Contribution of Clinical and Genetic Approaches for Diagnosing 209 Index Cases With 46,XY Differences of Sex Development

CONTEXT

Massively parallel sequencing (MPS) technologies have emerged as a first-tier approach for diagnosing several pediatric genetic syndromes. However, MPS has not been systematically integrated into the diagnostic workflow along with clinical/biochemical data for diagnosing 46,XY differences of sex development (DSD).

OBJECTIVE

To analyze the contribution of phenotypic classification either alone or in association with genetic evaluations, mainly MPS, for diagnosing a large cohort of 46,XY DSD patients.

DESIGN/PATIENTS

209 nonsyndromic 46,XY DSD index cases from a Brazilian DSD center were included. Patients were initially classified into 3 subgroups according to clinical and biochemical data: gonadal dysgenesis (GD), disorders of androgen secretion/action, and DSD of unknown etiology. Molecular genetic studies were performed by Sanger sequencing and/or MPS.

RESULTS

Clinical/biochemical classification into either GD or disorders of hormone secretion/action was obtained in 68.4% of the index cases. Among these, a molecular diagnosis was obtained in 36% and 96.5%, respectively. For the remainder 31.6% classified as DSD of clinically unknown etiology, a molecular diagnosis was achieved in 31.8%. Overall, the molecular diagnosis was achieved in 59.3% of the cohort. The combination of clinical/biochemical and molecular approaches diagnosed 78.9% of the patients. Clinical/biochemical classification matched with the genetic diagnosis in all except 1 case. DHX37 and NR5A1 variants were the most frequent genetic causes among patients with GD and DSD of clinical unknown etiology, respectively.

CONCLUSIONS

The combination of clinical/biochemical with genetic approaches significantly improved the diagnosis of 46,XY DSD. MPS potentially decreases the complexity of the diagnostic workup as a first-line approach for diagnosing 46,XY DSD.

Endocrine disruption caused by the aquatic exposure to aluminum and manganese in Astyanax altiparanae (Teleostei: Characidae) females during the final ovarian maturation

Aluminum (Al) and manganese (Mn) can be toxic to aquatic biota and cause endocrine disruption in fish, affecting reproduction. This study evaluates the physiological responses of the ray-finned teleost fish Astyanax altiparanae vitellogenic females after acute exposure (96 h) to Al and Mn (alone and combined) in acid pH followed by the same period of exposure to metal-free water in neutral pH. The aim of this second period of exposure was to assess the recovery capacity from the toxic effects these metals. Five experimental groups were established: a control in neutral pH (Ctrl), and acidic pH (Ac), aluminum (Al), manganese (Mn), and Al + Mn groups, maintaining the acidic pH in the groups to which metals were added. The following biological parameters were evaluated: metal tissue concentration, relative fecundity (RF: absolute fecundity/body mass). Plasma levels of cortisol (proxy for stress) and 17α hydroxyprogesterone (17α-OHP), and gene expression of pituitary lhβ mRNA (proxies for final maturation) were measured to evaluate endocrine disruption. In the synchronic exposure, the presence of Mn potentiated the accumulation of Al in gills. The females from acidic pH and Al groups showed a reduced RF. Exposure to Al and Mn triggered an endocrine disruption response, evidenced by a decrease in the plasma concentration of 17α-OHP and cortisol. Despite this anti-steroidogenic effect, no changes occurred in the pituitary gene expression of lhβ. The endocrine changes and the metal accumulation were temporary, while the impacts on RF under the experimental conditions suggest permanent impairment in the reproduction of this species.

Variants in 46,XY DSD-Related Genes in Syndromic and Non-Syndromic Small for Gestational Age Children with Hypospadias

Hypospadias is a common congenital disorder of male genital formation. Children born small for gestational age (SGA) present a high frequency of hypospadias of undetermined etiology. No previous study investigated the molecular etiology of hypospadias in boys born SGA using massively parallel sequencing. Our objective is to report the genetic findings of a cohort of patients born SGA with medium or proximal hypospadias. We identified 46 individuals with this phenotype from a large cohort of 46,XY DSD patients, including 5 individuals with syndromic features. DNA samples from subjects were studied by either whole exome sequencing or target gene panel approach. Three of the syndromic patients have 5 main clinical features of Silver-Russell syndrome (SRS) and were first studied by MLPA. Among the syndromic patients, loss of DNA methylation at the imprinting control region H19/IGF2 was identified in 2 individuals with SRS clinical diagnosis. Two novel pathogenic variants in compound heterozygous state were identified in the CUL7 gene establishing the diagnosis of 3M syndrome in one patient, and a novel homozygous variant in TRIM37 was identified in another boy with Mulibrey nanism phenotype. Among the non-syndromic subjects, 7 rare heterozygous variants were identified in 6 DSD-related genes. However, none of the variants found can explain the phenotype by themselves. In conclusion, a genetic defect that clarifies the etiology of hypospadias was not found in most of the non-syndromic SGA children, supporting the hypothesis that multifactorial causes, new genes, and/or unidentified epigenetic defects may have an influence in this condition.

Aluminum bioconcentration in female Nile tilapia Oreochromis niloticus (Perciformes: Cichlidae) and the effects on pituitary gonadotropins

In this study, we measured aluminum (Al) bioconcentration in the brain, ovaries, and liver of Oreochromis niloticus females, and analyzed the effects of exposure to Al and acidic pH on the gene expression of follicle-stimulating hormone (βfsh) and luteinizing hormone (βlh) in these animals. Mature females were divided into 4 groups, thus being maintained for 96 h in one of the following conditions: control at neutral pH (Ctr); Al at neutral pH (Al); acidic pH (Ac), and Al at acidic pH (Al-Ac). pH alone did not influence Al bioconcentration in the brain. The animals from the Al-Ac group bioconcentrated more Al in the ovaries than those from the Al group, while no differences were observed in the liver. Aluminum bioconcentration was higher in the brain than in the liver and ovaries in Al-exposed animals (Al and Al-Ac), and higher in the brain than in the ovaries in the Ctr and Ac groups. The liver bioconcentrates more Al than the ovaries in the females from the Ctr and Ac groups. Aluminum and/or acidic pH did not alter βfsh gene expression, while βlh gene expression decreased in females from the Al group. Aluminum acted as an endocrine disruptor, suggesting deleterious effects in reproduction that could result in ovulation failure. Aluminum can act directly and/or indirectly in the pituitary, affecting ovarian steroidogenesis and altering the reproductive endocrine axis of mature O. niloticus females in an acute period of exposure.

SUN-710 Custom Panel to Diagnosis Genetic Endocrine Disorders in a Tertiary Academic Hospital

Next-generation sequencing (NGS) has been transforming the endocrine diagnostic methodology allowing the genetic testing to assume an exploratory role rather than only a confirmatory one. This is possible due to lower costs and increased yield of information. A way to further increase efficiency and sensitivity for variant detection is the use of a sequencing custom panel selecting specific genes for screening. In endocrine disorders, the complex and intricate genotype-phenotype relations and occurrence of diverse comorbidities made the diagnosis challenging. Our aim is to analyze the efficiency of a multigenic panel for molecular diagnosis of endocrine disorders in patients assisted in a tertiary academic hospital, as well as to train academic and medical faculties in the use of molecular tools. Genomic DNA from 282 patients was extracted from blood sample using standard procedures. Sanger method was previously used to screen some candidate genes in half of the patients. The custom panel was designed with 651 genes using the SureDesign tool (Agilent technologies), either associated with the phenotype (OMIM) or candidate genes that englobes developmental (DD), metabolic (MD), and adrenal (AD) disorders. Libraries were prepared with SureSelect^XT Target Enrichment kit (Agilent Technologies). The enriched DNA libraries were sequenced in NextSeq 500 (Illumina) with High Output V2 kit (2 x 150 bp). The raw data was aligned to hg19 with BWA-MEM, variant calling was performed using FreeBayes and annotated with ANNOVAR. Filtering took into consideration the rarity (≤1%) of variants in population databases and those in exonic or splice site regions. Variants found were then classified according ACMG/AMP criteria. The categories of Pathogenic (P) and Likely Pathogenic (LP) were considered for molecular diagnosis, while variants of uncertain significance (VUS) were only reported. The average result of 3 runs was: 159Kmm² of cluster density, 76.5 % of Q30 and 76.6 Gb of data were generated. The mean coverage depth of the targeted regions in panel sequencing data was 237x (SD±110x), with at least 96.3% of the sequenced bases being covered more than 20-fold. Out of the 282 patients, we identified 65 LP/P variants (23%), 22 VUS (8%) and 195 remained undiagnosed (69%). Considering the solved cases, 54 (19.1%) have DD, 6 (2.1%) have MD and 5 (1.8%) have AD. Taking into account that half of the patients had already been previously screened, the data enable new findings in known genes. The application of a multigenic panel aids the training of medical faculty in an academic hospital by showing the big picture of the molecular pathways behind each disorder. This may be particularly helpful considering the higher diagnosis of DD cases. A precise genetic etiology provides improvement in understanding the disease, guides decisions about prevention or treatment, and brings comfort to the affected families.

SAT-155 High Prevalence Alterations on DNA Mismatch Repair Genes Related to Lynch Syndrome in Pediatric Patients with Adrenocortical Tumor Carried of the Germline Mutation on TP53

Background: Adrenocortical cancer (ACC) is a rare malignant neoplasia associated with a variable clinical presentation. Pediatric patients generally have a better prognosis when compared to adults. In addition, unlike in adults where ACC which is usually sporadic, 50-80% of pediatric ACC is associated with genetic disorders such as Beckwith-Wiedemann and Li-Fraumeni syndromes. Recently, was showed that 3-5% of adult patients with ACC presented germline variants in DNA mismatch repair genes such as MSH2 and MSH6, the cause of Lynch syndrome (LS). The prevalence of these alterations in pediatric ACC is unknown. We aimed to investigate the prevalence of germline alterations in DNA mismatch repair genes among pediatric and adult patients with adrenocortical tumors (benign and malignant) carriers of the germline TP53 p.R337H mutation. Methods: 35 patients selected (30 pediatric and 5 adult) with functional tumors. ACC was diagnosed in 4 pediatric and in all adult patients. NGS was performed in 35 DNA blood samples by HNPCC MASTR Plus for the identification of SNV in 4 genes (MLH1, MSH2, MSH6, and PMS2) and 3’ UTR of EPCAM. Copy number variation (CNV) analyses were done by Copy Number Targeted Resequencing Analysis (CONTRA) and MLPA. The variants were classified, according to ACMG (American College Medical Genome) by Varsome platform. The protein expression was evaluated by Immunohistochemistry (IHC): MLH1 (clone ES05), MSH2 (FE11), MSH6 (EP49), and PMS2 (EP51). All patients were evaluated for variants in TP53. Results: NGS: 2 children presented 2 pathogenic allelic variants associated with LS (2/30, 6.6%), both patients with benign outcome and follow up of 4 years: 1 deletion in MLH1 (c.1500_1502del) and 1 nonsense in the MSH6 gene (c.328C>T p.Arg110X. CNV: MLPA specific for MLH1/MSH2 showed a normal copy number. ICH: the loss of expression in MLH1/PMS2 was identified in only one case without allelic variants. Discussion: Although our cohort is small, we observed 2 allelic pathogenic variants associated with LS among pediatric with adrenocortical tumors. It is higher than the prevalence of colorectal and endometrial cancer (3.2%) in LS. A personal and family history of LS tumors should be strongly considered for genetic risk assessment in pediatric patients with ACT. If the association with TP53 alteration can influence the tumor’s behavior with early clinical presentation, as seen in hereditary nonpolyposis colorectal cancer, it needs to be investigated. The patients with both alterations must be followed with surveillance, according to the US Multi-Society task force guideline for Lynch syndrome and for Li-Fraumeni syndrome.

High Prevalence of Alterations in DNA Mismatch Repair Genes of Lynch Syndrome in Pediatric Patients with Adrenocortical Tumors Carrying a Germline Mutation on TP53

Adrenocortical cancer is a rare malignant neoplasm associated with a dismal prognosis. Identification of the molecular pathways involved in adrenal tumorigenesis is essential for a better understanding of the disease mechanism and improvement of its treatment. The aim of this study is to define the prevalence of alterations in DNA mismatch repair (MMR) genes in Lynch syndrome among pediatric patients with adrenocortical neoplasia from southern Brazil, where the prevalence of a specific TP53 germline mutation (p.Arg337His) is quite high. Thirty-six pediatric patients were retrospectively evaluated. Immunohistochemistry (IHC) for the MMR enzymes MLH1, MSH2, MSH6, and PMS2, as well as next-generation sequencing (NGS) were performed. For IHC, 36 pediatric tumors were tested. In all of them, the expression of all evaluated MMR proteins was well-preserved. For NGS, 35 patients with pediatric tumor were tested. Three patients (8.57%) with the TP53 p.Arg337His germline mutation presented pathogenic and likely pathogenic variants in the MMR genes (two in MLH1 and one in MSH6). The prevalence of altered MMR genes among pediatric patients was elevated (8.57%) and higher than in colorectal and endometrial cancer cohorts. Pediatric patients with adrenocortical tumors should, thus, be strongly considered as at genetic risk for Lynch syndrome.

SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo

OBJECTIVES

High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases.

METHODS

Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb.

RESULTS/CONCLUSIONS

Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at: http://intranet.fm.usp.br/sela.

The involvement of gonadotropins and gonadal steroids in the ovulatory dysfunction of the potamodromous Salminus hilarii (Teleostei: Characidae) in captivity

Potamodromous teleosts that require migration to reproduce show dysfunctions that block ovulation and spawning while in captivity. To understand the physiological basis of these reproductive dysfunctions, follicle-stimulating hormone b subunit (fshb) and luteinizing hormone b subunit (lhb) gene expression analyses by real-time quantitative PCR, together with measurements of estradiol (E 2), 17α-hydroxyprogesterone (17α-OHP) and 17α,20β-dihydroxy-4-pregnen-3-one (17α,20β-DHP) levels, were carried out throughout the reproductive cycle of the potamodromous Salminus hilarii. The following reproductive stages were evaluated in captive and wild females: previtellogenic (PV), advanced maturation/mature (AM) and regression/spent (REG/SPENT). In the wild females, fshb expression decreased from the PV to the AM stage, and the opposite pattern was detected for E 2, which increased from the PV to the AM stage. fshb was expressed at lower levels in captive than in wild females, and this difference did not change during the reproductive cycle. lhb expression also increased from the PV to the AM stage in both groups, but the wild females at the AM and REG/SPENT stages showed higher lhb expression levels than the captive females. The concentrations of 17α-OHP did not change during the reproductive cycle, and the levels were higher in the captive than in the wild females at all reproductive stages. 17α,20β-DHP levels did not change between wild and captive females. However, in captive females, the transition from PV to AM stage was followed by an increase in 17α,20β-DHP levels. These data indicate that dysfunctions in the gonadotropins and steroids synthesis pathways cause the ovulation failure in captive S. hilarii.