Broadening the phenotypic and molecular spectrum of FINCA syndrome: Biallelic NHLRC2 variants in 15 novel individuals

FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement.

Syndromic neurodevelopmental disorder associated with de novo variants in DDX23

The DEAD/DEAH box RNA helicases are a superfamily of proteins involved in the processing and transportation of RNA within the cell. A growing literature supports this family of proteins as contributing to various types of human disorders from neurodevelopmental disorders to syndromes with multiple congenital anomalies. This article presents a cohort of nine unrelated individuals with de novo missense alterations in DDX23 (Dead-Box Helicase 23). The gene is ubiquitously expressed and functions in RNA splicing, maintenance of genome stability, and the sensing of double-stranded RNA. Our cohort of patients, gathered through GeneMatcher, exhibited features including tone abnormalities, global developmental delay, facial dysmorphism, autism spectrum disorder, and seizures. Additionally, there were a variety of other findings in the skeletal, renal, ocular, and cardiac systems. The missense alterations all occurred within a highly conserved RecA-like domain of the protein, and are located within or proximal to the DEAD box sequence. The individuals presented in this article provide evidence of a syndrome related to alterations in DDX23 characterized predominantly by atypical neurodevelopment.

Proximal variants in CCND2 associated with microcephaly, short stature, and developmental delay: A case series and review of inverse brain growth phenotypes

Cyclin D2 (CCND2) is a critical cell cycle regulator and key member of the cyclin D2-CDK4 (DC) complex. De novo variants of CCND2 clustering in the distal part of the protein have been identified as pathogenic causes of brain overgrowth (megalencephaly, MEG) and severe cortical malformations in children including the megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome. Megalencephaly-associated CCND2 variants are localized to the terminal exon and result in accumulation of degradation-resistant protein. We identified five individuals from three unrelated families with novel variants in the proximal region of CCND2 associated with microcephaly, mildly simplified cortical gyral pattern, symmetric short stature, and mild developmental delay. Identified variants include de novo frameshift variants and a dominantly inherited stop-gain variant segregating with the phenotype. This is the first reported association between proximal CCND2 variants and microcephaly, to our knowledge. This series expands the phenotypic spectrum of CCND2-related disorders and suggests that distinct classes of CCND2 variants are associated with reciprocal effects on human brain growth (microcephaly and megalencephaly due to possible loss or gain of protein function, respectively), adding to the growing paradigm of inverse phenotypes due to dysregulation of key brain growth genes.

Correction: Diagnostic value of partial exome sequencing in developmental disorders

[This corrects the article DOI: 10.1371/journal.pone.0201041.].

Targeted capture-based NGS is superior to multiplex PCR-based NGS for hereditary BRCA1 and BRCA2 gene analysis in FFPE tumor samples

BACKGROUND

With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. In most cases only formalin-fixed paraffin-embedded (FFPE) samples, containing fragmented and chemically modified DNA of minor quality, are available. Thus, multiplex PCR-based sequencing is most commonly applied in routine molecular testing, which is predominantly focused on the identification of known hot spot mutations in oncogenes.

METHODS

We compared the overall performance of an adjusted targeted capture-based enrichment protocol and a multiplex PCR-based approach for calling of pathogenic SNVs and InDels using DNA extracted from 13 FFPE tissue samples. We further applied both strategies to seven blood samples and five matched FFPE tumor tissues of patients with known germline exon-spanning deletions and gene-wide duplications in BRCA1/2 to evaluate CNV detection based solely on panel NGS data. Finally, we analyzed DNA from FFPE tissues of 11 index patients from families suspected of having hereditary breast and ovarian cancer, of whom no blood samples were available for testing, in order to identify underlying pathogenic germline BRCA1/2 mutations.

RESULTS

The multiplex PCR-based protocol produced inhomogeneous coverage among targets of each sample and between samples as well as sporadic amplicon drop out, leading to insufficiently or non-covered nucleotides, which subsequently hindered variant detection. This protocol further led to detection of PCR-artifacts that could easily have been misinterpreted as pathogenic mutations. No such limitations were observed by application of an adjusted targeted capture-based protocol, which allowed for CNV calling with 86% sensitivity and 100% specificity. All pathogenic CNVs were confirmed in the five matched FFPE tumor samples from patients carrying known pathogenic germline mutations and we additionally identified somatic loss of the second allele in BRCA1/2. Furthermore we detected pathogenic BRCA1/2 variants in four the eleven FFPE samples from patients of whom no blood was available for analysis.

CONCLUSIONS

We demonstrate that an adjusted targeted capture-based enrichment protocol is superior to commonly applied multiplex PCR-based protocols for reliable BRCA1/2 variant detection, including CNV-detection, using FFPE tumor samples.

The CD98 Heavy Chain Is a Marker and Regulator of Head and Neck Squamous Cell Carcinoma Radiosensitivity

PURPOSE

The heavy chain of the CD98 protein (CD98hc) is encoded by the SLC3A2 gene. Together with the light subunit LAT1, CD98hc constitutes a heterodimeric transmembrane amino acid transporter. High SLC3A2 mRNA expression levels are associated with poor prognosis in patients with head and neck squamous cell carcinoma (HNSCC) treated with radiochemotherapy. Little is known regarding the CD98hc protein-mediated molecular mechanisms of tumor radioresistance.

EXPERIMENTAL DESIGN

CD98hc protein expression levels were correlated with corresponding tumor control dose 50 (TCD₅₀) in HNSCC xenograft models. Expression levels of CD98hc and LAT1 in HNSCC cells were modulated by siRNA or CRISPR/Cas9 gene editing. HNSCC cell phenotypes were characterized by transcription profiling, plasma membrane proteomics, metabolic analysis, and signaling pathway activation. Expression levels of CD98hc and LAT1 proteins were examined by IHC analysis of tumor tissues from patients with locally advanced HNSCC treated with primary radiochemotherapy (RCTx). Primary endpoint was locoregional tumor control (LRC).

RESULTS

High expression levels of CD98hc resulted in an increase in mTOR pathway activation, amino acid metabolism, and DNA repair as well as downregulation of oxidative stress and autophagy. High expression levels of CD98hc and LAT1 proteins were significantly correlated and associated with an increase in radioresistance in HNSCC in vitro and in vivo models. High expression of both proteins identified a poor prognosis subgroup in patients with locally advanced HNSCC after RCTx.

CONCLUSIONS

We found that CD98hc-associated signaling mechanisms play a central role in the regulation of HNSCC radioresistance and may be a promising target for tumor radiosensitization.

Diagnostic value of partial exome sequencing in developmental disorders

Although intellectual disability is one of the major indications for genetic counselling, there are no homogenous diagnostic algorithms for molecular testing. While whole exome sequencing is increasingly applied, we questioned whether analyzing a partial exome, enriched for genes associated with Mendelian disorders, might be a valid alternative approach that yields similar detection rates but requires less sequencing capacities. Within this context 106 patients with different intellectual disability forms were analyzed for mutations in 4.813 genes after pre-exclusion of copy number variations by array-CGH. Subsequent variant interpretation was performed in accordance with the ACMG guidelines. By this, a molecular diagnosis was established in 34% of cases and candidate mutations were identified in additional 24% of patients. Detection rates of causative mutations were above 30%, regardless of further symptoms, except for patients with seizures (23%). We did not detect an advantage from partial exome sequencing for patients with severe intellectual disability (36%) as compared to those with mild intellectual disability (44%). Specific clinical diagnoses pre-existed for 20 patients. Of these, 5 could be confirmed and an additional 6 cases could be solved, but showed mutations in other genes than initially suspected. In conclusion partial exome sequencing solved >30% of intellectual disability cases, which is similar to published rates obtained by whole exome sequencing. The approach therefore proved to be a valid alternative to whole exome sequencing for molecular diagnostics in this cohort. The method proved equally suitable for both syndromic and non-syndromic intellectual disability forms of all severity grades.

Abstract 1410: Pedigree analysis equally identifies cases of pancreatic cancer in families with BRCA1 and BRCA2 mutations

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in western countries, although lifetime risk is estimated at only 1.3% in the general population. BRCA2 mutations, however, have been attributed with a lifetime risk for PDAC development of 5-10%, while the risk for PDAC development in BRCA1 mutation carriers has been the subject of an ongoing scientific discussion, with current estimates of an increased PDAC risk of only 2-4-fold.

We retrospectively analyzed 180 pedigrees for occurrence of PDAC. All families were counselled for hereditary breast and ovarian cancer (HBOC) within three years (2015 to 2017) at the Center for Hereditary Breast and Ovarian Cancer in Dresden. The pedigrees of 111 families with a pathogenic

BRCA1 germline mutation and of 69 families with a pathogenic BRCA2 germline mutation were available for analysis. Whenever possible genetic testing (NGS or targeted sequencing) was performed using blood and/or tumor tissue of affected individuals. 14 “BRCA1 families” were identified to have at least one family member affected by PDAC (12.6% of families). Three of the patients were available for testing and carrier status could be confirmed in all of them. According to formal genetic risk calculation 6 of the PDAC patients had a mutation carrier risk of 50%, 5 of 25% and 1 of 12.5%. Age of onset (AO) of the disease was known in 13 of the families and the mean AO, calculated for these patients, was 58.7 years. Interestingly, two female Mutation carriers had both breast- and pancreatic cancer and one family with a BRCA1 mutation presented

with two sisters with PDAC. Tumor tissue was available from one of them and sequencing indicated loss-of-heterozygosity, supporting the assumption that the BRCA1 mutation might have been causative for tumorigenesis.

Of the “BRCA2 families” 10 (14,5%) were identified to have one family member each with PDAC. To date, however, none of them was available for genetic testing. 3 of the patients had a mutation carrier risk calculated at 50%, 5 at 25%, 1 at 12.5% and 1 at 6.25%. The mean AO was calculated to be 60.1 years. One female PDAC patient additionally had breast cancer and one of the male patients also suffered from prostate cancer. While the number of families represented in this retrospective study is limited, our observations indicate that BRCA1 mutations might be underdiagnosed in PDAC, especially in patients with an earlier AO. Extensive genetic analyses of PDAC patients will be necessary in order to elucidate this presumption and could also indicate whether additional genetic risk modifiers play a role in PAC development in BRCA1/2 families.

Citation Format: Evelin Schrock, Karl Hackmann, Franziska Kuhlee, Arne Jahn, Johannes Wagner, Anne-Karin Kahlert, Joseph Porrmann, Andreas Tzschach, Daniela Aust, Gustavo Baretton, Karin Kast, Pauline Wimberger, Michael Laniado, Christoph Kahlert, Thilo Welsch, Jürgen Weitz, Barbara Klink, Andreas Rump, Laura Gieldon. Pedigree analysis equally identifies cases of pancreatic cancer in families with BRCA1 and BRCA2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1410.

Novel truncating PPM1D mutation in a patient with intellectual disability

Truncating mutations in the last and penultimate exons of the PPM1D gene were recently described as a cause for mild to severe intellectual disability in fourteen patients. Feeding difficulties, periods of fever and vomiting as well as a high pain threshold were described as additional characteristic features and the disorder was subsequently termed "intellectual developmental disorder with gastrointestinal difficulties and high pain threshold (IDDGIP)" in the OMIM database (MIM # 617450). Here we report on an additional patient carrying a novel de novo truncating mutation NM_003620.3: c.1535del, p.(Asn512Ilefs*2) in the last exon of PPM1D. While the patient showed features overlapping with the reported phenotype, such as a short stature and small hands and feet, he also presented with additional features like cleft lip and palate and an aberrant right subclavian artery. Notably, the patient did not have any gastrointestinal difficulties or periods of fever, indicating variability of the phenotype of patients with PPM1D mutations.

Novel PRPS1 gain-of-function mutation in a patient with congenital hyperuricemia and facial anomalies

Phosphoribosylpyrophosphate synthetase (PRPPS) superactivity (OMIM 300661) is a rare inborn error of purine metabolism that is caused by gain-of-function mutations in the X-chromosomal gene PRPS1 (Xq22.3). Clinical characteristics include congenital hyperuricemia and hyperuricosuria, gouty arthritis, urolithiasis, developmental delay, hypotonia, recurrent infections, short stature, and hearing loss. Only eight families with PRPPS superactivity and PRPS1 gain-of-function mutations have been reported to date. We report on a 7-year-old boy with congenital hyperuricemia, urolithiasis, developmental delay, short stature, hypospadias, and facial dysmorphisms. His mother also suffered from hyperuricemia that was diagnosed at age 13 years. A novel PRPS1 missense mutation (c.573G>C, p.[Leu191Phe]) was detected in the proband and his mother. Enzyme activity analysis confirmed superactivity of PRPP synthetase. Analysis of the crystal structure of human PRPPS suggests that the Leu191Phe mutation affects the architecture of both allosteric sites, thereby preventing the allosteric inhibition of the enzyme. The family reported here broadens the clinical spectrum of PRPPS superactivity and indicates that this rare metabolic disorder might be associated with a recognizable facial gestalt.

Abstract LB-287: Identification of patients at risk for tumor predisposition syndromes based on the evaluation of sporadic cancer exome sequencing data: experiences from the NCT/DKTK MASTER program

The MASTER (Molecularly Aided Stratification for Tumor Eradication Research) Program of the NCT (National Center for Tumor Diseases) Heidelberg and the DKTK (German Cancer Consortium) is situated at the interface of cancer genomics and clinical oncology to provide whole exome/genome and transcriptome sequencing to selected patients with unmet medical need, and to evaluate the utility of such an approach regarding molecular stratification and individualized, biology-guided treatment. The program has enabled implementation of a shared, DKTK-wide workflow for rapid-turnaround clinical sequencing, comprising all steps from sample processing to reporting of results by a dedicated molecular tumor board. In clinical cancer genome sequencing programs, bioinformatics pipelines normally exclude germline variants detected in matched normal tissues to select for somatic mutations. However, in younger cancer patients (less than 51 years of age) and/or patients with rare cancer entities, which are eligible for analysis within MASTER, we anticipated an enrichment of patients with a possible hereditary background. If germline variants would be excluded in such cases a priori, relevant pathogenic mutations responsible for cancer development might be missed. Importantly, such mutations could also be therapeutically relevant. This applies in particular to tumors with mutations in genes involved in DNA damage response signaling, e.g. BRCA1/2, PALB2, ATM, and others, which respond to treatment with PARP inhibitors and platinum-based chemotherapy. Furthermore, germline mutations in these genes are responsible for hereditary breast and ovarian cancer and more than 120 tumor predisposition syndromes (TPS) known to date. Therefore analysis of germline variants of all known hereditary cancer genes was included as part of the NCT/DKTK MASTER workflow since 2015. A board-certified clinical geneticists experienced in evaluating rare private germline variants performed data interpretation. Recommendations were provided to the clinical oncologists for referral of patients to a TPS center for genetic counseling, further diagnostics, surveillance, and tumor prevention measures. We here present results from 321 NCT/DKTK MASTER patients analyzed thus far. Previously unknown pathogenic germline variants in 22 different tumor susceptibility genes, such as BRCA1/2, PALB2, ATM, NF1, MEN1, RB1, APC, SDHB, CDH1, and others, were detected in 36 patients (11%) with various cancers. We thus demonstrate the importance of evaluating germline variants obtained by “omics”-based molecular diagnostic approaches under clinical conditions. Furthermore, our results not only had implications for further surveillance of patients and their families, but also contributed to clinically “actionable” treatment recommendations.

Citation Format: Evelin Schrock, Barbara Hutter, Martina Fröhlich, Falk Zakrzewski, Sebastian Uhrig, Andreas Rump, Karl Hackmann, Joseph Porrmann, Laura Gieldon, Daniela Richter, Albrecht Stenzinger, Thomas Kindler, Wilko Weichert, Philipp J. Jost, Christian Brandts, Klaus Schulze-Osthoff, Johanna Falkenhorst, Sebastian Bauer, Frederick Klauschen, Konrad Klinghammer, Gunnar Folprecht, Martin Wermke, Karsten Spiekermann, Benedikt Brors, Stefan Gröschel, Christoph Heining, Peter Horak, Hanno Glimm, Stefan Fröhling, Barbara Klink. Identification of patients at risk for tumor predisposition syndromes based on the evaluation of sporadic cancer exome sequencing data: experiences from the NCT/DKTK MASTER program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-287. doi:10.1158/1538-7445.AM2017-LB-287

Novel peroxisome proliferator-activated receptor gamma mutation in a family with familial partial lipodystrophy type 3

OBJECTIVE

Familial partial lipodystrophy type 3 (FPLD3) is an autosomal dominant disorder with loss of subcutaneous adipose tissue at the extremities and metabolic complications such as insulin resistance, hypertriglyceridaemia and hypertension. The aim of this study was to characterize the molecular basis of a family of 5 affected members with FPLD3.

METHODS

A 61-year-old female index patient and her relatives were assessed by detailed clinical and biochemical examinations. Sequence analysis of the LMNA and PPARG gene was performed. Structure analysis of the identified mutation was carried out using published X-ray crystal structures.

RESULTS

A novel heterozygous PPARG mutation c.1040A>C was identified in all 5 patients of the family but not in unaffected controls. The resulting amino acid substitution p.Lys347Thr is located at the ligand-binding domain (LBD) of the protein and is predicted to disrupt critical molecular interactions to the helix 12 of the LBD.

CONCLUSIONS

A novel PPARG mutation leading to FPLD3 is described. The results emphasize the importance of the clinical diagnosis and of further molecular genetic analyses in patients with clinical signs of FPLD but unremarkable LMNA findings.