Flow cytometry (FCM) on peripheral blood was significant for increased granulocytes and a population of aberrant blasts (~7.3%) expressing CD5, CD11c, CD13, CD34, CD38, CD56 (partial), CD117, and HLA-DR. The initial Bone marrow biopsy showed a hypercellular marrow (90-100%), 3% blasts, dysgranulopoiesis, and dysmegakaryopoiesis. Fluorescence in situ hybridization (FISH) analysis for BCR-ABL1 fusion and MPN with Eosinophilia panel, including FIP1L1-CHIC2-PDGFRA; PDGFRB/5q33; FGFR1/8p12, were all negative. Next Generation sequencing (NGS) detected at least one variant of strong clinical significance (Tier I) including: ASXL1 c.1900_1922del23, NRAS c.35G&amp;gt;C, U2AF1 c.470A&amp;gt;C, potential clinical significance (Tier II) GATA2 c.1160_1165delCCATGA and unknown clinical significance (Tier III) SETBP1 c.2620G&amp;gt;A. The chromosomal analysis showed trisomy 14. The patient received Decitabine for 2 months, but follow-up FCM on the subsequent bone marrow examination revealed 40% blasts, with marked erythroid hyperplasia. The patient was diagnosed with acute myeloid leukemia. Despite receiving Venetoclax and Azacitidine, the patient deteriorated and expired in 10 months after the initial diagnosis of MDS/MPN with neutrophilia. Results (if a Case Study enter NA) NA Conclusion This case highlights the poor prognosis associated with MDS/MPN with neutrophilia. Optimal management strategies for these patients are still evolving, and new targeted therapies are needed to improve outcomes.

Branchioma: immunohistochemical and molecular genetic study of 23 cases highlighting frequent loss of retinoblastoma 1 immunoexpression.

Branchioma is an uncommon benign neoplasm with an adult male predominance, typically occurring in the lower neck region. Different names have been used for this entity in the past (ectopic hamartomatous thymoma, branchial anlage mixed tumor, thymic anlage tumor, biphenotypic branchioma), but currently, the term branchioma has been widely accepted. Branchioma is composed of endodermal and mesodermal lineage derivatives, in particular epithelial islands, spindle cells, and mature adipose tissue without preexistent thymic tissue or evidence of thymic differentiation. Twenty-three branchiomas were evaluated morphologically. Eighteen cases with sufficient tissue were assessed by immunohistochemistry, next-generation sequencing (NGS) using the Illumina Oncology TS500 panel, and fluorescence in situ hybridization (FISH) using an RB1 dual-color probe. All cases showed a biphasic morphology of epithelial and spindle cells with intermingled fatty tissue. Carcinoma arising in branchioma was detected in three cases. The neoplastic cells showed strong AE1/3 immunolabeling (100%), while the spindle cells expressed CD34, p63, and SMA (100%); AR was detected in 40-100% of nuclei (mean, 47%) in 14 cases. Rb1 showed nuclear loss in ≥ 95% of neoplastic cells in 16 cases (89%), while two cases revealed retained expression in 10-20% of tumor cell nuclei. NGS revealed a variable spectrum of likely pathogenic variants (n = 5) or variants of unknown clinical significance (n = 6). Loss of Rb1 was detected by FISH in two cases. Recent developments support branchioma as a true neoplasm, most likely derived from the rudimental embryological structures of endoderm and mesoderm. Frequent Rb1 loss by immunohistochemistry and heterozygous deletion by FISH is a real pitfall and potential confusion with other Rb1-deficient head and neck neoplasms (i.e., spindle cell lipoma), especially in small biopsy specimens.

Abstract 18931: A PCSK9 and APOB Double Heterozygote Presenting Phenotypically Similar to Homozygous Familial Hypercholesterolemia

Introduction: Familial hypercholesterolemia (FH) is an inherited disorder associated with mutations in APOB, PCSK9 and LDLR genes. Heterozygous FH (HeFH) generally has one gene mutation. Homozygous FH (HoFH) has two mutations in the same gene and is characterized by vastly elevated plasma LDL-C, accelerated ASCVD and resistance to standard lipid-lowering therapy. Combinations of mutations can present with a phenotype similar to HoFH. We present a double heterozygous patient with unreported mutations in PCSK9 and APOB genes, exhibiting clinical features of HoFH. Hypothesis: Patients with multiple gene mutations for FH can present clinically similar to HoFH and would benefit from novel lipid lowering therapies Methods: 73-year-old female with a history of diabetes and hyperlipidemia presented in 2018 with dyspnea on exertion. Cholesterol (TC) and triglycerides (TG) were 430 and 715 mg/dl respectively, on rosuvastatin 40 mg and omega 3 fatty acids. Physical exam showed arcus senilis. A nuclear stress test showed ST depressions in inferolateral leads but normal scintigraphy. Genetic testing revealed APOB and PCSK9 mutations. She was then treated with rosuvastatin, icosapentyl ethyl, ezetimibe and fenofibrate. TC, LDL, TG and ApoB levels were 463, 236, 747 and &gt;240 mg/dl respectively. Evolocumab was added, with reduction of TC, TG and ApoB levels to 326, 432 and 182mg/dl, despite maximal available therapy. Results: Genetic testing revealed APOB variant NP_000375.2:p.Gln3378His and PCSK9 variant NP_777596.2:pAla544Thr, which were unreported mutations with unknown clinical significance. Genetically, this patient is a double heterozygote but expresses a phenotype similar to HoFH due to a poor response to maximum therapy. Conclusions: Although usually genetically defined, the phenotype of HoFH can present with different genetic variations. Chaudhry et al established genetic diagnosis of HoFH in 0.9% of patients initially diagnosed as HeFH, of which 3 were true homozygotes and 3 were compound heterozygotes. These findings support the idea that various heterozygous combinations of mutations in the genes for LDLR, APOB and PCSK9, may present clinically similar to HoFH. Patients with these mutations could benefit from novel agents such as evinacumab.

Abstract 18022: Multiplexed Generation and Functional Annotation of Hypertrophic Cardiomyopathy-Associated MYH7 Missense Variants in Isogenic Gene-Edited Stem Cell-Derived Cardiomyocytes

Hypertrophic cardiomyopathy (HCM) is an inheritable cardiac condition affecting 1:200-500 people and is characterized by left ventricular hypertrophy that can cause heart failure. Autosomal-dominant, missense mutations in MYH7 (encoding MHC-β) cause 33% of genotype + HCM cases. Despite this, 75% of MYH7 missense variants are of unknown clinical significance (VUS). Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) can elucidate the effect(s) of VUS, however, new variant identification by genetic testing outpaces methods to gene edit hiPSCs. Thus, we developed a method called CR ISPR a On- T arget E diting R etrieval (CRaTER) which increased successful gene-editing 25-fold over current methods. We leveraged CRaTER to enrich for edited hiPSCs, generating a library of 113 MYH7 missense variants. As mutations can reduce protein stability and abundance, we flow sorted MYH7 variant hiPSC-CMs into bins based on differing MHC-β protein abundance followed by next generation sequencing to calculate variant abundance scores. This multiplexed assay identified 31 residue substitutions as functionally abnormal, including all tested pathogenic variants and VUS. MHC-β depletion was validated in clonal hiPSC-CMs and by Western blotting of patient myocardium with a MYH7 mutation. Additionally, we found that severe MHC-β depletion is associated with increased cell size, a hallmark pathological phenotype of HCM. Finally, single-cell contractility analyses of hiPSC-CMs with a pathogenic MYH7 variant revealed hyperdynamic physiology relative to isogenic controls, suggesting an association between MHC-β loss and systolic dysfunction. Together, CRaTER enables the generation of isogenic hiPSC variant libraries at unprecedented scale for differentiation to disease-relevant cell types. Functional analyses of MYH7 variant hiPSC-CMs have revealed a novel correlation between MHC-β protein depletion and pathogenicity that accurately predicts MYH7 variant effect and has implications for future MYH7 variant effect interpretations.

Diagnostic pitfalls in a young adult with new diabetes.

A 20-year-old South Asian male presented with polyuria, polydipsia, HbA1c 81 mmol/mol, BMI 28.8 and family history of both type 1 and type 2 diabetes mellitus. As autoantibody testing was negative and c-peptide level demonstrated significant endogenous insulin secretion, type 1 diabetes was excluded. Given his age and family history, the differential diagnosis included maturity-onset diabetes of the young (MODY), a rare form of diabetes caused by a single-gene variant. A high probability of MODY was calculated and he was subsequently referred for genetic testing. Although a useful tool, the pre-test probability calculator for MODY is only validated in White Europeans. A heterogenous variant of unknown clinical significance of the NEUROD1 gene was detected, leading to gliclazide use with poor response. The patient responded well to metformin. Type 2 diabetes was considered the most likely diagnosis. This case highlights the diagnostic challenges in young patients of Asian ethnicity and the importance of interpreting genetic results of unknown significance within the clinical context. Ethnicity-specific BMI thresholds should be used when classifying patients as overweight or obese. Variants of unknown significance detected by genetic sequencing should be interpreted within the context of the patient's other clinical parameters. It is important to use ethnicity-specific BMI thresholds for obesity. Diagnosis of type 2 diabetes mellitus at younger ages is becoming increasingly common. The pre-test probability calculator for MODY is only validated in White Europeans; although a useful guide, results should be interpreted with caution in patients of other ethnicities.

The Incidence of Multiple Fusions in a Series of Pediatric Soft Tissue and Bone Tumors.

Next generation sequencing (NGS) has increased the detection of fusion genes in cancer. NGS has found multiple fusions in single tumor samples; however, the incidence of this in pediatric soft tissue and bone tumors (PSTBTs) is not well documented. The aim of this study is to catalogue the incidence of multiple fusions in a series of PSTBTs, and apply a modified gene fusion classification system to determine clinical relevance. RNA from 78 bone and soft tissue tumors and 7 external quality assessment samples were sequenced and analyzed using recently-described Metafusion (MF) software and classified using a modification of previously-published schema for fusion classification into 3 tiers: 1, strong clinical significance; 2, potential clinical significance; and 3, unknown clinical significance. One-hundred forty-five fusions were detected in 85 samples. Fifty-five samples (65%) had a single fusion and 30 (35%) had more than 1 fusion. No samples contained more than 1 tier 1 fusion. There were 40 tier 1 (28%), 36 tier 2 (24%), and 69 (48%) tier 3 fusions. A significant percentage of PSTBTs harbor more than 1 fusion, and by applying a modified fusion classification scheme, the potential clinical relevance of such fusions can be determined.

Molecular genetic diagnosis and treatment of congenital hyperinsulinism: results of observation of patients with variants in the genes &lt;i&gt;ABCC8&lt;/i&gt; and &lt;i&gt;KCNJ11&lt;/i&gt;

Congenital hyperinsulinism is a rare hereditary disease characterized by inadequate hypersecretion of insulin by pancreatic -cells, clinically manifested by persistent hypoglycemia, which poses a great threat to patient survival and a high risk of developing severe neurological complications.&#x0D; The article presents the results of clinical, hormonal and molecular genetic examination and treatment of 10 patients with congenital hyperinsulinism caused by mutations in the genes of ATP-dependent potassium channels (KCNJ11, ABCC8), hospitalized in Saint Petersburg State Pediatric Medical University clinic in 20102023. In all the studied patients, the disease manifested from the 1st to the 3rd day of life, and the median age of diagnosis of congenital hyperinsulinism in the study group was 1 month (min 14 days; max 3 years 9 months). In 8 out of 10 patients, a severe course of hypoglycemic syndrome was noted at the onset of the disease. According to the molecular genetic investigation results, 8 different mutations were identified: in the KCNJ11 (2/8) and ABCC8 (6/8) genes. Identical variants were found in two pairs of related patients. In children with mutations in the ABCC8 gene (n = 8), 2 variants with unknown clinical significance were identified, which were not previously described in allelic databases and scientific literature. According to the analysis of anamnestic and clinical and laboratory data, 80.0% of children, including patients with new, previously not described in the scientific literature, variants in the ABCC8 gene have a severe progressive course of congenital hyperinsulinism, requiring the appointment of insulinostatic therapy.