Splice-site mutation causing partial retention of intron in the FLCN gene in Birt-Hogg-Dubé syndrome: a case report

A Novel FLCN Variant in a Suspected Birt-Hogg-Dubè Syndrome Patient

Subjects with pathogenic (PV) and likely pathogenic (LPV) FLCN variants have an increased risk of manifesting benign and malignant disorders that are related to Birt-Hogg-Dubé syndrome (BHDS): an autosomal dominantly inherited disorder whose severity can vary significantly. Renal cell carcinoma (RCC) development in BHD (Birt-Hogg-Dubé) patients has a very high incidence; thus, identifying this rare syndrome at early stages and preventing metastatic spread is crucial. Over the last decade, the advancement of Next Generation Sequencing (NGS) and the implementation of multigene panels for hereditary cancer syndromes (HCS) have led to a subsequent focus on additional genes and variants, including those of uncertain significance (VUS). Here, we describe a novel FLCN variant observed in a subject manifesting disorders that were suspected to be related to BHDS and with a family history of multiple cancers.

Case report: Identification of a novel heterozygous germline ERCC2 mutation in a patient with dermatofibrosarcoma protuberans

Dermatofibrosarcoma protuberans (DFSP) is a kind of soft tissue sarcoma, mostly occurs in the trunk, followed by proximal extremities and head and neck. Surgical resection is the most important treatment for DFSP, but the local recurrence rate of DFSP is high. Except reported specific chromosomal tran7slocations occurred in DFSP, the association between DNA repair gene mutations and DFSP still unknown. In this report we found a 19-year-old boy with DFSP carries a novel heterozygous germline ERCC2 mutation, which belongs to the nucleotide excision repair (NER) pathway and genetic defects in ERCC2 may contribute to the cancer susceptibility xeroderma pigmentosum (XP), Cocaine syndrome (CS), and trichothiodystrophy (TTD). Different mutations of the ERCC2 gene can lead to diverse diseases, but there are no targeted therapies. In summary, our results enlarged the mutation spectrum of the DFSP patients. It also provides new insights into genetic counseling and targeted therapeutic strategies for patients with DFSP.

Comment on Balsamo et al.: “Birt–Hogg–Dubé syndrome with simultaneous hyperplastic polyposis of the gastrointestinal tract: case report and review of the literature”

In this comment, we highlight the diagnosis of Birt–Hogg–Dubé (BHD) in a 60-year-old man was made from identification and removal of normochromic papular cutaneous lesions whose histological examination indicated trichodyscomas and which are considered equivalent to fibrofolliculomas, presence of bilateral renal mass suggestive of angiomyolipomas by imaging exams. A benign/likely benign variant of FLCN in the intron 13 was also detected. Still, his previous pathological history presented other relevant data such as the prior removal of vocal cord angioma, total thyroidectomy, and left parotidectomy due to a cystic lesion whose histopathological examination revealed the presence of oncocytoma and lipomatosis, in addition to basal cell cutaneous carcinoma. Simultaneous gastrointestinal hyperplastic polyposis was found in this patient. The case we reported does not have the genotypic and phenotypic expressions most present in BHDS. These facts make it important for readers to know the clinical and genetic presentation facets of this unusual syndrome.

Reanalysis of Exome Data Identifies Novel SLC25A46 Variants Associated with Leigh Syndrome

SLC25A46 (solute carrier family 25 member 46) mutations have been linked to various neurological diseases with recessive inheritance, including Leigh syndrome, optic atrophy, and lethal congenital pontocerebellar hypoplasia. SLC25A46 is expressed in the outer membrane of mitochondria, where it plays a critical role in mitochondrial dynamics. A deceased 7-month-old female infant was suspected to have Leigh syndrome. Clinical exome sequencing was non-diagnostic, but research reanalysis of the sequencing data identified two novel variants in SLC25A46: a missense (c.1039C>T, p.Arg347Cys; NM_138773, hg19) and a donor splice region variant (c.283+5G>A) in intron 1. Both variants were predicted to be damaging. Sanger sequencing of cDNA detected a single missense allele in the patient compared to control, and the SLC25A46 transcript levels were also reduced due to the splice region variant. Additionally, Western blot analysis of whole-cell lysate showed a decrease of SLC25A46 expression in proband fibroblasts, relative to control cells. Further, analysis of mitochondrial morphology revealed evidence of increased fragmentation of the mitochondrial network in proband fibroblasts, compared to control cells. Collectively, our findings suggest that these novel variants in SLC24A46, the donor splice one and the missense variant, are the cause of the neurological phenotype in this proband.

Different mutations in the MMUT gene are associated with the effect of vitamin B12 in a cohort of 266 Chinese patients with mut-type methylmalonic acidemia: A retrospective study

BACKGROUND

To summarize the relationship between different MMUT gene mutations and the response to vitamin B12 in MMA.

METHODS

This was a retrospective study of patients diagnosed with mut-type MMA. All patients with mut-type MMA were tested for responsiveness to vitamin B12.

RESULTS

There were 81, 27, and 158 patients in the completely responsive, partially responsive, and nonresponsive groups, respectively, and the proportions of symptom occurrence were 30/81 (37.0%), 21/27 (77.8%), and 131/158 (82.9%), respectively (p < .001). The median levels of posttreatment propionyl carnitine (C3), C3/acetyl carnitine (C2) ratio in the blood, and methylmalonic acid in the urine were all lower than pretreatment, and the median level of C3/C2 ratio in the completely responsive group was within the normal range. In 266 patients, 144 different mutations in the MMUT gene were identified. Patients with the mutations of c.1663G>A, c.2080C>T, c.1880A>G, c.1208G>A, etc. were completely responsive and with the mutations of c.1741C>T, c.1630_1631GG>TA, c.599T>C, etc. were partially responsive. The proportions of healthy/developmental delay outcomes in the three groups were 63.0%/23.5%, 33.3%/40.7%, and 13.3%/60.1%, respectively (p < .001).

CONCLUSION

Different mutations in the MMUT gene are associated with the effect of vitamin B12 treatment.

The clinical characteristics of East Asian patients with Birt-Hogg-Dubé syndrome

Background

Birt-Hogg-Dube (BHD) syndrome is an autosomal dominant disease that has been characterized by skin lesions, multiple pulmonary cysts, spontaneous pneumothorax, and renal tumors, but the patients in Asian countries may show fewer symptoms. We aimed to explore and summarize the clinical features of BHD patients in East Asia to facilitate early diagnosis and timely interventions.

Methods

We collected and analyzed the clinical data of patients diagnosed with BHD in our hospital by reviewing medical records. We performed a systematic literature search regarding the presenting clinical features in BHD patients from China, Japan, and Korea and then reviewed the publications that were identified.

Results

In our hospital, 10 patients were diagnosed with BHD from April 2015 to September 2019. After reviewing the literature, we recruited 38 articles, including 12, 20, and 6 reports from China, Japan, and Korea, respectively. A total of 166 patients were included in this study, and 100 of them (60.2%) were females. Multiple pulmonary cysts were present in 145 patients (87.3%), and 124 patients (74.7%) had a history of pneumothorax on at least one occasion. Skin biopsy confirmed fibrofolliculomas (FFs) alone in 22 patients (13.3%), trichodiscomas (TDs) alone in 3 patients (1.8%), and both FFs and TDs in 7 patients (4.2%). Renal carcinoma only occurred in 12 (7.2%) patients. The most frequent genetic mutations in East Asian patients were c.1285delC on exon 11 (18.4%), c.1285dupC on exon 11 (18.4%), and c.1347_1353dupCCACCCT on exon 12 (8.2%).

Conclusions

Our findings suggested that pulmonary cysts are the most frequent radiological findings, and pneumothorax is the most common symptom in East Asian patients with BHD, and that skin lesions and kidney involvement are less frequent. To make an early diagnosis and minimize the severity of complications, careful observation, and timely genetic examination of the FLCN gene is essential.

iREAD: a tool for intron retention detection from RNA-seq data

BACKGROUND

Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection.

RESULTS

Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR events by analyzing the features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. iREAD provides significant added value in detecting IR compared with output from IRFinder with a higher AUC on all datasets tested. Both methods showed low false positive rates and high false negative rates in different regimes, indicating that use together is generally beneficial. The output from iREAD can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. The software is freely available at https://github.com/genemine/iread.

CONCLUSION

Being complementary to existing tools, iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions. Intron retention analysis provides a complementary approach for understanding transcriptome.

Novel GLI3 variant causes Greig cephalopolysyndactyly syndrome in three generations of a Lithuanian family

Background

Preaxial polydactyly type IV, also referred as polysyndactyly, has been described in a few syndromes. We present three generations of a family with preaxial polydactyly type IV and other clinical features of Greig cephalopolysyndactyly syndrome (GCPS).

Methods and results

Sequencing analysis of the GLI3 coding region identified a novel donor splice site variant NC_000007.14(NM_000168.6):c.473+3A>T in the proband and the same pathogenic variant was subsequently identified in other affected family members. Functional analysis based on Sanger sequencing of the proband's complementary DNA (cDNA) sample revealed that the splice site variant c.473+3A>T disrupts the original donor splice site, thus leading to exon 4 skipping. Based on further in silico analysis, this pathogenic splice site variant consequently results in a truncated protein NP_000159.3:p.(His123Argfs*57), which lacks almost all functionally important domains. Therefore, functional cDNA analysis confirmed that the haploinsufficiency of the GLI3 is the cause of GCPS in the affected family members.

Conclusion

Despite the evidence provided, pathogenic variants in the GLI3 do not always definitely correlate with syndromic or nonsyndromic clinical phenotypes associated with this gene. For this reason, further transcriptomic and proteomic evaluation could be suggested.

Predicting the change of exon splicing caused by genetic variant using support vector regression

Alternative splicing can be disrupted by genetic variants that are related to diseases like cancers. Discovering the influence of genetic variations on the alternative splicing will improve the understanding of the pathogenesis of variants. Here, we developed a new approach, PredPSI-SVR to predict the impact of variants on exon skipping events by using the support vector regression. From the sequence of a particular exon and its flanking regions, 42 comprehensive features related to splicing events were extracted. By using a greedy feature selection algorithm, we found eight features contributing most to the prediction. The trained model achieved a Pearson correlation coefficient (PCC) of 0.570 in the 10-fold cross-validation based on the training data set provided by the "vex-seq" challenge of the 5th Critical Assessment of Genome Interpretation. In the blind test also held by the challenge, our prediction ranked the 2nd with a PCC of 0.566 that demonstrates the robustness of our method. A further test indicated that the PredPSI-SVR is helpful in prioritizing deleterious synonymous mutations. The method is available on https://github.com/chenkenbio/PredPSI-SVR.

Pathology of Birt-Hogg-Dubé syndrome: A special reference of pulmonary manifestations in a Japanese population with a comprehensive analysis and review

Birt-Hogg-Dubé (BHD) syndrome is a rare genetic disorder characterized by cutaneous fibrofolliculomas, pulmonary cysts and renal cell carcinomas. Affected individuals inherit germline mutations in the folliculin gene (FLCN). Approximately 150 pathogenic FLCN variants have been identified worldwide. Many Japanese probands of BHD syndrome were first identified by pulmonologists and/or radiologists during treatment of pneumothoraces. Lung specimens obtained through video-assisted thoracoscopic surgery (VATS) have characteristic features unique to BHD syndrome; however, pathologists often miss key findings and diagnose patients with "bullae/blebs". The pleural and subpleural cysts of BHD syndrome-associated lung diseases are often modified by tissue remodeling and can be difficult to distinguish from emphysematous bullae/blebs. Intraparenchymal unruptured cysts tend to retain distinctive features that are different from other cystic lung diseases. Here, we review the clinicopathological findings of BHD syndrome in a Japanese population based on data from 200 probands diagnosed by genetic testing and a total of 520 symptomatic family members identified through BHD-NET Japan (http://www.bhd-net.jp/). Detailed morphology of pulmonary cysts obtained from VATS and autopsied lung specimens are described, and pathological clues for differentiating miscellaneous cystic lung disorders are discussed.