Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones

High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here, we use spatial transcriptomics to identify HGSOC subclones and study their association with infiltrating cell populations. Visium spatial transcriptomics reveals multiple tumour subclones with different copy number alterations present within individual tumour sections. These subclones differentially express various ligands and receptors and are predicted to differentially associate with different stromal and immune cell populations. In one sample, CosMx single molecule imaging reveals subclones differentially associating with immune cell populations, fibroblasts, and endothelial cells. Cell-to-cell communication analysis identifies subclone-specific signalling to stromal and immune cells and multiple subclone-specific autocrine loops. Our study highlights the high degree of subclonal heterogeneity in HGSOC and suggests that subclone-specific ligand and receptor expression patterns likely modulate how HGSOC cells interact with their local microenvironment.

Molecular characterization of 13 patients with PIK3CA-related overgrowth spectrum using a targeted deep sequencing approach

Activating variants in the PIK3CA gene cause a heterogeneous spectrum of disorders that involve congenital or early-onset segmental/focal overgrowth, now referred to as PIK3CA-related overgrowth spectrum (PROS). Historically, the clinical diagnoses of patients with PROS included a range of distinct syndromes, including CLOVES syndrome, dysplastic megalencephaly, hemimegalencephaly, focal cortical dysplasia, Klippel-Trenaunay syndrome, CLAPO syndrome, fibroadipose hyperplasia or overgrowth, hemihyperplasia multiple lipomatosis, and megalencephaly capillary malformation-polymicrogyria (MCAP) syndrome. MCAP is a sporadic overgrowth disorder that exhibits core features of progressive megalencephaly, vascular malformations, distal limb malformations, cortical brain malformations, and connective tissue dysplasia. In 2012, our research group contributed to the identification of predominantly mosaic, gain-of-function variants in PIK3CA as an underlying genetic cause of the syndrome. Mosaic variants are technically more difficult to detect and require implementation of more sensitive sequencing technologies and less stringent variant calling algorithms. In this study, we demonstrated the utility of deep sequencing using the Illumina TruSight Oncology 500 (TSO500) sequencing panel in identifying variants with low allele fractions in a series of patients with PROS and suspected mosaicism: pathogenic, mosaic PIK3CA variants were identified in all 13 individuals, including 6 positive controls. This study highlights the importance of screening for low-level mosaic variants in PROS patients. The use of targeted panels with deep sequencing in clinical genetic testing laboratories would improve diagnostic yield and accuracy within this patient population.

Reclassification of two germline DICER1 splicing variants leads to DICER1 syndrome diagnosis

DICER1 syndrome is an inherited condition associated with an increased risk of developing hamartomatous and neoplastic lesions in diverse organs, mainly at early ages. Germline pathogenic variants in DICER1 cause this condition. Detecting a variant of uncertain significance in DICER1 or finding uncommon phenotypes complicate the diagnosis and can negatively impact patient care. We present two unrelated patients suspected to have DICER1 syndrome. Both females (aged 13 and 15 years) presented with multinodular goiter (thyroid follicular nodular disease) and ovarian tumours. One was diagnosed with an ovarian Sertoli-Leydig cell tumour (SLCT) and the other, with an ovarian juvenile granulosa cell tumour, later reclassified as a retiform variant of SLCT. Genetic screening showed no germline pathogenic variants in DICER1. However, two potentially splicing variants were found, DICER1 c.5365-4A>G and c.5527+3A>G. Also, typical somatic DICER1 RNase IIIb hotspot mutations were detected in the thyroid and ovarian tissues. In silico splicing algorithms predicted altered splicing for both germline variants and skipping of exon 25 was confirmed by RNA assays for both variants. The reclassification of the ovarian tumour, leading to recognition of the association with DICER1 syndrome and the characterization of the germline intronic variants were all applied to recently described DICER1 variant classification rules. This ultimately resulted in confirmation of DICER1 syndrome in the two teenage girls.

Bridging clinical care and research in Ontario, Canada: Maximizing diagnoses from reanalysis of clinical exome sequencing data

We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.

Molecular characterization of DICER1-mutated pituitary blastoma

Pituitary blastoma (PitB) has recently been identified as a rare and potentially lethal pediatric intracranial tumor. All cases that have been studied molecularly possess at least one DICER1 pathogenic variant. Here, we characterized nine pituitary samples, including three fresh frozen PitBs, three normal fetal pituitary glands and three normal postnatal pituitary glands using small-RNA-Seq, RNA-Seq, methylation profiling, whole genome sequencing and Nanostring® miRNA analyses; an extended series of 21 pituitary samples was used for validation purposes. These analyses demonstrated that DICER1 RNase IIIb hotspot mutations in PitBs induced improper processing of miRNA precursors, resulting in aberrant 5p-derived miRNA products and a skewed distribution of miRNAs favoring mature 3p over 5p miRNAs. This led to dysregulation of hundreds of 5p and 3p miRNAs and concomitant dysregulation of numerous mRNA targets. Gene expression analysis revealed PRAME as the most significantly upregulated gene (500-fold increase). PRAME is a member of the Retinoic Acid Receptor (RAR) signaling pathway and in PitBs, the RAR, WNT and NOTCH pathways are dysregulated. Cancer Hallmarks analysis showed that PI3K pathway is activated in the tumors. Whole genome sequencing demonstrated a quiet genome with very few somatic alterations. The comparison of methylation profiles to publicly available data from ~ 3000 other central nervous system tumors revealed that PitBs have a distinct methylation profile compared to all other tumors, including pituitary adenomas. In conclusion, this comprehensive characterization of DICER1-related PitB revealed key molecular underpinnings of PitB and identified pathways that could potentially be exploited in the treatment of this tumor.

Intrathyroidal Thymus (Incidentaloma) Mimicking Thyroid Neoplasia in DICER1 Syndrome

INTRODUCTION

With the use of ultrasonography for the evaluation of thyroid and nonthyroid neck diseases, the incidental discovery of previously unsuspected thyroid nodules/nonpalpable lesions has increased. Intrathyroidal thymus arises due to aberrant thymic migration during embryogenesis. It is thought to be rare, fulfils the classiccriteria for diagnosis of an incidentaloma and it can be mistaken for a thyroid nodule. Multinodular goiter is the main endocrine manifestation of DICER1 syndrome, a tumor predisposition syndrome. Careful thyroid examination including ultrasound is thus necessary for DICER1 syndrome patients.

CASE REPORT

A 4-year-old prepubertal boy was referred to the pediatric endocrinology department following an earlier diagnosis of pleuropulmonary blastoma (PPB) type III, which is a hallmark component of DICER1 syndrome. The patient underwent surgery followed by chemotherapy. Genetic analysis identified a germline DICER1 pathogenic variant (c.2062C>T, p.R688*)in the child and in 5 relatives. A second somatic DICER1 RNase IIIb hotspot mutation(c.5438A>G, p.E1813G) was identified in DNA extracted from the proband's PPB. He had no goiter on clinical examination, but a heterogenous, well-delineated, avascular, solid and hypoechogenic lesion with pseudomicrocalcifications was observed in the right lobe (4.1 × 3.1 × 2.6 mm), suggestive of thyroid neoplasia. Diagnostic work-up and a 3-year follow-up excluded thyroid neoplasia and confirmed the diagnosis of an intrathyroid benign thymic lesion.

DISCUSSION AND CONCLUSION

This case exemplifies that thyroid incidentalomas in DICER1 syndrome patients should be viewed with great suspicion, but that not all thyroid disorders are indeed DICER1-related in these patients.

Endometrial Stem/Progenitor cell (ES/PC) Marker Expression Profile in Adenosarcoma and Endometrial Stromal Sarcoma

BACKGROUND

The uterus is one of the most dynamic organs in the human body, and this dynamic homeostasis is supported by endometrial stem/progenitor cells (ES/PCs), which are heterogeneous in their phenotype and degree of differentiation. ES/PCs are generally localized in the endometrial stroma, the site of origin for adenosarcoma and endometrial stromal sarcoma (ESS). Subsets of ESSs and adenosarcomas harbor SUZ12 or DICER1 gene alterations, two genes with roles in embryonic stem cell biology. However, the possible contribution of ES/PCs to tumorigenesis is unexplored.

METHOD

We examined the expression of eleven ES/PC markers, along with three proteins expressed in the mature endometrial stroma (ER, PR and CD10) in 60 uterine tumors (24 low-, 11 high-grade ESS, 25 adenosarcomas). Protein expression profiles were assessed by unsupervised hierarchical clustering. miRNA expression profiles were examined in a subset of adenosarcoma with/without DICER1 mutations, using the NanoString platform.

RESULTS

ES/PC markers were variably expressed, and the tumors exhibited limited immunophenotypic resemblance to different ES/PCs. Within the ESSs, the ES/PC marker clustering pattern was prognostic for both overall and disease-free survival. Comparing adenosarcomas and ESSs, most high-grade ESSs clustered with one another, while low-grade ESSs and adenosarcomas tended to cluster with one another. Among the adenosarcomas, the miRNA expression profiles were varied with respect to the DICER1 mutation status, with pathway analysis pointing to dysregulated signal transduction and stem cell biology.

CONCLUSIONS

ESSs and adenosarcomas exhibit varying immunophenotypic resemblance to ES/PCs. These expression profiles have prognostic implications and may be genetically driven.

Clinical Outcomes and Complications of Pituitary Blastoma

CONTEXT

Pituitary blastoma is a rare, dysontogenetic hypophyseal tumor of infancy first described in 2008, strongly suggestive of DICER1 syndrome.

OBJECTIVE

This work aims to describe genetic alterations, clinical courses, outcomes, and complications in all known pituitary blastoma cases.

DESIGN AND SETTING

A multi-institutional case series is presented from tertiary pediatric oncology centers.

PATIENTS

Patients included children with pituitary blastoma.

INTERVENTIONS

Genetic testing, surgery, oncologic therapy, endocrine support are reported.

OUTCOME MEASURES

Outcome measures included survival, long-term morbidities, and germline and tumor DICER1 genotypes.

RESULTS

Seventeen pituitary blastoma cases were studied (10 girls and 7 boys); median age at diagnosis was 11 months (range, 2-24 months). Cushing syndrome was the most frequent presentation (n = 10). Cushingoid stigmata were absent in 7 children (2 with increased adrenocorticotropin [ACTH]; 5 with normal/unmeasured ACTH). Ophthalmoplegia and increased intracranial pressure were also observed. Surgical procedures included gross/near-total resection (n = 7), subtotal resection (n = 9), and biopsy (n = 1). Six children received adjuvant therapy. At a median follow-up of 6.7 years, 9 patients were alive; 8 patients died of the following causes: early medical/surgical complications (n = 3), sepsis (n = 1), catheter-related complication (n = 1), aneurysmal bleeding (n = 1), second brain tumor (n = 1), and progression (n = 1). Surgery was the only intervention for 5 of 9 survivors. Extent of resection, but neither Ki67 labeling index nor adjuvant therapy, was significantly associated with survival. Chronic complications included neuroendocrine (n = 8), visual (n = 4), and neurodevelopmental (n = 3) deficits. Sixteen pituitary blastomas were attributed to DICER1 abnormalities.

CONCLUSIONS

Pituitary blastoma is a locally destructive tumor associated with high mortality. Surgical resection alone provides long-term disease control for some patients. Quality survival is possible with long-term neuroendocrine management.

A complex DICER1 syndrome phenotype associated with a germline pathogenic variant affecting the RNase IIIa domain of DICER1

Background

Germline pathogenic variants in DICER1 cause DICER1 syndrome, an autosomal dominant, pleiotropic tumour predisposition syndrome with variable expressivity and reduced penetrance for specific dysplastic and neoplastic lesions. Recently, a syndrome with the acronym GLOW (Global developmental delay, Lung cysts, Overgrowth, Wilms tumour) was described in two children with mosaic missense mutations in hotspot residues of the DICER1 RNase IIIb domain.

Methods

Whole genome sequencing, exome sequencing, Sanger sequencing, digital PCR and a review of Wilms tumours with DICER1 RNase III domain mutations were performed.

Results

A de novo heterozygous c.4031C>T (p.S1344L) variant in the sequence encoding the RNase IIIa domain of DICER1 was detected. Clinical investigations revealed a phenotype that resembles the GLOW subphenotype of DICER1 syndrome.

Conclusion

The phenotypic overlap between patients with p.S1344L mutation and GLOW syndrome provide clinical support for recent discoveries that RNase IIIa-Ser1344 site mutations impede miRNA-5p biogenesis analogous to DICER1 hotspot mutations in the RNase IIIb domain. We show that an individual with a heterozygous germline p.S1344L mutation has a severe form of DICER1 syndrome (‘DICER1 syndrome plus’), with notable features of intellectual disability, macrocephaly, physical abnormalities, Wilms tumour and a well-differentiated fetal adenocarcinoma of the lung.

DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis

BACKGROUNDDICER1 is the only miRNA biogenesis component associated with an inherited tumor syndrome, featuring multinodular goiter (MNG) and rare pediatric-onset lesions. Other susceptibility genes for familial forms of MNG likely exist.METHODSWhole-exome sequencing of a kindred with early-onset MNG and schwannomatosis was followed by investigation of germline pathogenic variants that fully segregated with the disease. Genome-wide analyses were performed on 13 tissue samples from familial and nonfamilial DGCR8-E518K-positive tumors, including MNG, schwannomas, papillary thyroid cancers (PTCs), and Wilms tumors. miRNA profiles of 4 tissue types were compared, and sequencing of miRNA, pre-miRNA, and mRNA was performed in a subset of 9 schwannomas, 4 of which harbor DGCR8-E518K.RESULTSWe identified c.1552G>A;p.E518K in DGCR8, a microprocessor component located in 22q, in the kindred. The variant identified is a somatic hotspot in Wilms tumors and has been identified in 2 PTCs. Copy number loss of chromosome 22q, leading to loss of heterozygosity at the DGCR8 locus, was found in all 13 samples harboring c.1552G>A;p.E518K. miRNA profiling of PTCs, MNG, schwannomas, and Wilms tumors revealed a common profile among E518K hemizygous tumors. In vitro cleavage demonstrated improper processing of pre-miRNA by DGCR8-E518K. MicroRNA and RNA profiling show that this variant disrupts precursor microRNA production, impacting populations of canonical microRNAs and mirtrons.CONCLUSIONWe identified DGCR8 as the cause of an unreported autosomal dominant mendelian tumor susceptibility syndrome: familial multinodular goiter with schwannomatosis.FUNDINGCanadian Institutes of Health Research, Compute Canada, Alex's Lemonade Stand Foundation, the Mia Neri Foundation for Childhood Cancer, Cassa di Sovvenzioni e Risparmio fra il Personale della Banca d'Italia, and the KinderKrebsInitiative Buchholz/Holm-Seppensen.

Somatic tumour testing establishes that bilateral DICER1-associated ovarian Sertoli-Leydig cell tumours represent independent primary neoplasms

AIMS

Sertoli-Leydig cell tumours (SLCTs) are rare ovarian neoplasms that are commonly associated with somatic or germline DICER1 mutations, especially when of the moderately or poorly differentiated type. A large majority are unilateral, but bilateral neoplasms have been reported, sometimes in the context of germline DICER1 mutations (DICER1 syndrome). It is currently unknown whether these represent independent neoplasms or metastasis from one ovary to the other and we aimed to elucidate this.

METHODS AND RESULTS

We report three cases of bilateral ovarian SLCT (all in patients with DICER1 syndrome) and review all reported cases of bilateral neoplasms. In the three cases (all moderately or poorly differentiated neoplasms), the time interval between the discovery of the tumours in each ovary ranged from 2.7 years to 6 years. In all cases, different DICER1 somatic hotspot mutations within the two tumours provided definitive proof that they represent independent neoplasms; this may be important clinically. Our literature review revealed that, when this information was available, all patients with bilateral SLCT had a germline DICER1 mutation.

CONCLUSIONS

Bilateral ovarian SLCTs represent independent rather than metastatic neoplasms, and essentially always occur in the context of DICER1 syndrome.

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

BACKGROUND

Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits.

RESULTS

Here, we compare gene expression and cellular composition of single-cell suspensions prepared from adult mouse kidney using two tissue dissociation protocols. For each sample, we also compare fresh cells to cryopreserved and methanol-fixed cells. Lastly, we compare this single-cell data to that generated using three single-nucleus RNA sequencing workflows. Our data confirms prior reports that digestion on ice avoids the stress response observed with 37 °C dissociation. It also reveals cell types more abundant either in the cold or warm dissociations that may represent populations that require gentler or harsher conditions to be released intact. For cell storage, cryopreservation of dissociated cells results in a major loss of epithelial cell types; in contrast, methanol fixation maintains the cellular composition but suffers from ambient RNA leakage. Finally, cell type composition differences are observed between single-cell and single-nucleus RNA sequencing libraries. In particular, we note an underrepresentation of T, B, and NK lymphocytes in the single-nucleus libraries.

CONCLUSIONS

Systematic comparison of recovered cell types and their transcriptional profiles across the workflows has highlighted protocol-specific biases and thus enables researchers starting single-cell experiments to make an informed choice.

An update on the central nervous system manifestations of DICER1 syndrome

DICER1 syndrome is a rare tumor predisposition syndrome with manifestations that predominantly affect children and young adults. The syndrome is typically caused by heterozygous germline loss-of-function DICER1 alterations accompanied on the other allele by somatic missense mutations occurring at one of a few mutation hotspots within the sequence encoding the RNase IIIb domain. DICER1 encodes a member of the microRNA biogenesis machinery. The syndrome spectrum is highly pleiotropic and features a unique constellation of benign and malignant neoplastic and dysplastic lesions. Pleuropulmonary blastoma (PPB), the most common primary lung cancer in children, is the hallmark tumor of the syndrome. Other manifestations include ovarian Sertoli-Leydig cell tumor, cystic nephroma arising in childhood, multinodular goiter, thyroid carcinoma, anaplastic sarcoma of the kidney, embryonal rhabdomyosarcoma, and nasal chondromesenchymal hamartoma, in addition to other rare entities. Several central nervous system (CNS) manifestations have also been defined, including metastases of PPB to the cerebrum, pituitary blastoma, pineoblastoma, ciliary body medulloepithelioma, and most recently primary DICER1-associated CNS sarcomas and ETMR-like infantile cerebellar embryonal tumor. Macrocephaly is a recently reported non-neoplastic, haploinsufficient phenotype. In this manuscript, we review the CNS manifestations of DICER1 syndrome.

Clinical and Molecular Characteristics May Alter Treatment Strategies of Thyroid Malignancies in DICER1 Syndrome

CONTEXT

DICER1 syndrome is a rare autosomal-dominantly inherited disorder that predisposes to a variety of cancerous and noncancerous tumors of mostly pediatric and adolescent onset, including differentiated thyroid carcinoma (DTC). DTC has been hypothesized to arise secondarily to the increased prevalence of thyroid hyperplastic nodules in syndromic patients.

OBJECTIVE

To determine somatic alterations in DICER1-associated DTC and to study patient outcomes.

DESIGN

Retrospective series.

SETTING

Tertiary referral centers.

PATIENTS

Ten patients with germline pathogenic DICER1 variants and early-onset DTC.

METHODS

Somatic DICER1 mutation analysis, extensive somatic DNA variant and gene fusion analyses were performed on all tumors.

RESULTS

Median age at DTC diagnosis was 13.5 years and there was no recurrent or metastatic disease (median follow-up, 8 years). All thyroid specimens showed diffuse nodular hyperplasia with at least one focus suspicious of DTC but without infiltrative growth, extrathyroidal extension, vascular invasion, or lymph node metastasis. Most of the individual nodules (benign and malignant) sampled from the 10 tumors harbored distinct DICER1 RNase IIIb hotspot mutations, indicating a polyclonal composition of each tumor. Furthermore, nine of 10 DICER1-related DTCs lacked well-known oncogenic driver DNA variants and gene rearrangements.

CONCLUSION

On the basis of our clinical, histological, and molecular data, we consider that most DICER1-related DTCs form a low-risk subgroup. These tumors may arise within one of multiple benign monoclonal nodules; thus, hemi-thyroidectomy or, more likely, total thyroidectomy may often be required. However, radioiodine treatment may be unnecessary given the patients' ages and the tumors' low propensity for metastases.

DICER1 Mutations Are Frequent in Adolescent-Onset Papillary Thyroid Carcinoma

CONTEXT

Papillary thyroid carcinoma (PTC) is a common malignancy in adolescence and is molecularly and clinically distinct from adult PTC. Mutations in the DICER1 gene are associated with thyroid abnormalities, including multinodular goiter and differentiated thyroid carcinoma.

OBJECTIVE

In this study, we sought to characterize the prevalence of DICER1 variants in pediatric PTC, specifically in tumors without conventional PTC oncogenic alterations.

PATIENTS

Patients (N = 40) who underwent partial or total thyroidectomy and who were <18 years of age at the time of surgery were selected.

DESIGN

The 40 consecutive thyroidectomy specimens (30 malignant, 10 benign) underwent genotyping for 17 PTC-associated variants, as well as full sequencing of the exons and exon-intron boundaries of DICER1.

RESULTS

Conventional alterations were found in 12 of 30 (40%) PTCs (five BRAFV600E, three RET/PTC1, four RET/PTC3). Pathogenic DICER1 variants were identified in 3 of 30 (10%) PTCs and in 2 of 10 (20%) benign nodules, all of which lacked conventional alterations and did not recur during follow-up. DICER1 alterations thus constituted 3 of 18 (16.7%) PTCs without conventional alterations. The three DICER1-mutated carcinomas each had two somatic DICER1 alterations, whereas two follicular-nodular lesions arose in those with germline DICER1 mutations and harbored characteristic second somatic RNase IIIb "hotspot" mutations.

CONCLUSIONS

DICER1 is a driver of pediatric thyroid nodules, and DICER1-mutated PTC may represent a distinct class of low-risk malignancies. Given the prevalence of variants in children, we advocate for inclusion of DICER1 sequencing and gene dosage determination in molecular analysis of pediatric thyroid specimens.

Familial multinodular goiter and Sertoli-Leydig cell tumors associated with a large intragenic in-frame DICER1 deletion

OBJECTIVE

Familial multinodular goiter (MNG), with or without ovarian Sertoli-Leydig cell tumor (SLCT), has been linked to DICER1 syndrome. We aimed to search for the presence of a germline DICER1 mutation in a large family with a remarkable history of MNG and SLCT, and to further explore the relevance of the identified mutation.

DESIGN AND METHODS

Sanger sequencing, Fluidigm Access Array and multiplex ligation-dependent probe amplification (MLPA) techniques were used to screen for DICER1 mutations in germline DNA from 16 family members. Where available, tumor DNA was also studied. mRNA and protein extracted from carriers' lymphocytes were used to characterize the expression of the mutant DICER1.

RESULTS

Nine of 16 tested individuals carried a germline, in-frame DICER1 deletion (c.4207-41_5364+1034del), which resulted in the loss of exons 23 and 24 from the cDNA. The mutant transcript does not undergo nonsense-mediated decay and the protein is devoid of specific metal ion-binding amino acids (p.E1705 and p.D1709) in the RNase IIIb domain. In addition, characteristic somatic 'second hit' mutations in this region were found on the other allele in tumors.

CONCLUSIONS

Patients with DICER1 syndrome usually present a combination of a typically truncating germline DICER1 mutation and a tumor-specific hotspot missense mutation within the sequence encoding the RNase IIIb domain. The in-frame deletion found in this family suggests that the germline absence of p.E1705 and p.D1709, which are crucial for RNase IIIb activity, may be enough to permit DICER1 syndrome to occur.

A case of neuroblastoma in DICER1 syndrome: Chance finding or noncanonical causation?

DICER1 syndrome is an inherited disorder associated with at least a dozen rare, mainly pediatric-onset tumors. Its characterization remains incomplete. Some studies suggested that neuroblastoma (NB) may be involved in this syndrome. Here, we describe the case of a 14-year-old female presenting with a multinodular goiter (MNG) and a collision tumor composed of NB and cystic nephroma (CN). She is a carrier of a deleterious germline mutation in exon 23 of DICER1 and harbored different somatic mutations in the CN and MNG. However, no second hit was found in the NB, questioning its status as a DICER1-related tumor.

A Case Report of Syndromic Multinodular Goitre in Adolescence: Exploring the Phenotype Overlap between Cowden and DICER1 Syndromes

BACKGROUND

Hereditary tumour predisposition syndromes may increase the risk for development of thyroid nodules at a young age. We present the case of an adolescent female with Cowden syndrome who had some atypical phenotypic features which overlapped with the DICER1 syndrome.

MATERIAL AND METHODS

A 17-year-old female presented with a 3-month history of progressive right neck swelling. Fine needle cytology of the thyroid revealed a follicular neoplasm with features suggestive of follicular variant of papillary thyroid carcinoma and she underwent a hemithyroidectomy. Enlarging nodules in the remaining thyroid led to a completion thyroidectomy at 19 years of age. The patient's past medical history included an ovarian mixed malignant germ cell tumour, pulmonary nodules and cysts, renal cysts, mucocutaneous lesions, an arachnoid cyst, and a fibrous breast lesion. Macrocephaly was noted on physical examination.

RESULTS

Based on the patient's complex phenotype and young age, a hereditary predisposition syndrome was suspected and genetic testing of PTEN and DICER1 was undertaken. A heterozygous truncating germ-line PTEN mutation was identified, which combined with clinical findings, met criteria for the diagnosis of Cowden syndrome. Additional loss of heterozygosity of the wild-type PTEN allele was detected in the right thyroid lesion and ovarian tumour. No DICER1 mutations were identified.

CONCLUSIONS

Genetic testing was crucial in elucidating this patient's predisposition to the early development of neoplastic and non-neoplastic conditions. Our report also highlights the phenotypic overlap between the Cowden and DICER1 syndromes and illustrates the importance of recognising the variable phenotypic features of hereditary syndromes in order to enable timely implementation of appropriate care.

Sequencing of DICER1 in sarcomas identifies biallelic somatic DICER1 mutations in an adult-onset embryonal rhabdomyosarcoma

Background:

Sarcomas are rare and heterogeneous cancers. We assessed the contribution of DICER1 mutations to sarcoma development.

Methods:

The coding region of DICER1 was sequenced in 67 sarcomas using a custom Fluidigm Access Array. The RNase III domains were Sanger sequenced in six additional sarcomas to identify hotspot DICER1 variants.

Results:

The median age of sarcoma diagnosis was 45.7 years (range: 3 months to 87.4 years). A recurrent embryonal rhabdomyosarcoma (ERMS) of the broad ligament, first diagnosed at age 23 years, harboured biallelic pathogenic somatic DICER1 variants (1 truncating and 1 RNase IIIb missense). We identified nine other DICER1 variants. One somatic variant (p.L1070V) identified in a pleomorphic sarcoma and one germline variant (c.2257-7A>G) may be pathogenic, but the others are considered to be benign.

Conclusions:

We show that deleterious DICER1 mutations underlie the genetic basis of only a small fraction of sarcomas, in particular ERMS of the urogenital tract.

Deep Sequencing Reveals Spatially Distributed Distinct Hot Spot Mutations in DICER1-Related Multinodular Goiter

CONTEXT

Nontoxic multinodular goiter (MNG) occurs frequently, but its genetic etiology is not well established. Familial MNG and MNG occurring with ovarian Sertoli-Leydig cell tumor are associated with germline DICER1 mutations. We recently identified second somatic DICER1 ribonuclease (RNase) IIIb mutations in two MNGs.

OBJECTIVE

The objective of the study was to investigate the occurrence of somatic DICER1 mutations and mutational clonality in MNG.

PATIENTS

MNGs from 15 patients (10 with and five without germline DICER1 mutations) were selected based on tissue availability.

DESIGN

Core biopsies/scrapings (n = 70) were obtained, sampling areas of follicular hyperplasia, hyperplasia within colloid pools, unremarkable thyroid parenchyma, and areas of thyroid parenchyma, not classified. After capture with a Fluidigm access array, the coding sequence of DICER1 was deep sequenced using DNA from each core/scraping.

RESULTS

All germline DICER1-mutated cases were found to harbor at least one RNase III mutation. Specifically, we identified 12 individually distinct DICER1 RNase IIIb hot spot mutations in 32 of the follicular hyperplasia or hyperplasia within colloid pools cores/scrapings. These mutations are predicted to affect the metal-ion binding residues at positions p.Glu1705, p.Asp1709, p.Gly1809, p.Asp1810, and p.Glu1813. Somatic RNase IIIb mutations were identified in the 10 DICER1 germline mutated MNGs as follows: two cases contained one somatic mutation, five cases contained two mutations, and three cases contained three distinct somatic hot spot mutations. No RNase IIIb mutations were identified in the MNGs from individuals without germline DICER1 mutations.

CONCLUSIONS

This study demonstrates that nodules within MNG occurring in DICER1 syndrome are associated with spatially distributed somatic DICER1 RNase IIIb mutations.

Abstract 2390: The polyclonal nature of multinodular goitre revealed by DICER1 sequencing

Nontoxic multinodular goitre (MNG) occurs frequently in the general population and is characterised by nodular enlargement of the thyroid gland. In 2011, Rio Frio et al discovered that familial MNG and MNG occurring with Sertoli-Leydig cell tumours were associated with germ-line mutations in the microRNA-processing gene, DICER1. We recently reported the first instance of biallelic DICER1 mutations in an MNG. This prompted us to further investigate the role of DICER1 mutations in MNG pathogenesis.

Given that MNG may either be a monoclonal or polyclonal disease, we set out to investigate whether the molecular landscape was correspondingly heterogeneous. We obtained core biopsies (n = 27) from 9 MNGs. 1mm cores were excised from morphologically distinct regions, including from areas of follicular hyperplasia (FH), hyperplasia within colloid pools (HC) and/or otherwise unremarkable areas. DNA extracted from each core was processed using a custom Fluidigm Access Array followed by deep sequencing. We focused our investigation on the RNase IIIb domain of DICER1 to identify known hotspot mutations. All mutations were validated by Sanger sequencing.

We identified 6 individually distinct DICER1 RNase IIIb hotspot mutations in 14 (of 27) cores consisting of FH or HC (Table 1). These mutations affected the metal-ion binding residues at positions 1705, 1709, 1810 & 1813. Two MNGs that arose in individuals without germ-line DICER1 mutations did not carry any RNase IIIb hits. Of the remaining 7 germ-line DICER1-mutated cases, 2 carried 1 RNase IIIb mutation; 4 carried 2 different RNase IIIb mutations and one case did not carry any successfully-validated RNase IIIb mutations.

We demonstrate that spatial heterogeneity of RNase IIIb DICER1 mutations exists in MNG. We postulate that cyclic hyperplasia followed by regression over time in response to external stimuli, particularly in germ-line DICER1 mutation carriers, contributes to the polyclonal accumulation of RNase IIIb mutations in MNG. Table 1:DICER1 RNase IIIb Mutation FrequenciesCaseGerm-line DICER1 StatusMorphologyc.5113G&gt;A p.E1705Kc.5125G&gt;A p.D1709Nc.5126A&gt;G p.D1709Gc.5428G&gt;T p.D1810Yc.5429A&gt;T p.D1810Vc.5437G&gt;C p.E1813Q1PositiveHC41.7–––––FH–––––22.12PositiveFH––––––UR––––––HC––––––UR––––––HC––Sanger–––HC––Sanger–––3PositiveHC––––29.2–FH–43.7––––FH–28.8––––4PositiveHC––30.6–––UR––––––HC––33.1–––FH–––52.3––5PositiveHC––––––HC with FH––––––6PositiveFH–––––39.3FH–––––13.1FH––––––7PositiveFH–––41.8––FH28.0–––––8NegativeFH––––––HC––––––9NegativeFH––––––PTC––––––FH––––––Abbreviations: FH, follicular hyperplasia; HC, hyperplasia within colloid pools; UR, unremarkable; PTC, papillary thyroid ca. Notes: Each row corresponds to a separate core. Mutant allele frequencies are indicated in each cell (all &gt;10%); ‘‘–’’ indicates mutation not observed in core DNA; Sanger, indicates mutations previously identified in an independent PCR from bulk MNG DNA, tested by Sanger sequencing. All Fluidigm positives were confirmed by Sanger sequencing from the same DNA that was used to do the Fluidigm analysis.

Citation Format: Leanne de Kock, Ismaël Bah, Mona Wu, John R. Priest, Jiannis Ragoussis, William D. Foulkes. The polyclonal nature of multinodular goitre revealed by DICER1 sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2390.

Effect of short and long range order on crystal structure interpretation: Raman and powder X-ray diffraction of LiPF₆

The structure of LiPF6 has been probed using Raman scattering as well as pXRD and the results are compared and contrasted. The conventional Bragg angle scattering pXRD determines that dry LiPF6 crystallizes in a trigonal structure (Space Group R-3 (148)), while Raman data suggests that the observed structure is close to cubic (Space Group Fm-3m (225)), similar to NaPF6 and KPF6. DFT heat capacity calculations using ab-initio methods for both R-3 and Fm-3m structures show better correlation with the Raman observations. The differences between Raman and pXRD data in LiPF6 appear to be in common with that observed in other materials that are close to phase transitions at the temperature where order/disorder and phase transition processes are known to occur. In these circumstances, Raman spectroscopy emerges as a more sensitive probe of local structural changes than pXRD, which is known to probe the overall average long range order of crystalline materials. The results are interpreted through the relationship between the local symmetry, internal energy and the heat capacity.

Abstract 4934: Mosaic RNase IIIb domain DICER1 mutations in children with multiple primary tumors

The DICER1 syndrome or pleuropulmonary blastoma (PPB) familial tumor and dysplasia syndrome (PPB FTDS) (OMIM #601200) is caused by heterozygous germ-line mutations in the microRNA maturation pathway gene, DICER1. Several rare phenotypes constitute the syndrome including PPB, cystic nephroma (CN), ovarian Sertoli-Leydig cell tumors (SLCT), intra-ocular medulloepithelioma, nasal chondromesenchymal hamartoma (NCMH), pineoblastoma, pituitary blastoma, multinodular goitre (MNG) and other rare childhood sarcomas and dysplasias. Highly characteristic second somatic mutations have been identified in DICER1-associated tumors, affecting amino acid residues central to the catalytic activity of the RNase IIIb domain.

We describe four children with multiple primary tumours associated with the DICER1 syndrome. Sanger sequencing of constitutional DNA obtained from peripheral blood lymphocytes and/or saliva revealed no likely deleterious germ-line DICER1 mutations. We subsequently sequenced the region encoding the DICER1 RNase IIIa and RNase IIIb domains in gDNA extracted from the tumor samples, and noted the presence of the same RNase IIIb missense mutation in multiple tumors from each patient (Patient A: c.5437G&gt;C; Patient B: c.5125G&gt;A; Patient C: c.5439G&gt;C; Patient D: c.5425G&gt;A). We performed targeted capture followed by deep sequencing on DNA extracted from both normal and tumor tissue, which revealed the presence of the respective RNase IIIb mutations in a low percentage of sequencing reads (0.2 - 13%) in constitutional DNA from three of the four patients (Patients A, B and C). The relative abundance of the allele harboring the DICER1 RNase IIIb mutation was significantly higher in the tumors compared to normal tissue from the surrounding organ and/or distant sites. Taken together, these findings indicate a mosaic origin of the DICER1 RNase IIIb missense mutations. The mosaic origin of Patient D's mutation remains to be unequivocally established.

We further hypothesized that, in the setting of a mosaic DICER1 RNase IIIb mutations, we might discover second somatic mutations outside of the RNase IIIb domain which initiate two-hit tumorigenesis as seen in most DICER1-related tumors. Sequencing data identified individually distinct second somatic, likely-deleterious DICER1 mutations in Patient A's left ovary SLCT and sinonasal inflammatory polyp, in Patient C's NCMH, and in Patient D's Type II PPB which arose in a pre-existing lung cyst. Each of these second somatic mutations are predicted to prematurely truncate the DICER1 protein.

We demonstrate that mosaic DICER1 RNase IIIb missense mutations are an occasional and important genetic cause of the DICER1 syndrome in patients presenting with multiple primary tumors associated with the syndrome, and that for tumor initiation, they appear to be accompanied by second somatic truncating non-RNase IIIb DICER1 mutations.

Citation Format: Leanne de Kock, Barbara Rivera Polo, Mona Wu, Evan Weber, Claudio Sandoval, Saskia M. J. Hopman, J. Hans M. Merks, Annet van Hagen, D. A. Plager, Nelly Sabbaghian, Nancy Hamel, Dorothée Bouron-Dal Soglio, John R. Priest, William D. Foulkes. Mosaic RNase IIIb domain DICER1 mutations in children with multiple primary tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4934. doi:10.1158/1538-7445.AM2015-4934

Ovarian embryonal rhabdomyosarcoma is a rare manifestation of the DICER1 syndrome

Embryonal rhabdomyosarcoma (ERMS), a soft tissue sarcoma, is one of the most common pediatric cancers. Certain ERMSs are associated with the DICER1 syndrome, a tumor predisposition syndrome caused by germ-line DICER1 mutations. Characteristic somatic mutations have also been identified in DICER1-associated tumor types. These "hotspot" mutations affect the catalytic activity of the DICER1 ribonuclease IIIb domain. Primary ovarian ERMS (oERMS) is extremely rare. We present a case of a 6-year-old girl with an oERMS harboring 2 DICER1 mutations. The girl also exhibited other DICER1 phenotypes: cystic nephroma (CN) and multinodular goiter. Somatic investigations of the CN identified a hotspot DICER1 mutation different from that in the oERMS. Significantly, the CN presented at 12 years of age, which is much older than the previously reported age range of susceptibility. This report documents the occurrence of DICER1 mutations in a case of oERMS, expanding the spectrum of DICER1-associated tumors.

Germ-line and somatic DICER1 mutations in pineoblastoma

Germ-line RB-1 mutations predispose to pineoblastoma (PinB), but other predisposing genetic factors are not well established. We recently identified a germ-line DICER1 mutation in a child with a PinB. This was accompanied by loss of heterozygosity (LOH) of the wild-type allele within the tumour. We set out to establish the prevalence of DICER1 mutations in an opportunistically ascertained series of PinBs. Twenty-one PinB cases were studied: Eighteen cases had not undergone previous testing for DICER1 mutations; three patients were known carriers of germ-line DICER1 mutations. The eighteen PinBs were sequenced by Sanger and/or Fluidigm-based next-generation sequencing to identify DICER1 mutations in blood gDNA and/or tumour gDNA. Testing for somatic DICER1 mutations was also conducted on one case with a known germ-line DICER1 mutation. From the eighteen PinBs, we identified four deleterious DICER1 mutations, three of which were germ line in origin, and one for which a germ line versus somatic origin could not be determined; in all four, the second allele was also inactivated leading to complete loss of DICER1 protein. No somatic DICER1 RNase IIIb mutations were identified. One PinB arising in a germ-line DICER1 mutation carrier was found to have LOH. This study suggests that germ-line DICER1 mutations make a clinically significant contribution to PinB, establishing DICER1 as an important susceptibility gene for PinB and demonstrates PinB to be a manifestation of a germ-line DICER1 mutation. The means by which the second allele is inactivated may differ from other DICER1-related tumours.

Exploring the association Between DICER1 mutations and differentiated thyroid carcinoma

CONTEXT

Carriers of germline DICER1 mutations are predisposed to a rare cancer syndrome, the DICER1 syndrome. Thyroid abnormalities are a common finding in DICER1 syndrome with multinodular goiter frequently present in many families in which a germline DICER1 mutation is segregating. Differentiated thyroid carcinoma (DTC) is infrequently seen in such pedigrees. In addition to germline DICER1 mutations, specific somatic mutations have been identified in the DICER1 ribonuclease IIIb catalytic domain in several tumor types.

OBJECTIVE

We aimed to determine whether such characteristic somatic DICER1 mutations are present in DTCs that arise within germline DICER1 mutation carriers.

DESIGN AND SETTING

The study involved an opportunistic collection of 3 cases of DTC arising in individuals suspected to have DICER1 syndrome and hospital-based ascertainment and testing was implemented.

RESULTS

We identified somatic DICER1 mutations in 3 DTCs arising in unrelated germline DICER1 mutation carriers, all of whom had been diagnosed in infancy with pleuropulmonary blastoma (PPB), were treated with chemotherapy, exposed frequently to diagnostic radiation, and subsequently developed DTC. The somatic mutations occurred within the DICER1 ribonuclease IIIb domain, affecting highly conserved amino acid residues central to the catalytic activity of the domain.

CONCLUSION

This report of somatic DICER1 mutations in DTC strengthens the association between DTC and the DICER1 syndrome. The possible association between germline DICER1 mutations, PPB treatment, and the risk of subsequent DTC must be considered by clinicians when treating PPB.

Raman analysis of ancient pigments on a tile from the Citadel of Algiers

A micro-Raman spectroscopy study of a multi-coloured (yellow, blue, white, redish-brown and brown-black) tile shard from the Citadel of Algiers was undertaken. XRD and EDX were used as complementary techniques. The study shows that the heterogeneous three-shade yellow pigment on the tile is composed largely of the ancient ternary (Pb-Sn-Sb) pyrochlore oxide with a dominant Pb-O vibration at 127 cm(-1) consistent with the Pb2SnSbO6.5 structure as verified by XRD. The literature assignment of this band at 132 cm(-1) probably comes from a mixture of pigments. The redish-brown and the brown-black pigments are found to be Naples yellow (Pb2Sb2O7) and lead(II) stannate (Pb2SnO4), respectively, while cobalt blue (CoAl2O4) gives the blue colour and cassiterite (SnO2) is the origin of the white colour. The bulk of the tile body is composed mainly of hematite (alpha-Fe2O3), maghemite (gamma-Fe2O3), magnetite (Fe3O4) and Quartz (alpha-SiO2) with traces of calcite (CaCO3) and amorphous carbon. Micro-Raman spectroscopy proved to be very useful in the characterization of pigments as well as the tile body. These results further establish Raman spectroscopy as a technique of choice for the analysis of pigments on archaeological artifacts. The results obtained here could be used in the restoration and preservation programme of the Citadel itself which stands today as a symbol of pre-colonial Algerian heritage.