Epidermoid cyst of spleen, an unusual cause of massive splenomegaly

Large epidermoid cyst of the spleen causing massive splenomegaly: A case report

Splenic cysts are uncommon and are classified as primary cysts or secondary cysts based on the presence or absence of an intact epithelial lining, respectively. Epidermoid cysts have an epithelial lining of stratified squamous epithelium and have been reported in normal and intra-pancreatic accessory spleens. An 18-year-old girl presented with a symptomatic, uncomplicated splenic cyst causing massive splenomegaly and symptoms due to mass effect. Peripheral cytopaenias and lymphoproliferative neoplasm were excluded. Preoperative computed tomography was suggestive of a large splenic cyst causing massive splenomegaly and marked loco-regional pressure effects. Open splenectomy was performed and histology confirmed an epidermoid cyst with no features of malignancy. Splenic epidermoid cysts are a rare cause of massive splenomegaly. Surgical intervention is recommended due to symptoms and the risk of complications.

Disease variant prediction with deep generative models of evolutionary data

Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences^1-3. In principle, computational methods could support the large-scale interpretation of genetic variants. However, state-of-the-art methods^4-10 have relied on training machine learning models on known disease labels. As these labels are sparse, biased and of variable quality, the resulting models have been considered insufficiently reliable¹¹. Here we propose an approach that leverages deep generative models to predict variant pathogenicity without relying on labels. By modelling the distribution of sequence variation across organisms, we implicitly capture constraints on the protein sequences that maintain fitness. Our model EVE (evolutionary model of variant effect) not only outperforms computational approaches that rely on labelled data but also performs on par with, if not better than, predictions from high-throughput experiments, which are increasingly used as evidence for variant classification^12-16. We predict the pathogenicity of more than 36 million variants across 3,219 disease genes and provide evidence for the classification of more than 256,000 variants of unknown significance. Our work suggests that models of evolutionary information can provide valuable independent evidence for variant interpretation that will be widely useful in research and clinical settings.

The promise of automated machine learning for the genetic analysis of complex traits

The genetic analysis of complex traits has been dominated by parametric statistical methods due to their theoretical properties, ease of use, computational efficiency, and intuitive interpretation. However, there are likely to be patterns arising from complex genetic architectures which are more easily detected and modeled using machine learning methods. Unfortunately, selecting the right machine learning algorithm and tuning its hyperparameters can be daunting for experts and non-experts alike. The goal of automated machine learning (AutoML) is to let a computer algorithm identify the right algorithms and hyperparameters thus taking the guesswork out of the optimization process. We review the promises and challenges of AutoML for the genetic analysis of complex traits and give an overview of several approaches and some example applications to omics data. It is our hope that this review will motivate studies to develop and evaluate novel AutoML methods and software in the genetics and genomics space. The promise of AutoML is to enable anyone, regardless of training or expertise, to apply machine learning as part of their genetic analysis strategy.

Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

BACKGROUND

Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 (BMPR2) are the cause of most heritable cases but the vast majority of other cases are genetically undefined.

METHODS

To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource - Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD.

RESULTS

Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes (BMPR2, GDF2, and TBX4), two recently identified candidate genes (SOX17, KDR), and two new candidate genes (fibulin 2, FBLN2; platelet-derived growth factor D, PDGFD). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e-5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development.

CONCLUSIONS

Rare variant analysis of a large international consortium identified two new candidate genes-FBLN2 and PDGFD. The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.

Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing

The various malformations of the aerodigestive tract collectively known as esophageal atresia/tracheoesophageal fistula (EA/TEF) constitute a rare group of birth defects of largely unknown etiology. Previous studies have identified a small number of rare genetic variants causing syndromes associated with EA/TEF. We performed a pilot exome sequencing study of 45 unrelated simplex trios (probands and parents) with EA/TEF. Thirteen had isolated and 32 had nonisolated EA/TEF; none had a family history of EA/TEF. We identified de novo variants in protein-coding regions, including 19 missense variants predicted to be deleterious (D-mis) and 3 likely gene-disrupting (LGD) variants. Consistent with previous studies of structural birth defects, there is a trend of increased burden of de novo D-mis in cases (1.57-fold increase over the background mutation rate), and the burden is greater in constrained genes (2.55-fold, p = 0.003). There is a frameshift de novo variant in EFTUD2, a known EA/TEF risk gene involved in mRNA splicing. Strikingly, 15 out of 19 de novo D-mis variants are located in genes that are putative target genes of EFTUD2 or SOX2 (another known EA/TEF gene), much greater than expected by chance (3.34-fold, p value = 7.20e-5). We estimated that 33% of patients can be attributed to de novo deleterious variants in known and novel genes. We identified APC2, AMER3, PCDH1, GTF3C1, POLR2B, RAB3GAP2, and ITSN1 as plausible candidate genes in the etiology of EA/TEF. We conclude that further genomic analysis to identify de novo variants will likely identify previously undescribed genetic causes of EA/TEF.

Role of POLE and POLD1 in familial cancer

Purpose

Germline pathogenic variants in the exonuclease domain (ED) of polymerases POLE and POLD1 predispose to adenomatous polyps, colorectal cancer (CRC), endometrial tumors, and other malignancies, and exhibit increased mutation rate and highly specific associated mutational signatures. The tumor spectrum and prevalence of POLE and POLD1 variants in hereditary cancer are evaluated in this study.

Methods

POLE and POLD1 were sequenced in 2813 unrelated probands referred for genetic counseling (2309 hereditary cancer patients subjected to a multigene panel, and 504 patients selected based on phenotypic characteristics). Cosegregation and case–control studies, yeast-based functional assays, and tumor mutational analyses were performed for variant interpretation.

Results

Twelve ED missense variants, 6 loss-of-function, and 23 outside-ED predicted-deleterious missense variants, all with population allele frequencies <1%, were identified. One ED variant (POLE p.Met294Arg) was classified as likely pathogenic, four as likely benign, and seven as variants of unknown significance. The most commonly associated tumor types were colorectal, endometrial and ovarian cancers. Loss-of-function and outside-ED variants are likely not pathogenic for this syndrome.

Conclusions

Polymerase proofreading–associated syndrome constitutes 0.1–0.4% of familial cancer cases, reaching 0.3–0.7% when only CRC and polyposis are considered. ED variant interpretation is challenging and should include multiple pieces of evidence.

Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex

Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.

Epidermoid cyst of the spleen

BACKGROUND

The aim of this study is to elucidate the characteristics, clinical presentations, and management of epidermoid cysts located in the spleen and the intrapancreatic accessory spleen.

METHODS

Data pooled for analysis were collected from epidermoid cyst cases encountered in the study institution and sporadic case reports obtained from the English literature.

RESULTS

There were 115 cases of epidermoid cyst. Seventy eight (67.8 %) were found in the spleen, whereas 37 (32.2 %) were found in the intrapancreatic accessory spleen. Comparing between the two groups, the splenic group showed female predominance, younger age, and larger cystic size. For symptoms, left upper abdominal mass (57.7 %) and left upper abdominal pain (39.0 %) were more commonly found in the spleen group. Meanwhile, the intrapancreatic accessory spleen group had higher percentage of asymptomatic cysts (59.5 %). As for surgical indication, majority of patients in the spleen group underwent surgery for symptomatic relief (75.4 %), while the intrapancreatic accessory spleen group underwent surgery mainly for suspicious malignancy (90.0 %).

CONCLUSIONS

Surgical treatment for epidermoid cysts of the spleen is considered the optimal treatment for either alleviating the symptoms caused by a bulky cyst or for determining the histopathologic nature of a suspicious malignant cystic neoplasm.

Lymphoepithelial cysts of the pancreas: demonstration of lipid component using CT and MRI

We present two cases of surgically proven lymphoepithelial cyst (LEC) of the pancreas that had a lipid component visualized by CT and MRI. Identification of this component in a pancreatic cystic lesion is a key to favor the diagnosis of LEC or splenic epidermoid cyst over other cystic lesions when the lesion is noted in an elderly patient.

Splenic cyst carcinoma presenting in pregnancy

A case report of squamous cell carcinoma in an epidermoid cyst of the spleen is diagnosed in a pregnant female. Elaboration on the clinical, radiological, and pathological findings is presented to emphasize the distinguishing features of benign and malignant cysts.

Solitary epidermoid splenic cysts: occurrence in sibs

The case reports of two siblings with solitary epidermoid cysts of the spleen are presented. This improbable chance occurrence raises the possibility of a transmissible genetic defect accounting for the formation of these cysts.

Congenital epithelial splenic cysts in children. Emphasis on sonographic appearances and some unusual features

The clinical, radiographic and sonographic features of four children with congenital epithelial splenic cysts are described. All four cases presented with a left upper quadrant mass and few symptoms. In one case the spleen descended into the pelvis in the upright position. In three cases the sonographic findings showed the mass to be completely sonolucent. In the fourth case the mass was echogenic and echoes were distributed homogeneously throughout the mass. These internal echoes were due to the presence of fat droplets within the cyst fluid. Internal echoes may also be due to hemorrhage into the cyst. In all four cases a rim of splenic tissue was visible around part of the cyst.

Preoperative diagnosis of splenic cysts in children by gray scale ultrasonography

Ultrasonography is a useful noninvasive modality for the diagnosis of splenic cysts in children. Characteristic features plus the typical clinical and radiographic presentation should obviate the need for further more invasive and costly techniques which add little to diagnostic accuracy. Additional advantages offered by ultrasound a minimal patient discomfort, no ionizing radiation, and immediate reassurance to parents that the mass is a cyst. We report two cases of epidermoid splenic cysts preoperatively diagnosed by ultrasonography. The typical sonographic characteristics are presented and the sonographic differential diagnosis is discussed.