What's new in adipocytic neoplasia?

Adipocytic tumours are among the most common mesenchymal neoplasms, and constitute a clinically, biologically and pathologically diverse group. Their wide histological spectrum and frequent morphological overlap have made classification and diagnosis challenging, with accurate classification being critical because of the considerable differences in prognosis and management between morphologically overlapping neoplasms. Ongoing advances in molecular genetics have aided significantly to our understanding of these neoplasms, with continuing evolution in classification. This review summarises the new developments in benign and malignant adipocytic neoplasms, with discussion of new entities and genetic findings, updates on the clinical and morphological spectrum, and the use of diagnostic immunohistochemistry and molecular markers in the differential diagnosis.

Long-read genome sequencing resolves a complex 13q structural variant associated with syndromic anophthalmia.

Microphthalmia, anophthalmia, and coloboma (MAC) are a heterogeneous spectrum of anomalous eye development and degeneration with genetic and environmental etiologies. Structural and copy number variants of chromosome 13 have been implicated in MAC; however, the specific loci involved in disease pathogenesis have not been well-defined. Herein we report a newborn with syndromic degenerative anophthalmia and a complex de novo rearrangement of chromosome 13q. Long-read genome sequencing improved the resolution and clinical interpretation of a duplication-triplication/inversion-duplication (DUP-TRP/INV-DUP) and terminal deletion. Sequence features at the breakpoint junctions suggested microhomology-mediated break-induced replication (MMBIR) of the maternal chromosome as the origin. Comparing this rearrangement to previously reported copy number alterations in 13q, we refine a putative dosage-sensitive critical region for MAC that might provide new insights into its molecular etiology.

Cytogenetic and molecular characterization of a patient having infertility and mild intellectual disability with a very rare unstable ring chromosome 13.

INTRODUCTION: Ring chromosomes arise from breakage and fusion at distal regions of short and long arms of the chromosomes. The effect of the ring chromosome on the phenotype may vary widely depending on the amount of the deletion in the chromosomal areas and genes implicated in these regions. CASE PRESENTATION: We present a 35-year-old male patient with infertility and mild intellectual disability (MID) who has de novo ring 13 (r(13)) chromosomes. To determine chromosomal abnormality, we performed karyotype analysis, Y chromosome microdeletion analysis, FISH, and aCGH techniques. CONCLUSION: The patient's karyotype analysis result was mos46,XY,r(13)(p13q34)[75]/45,XY,-13[14]/46,XY,dic (13;13)[8]/47,XY,r(13), + r(13)[2]/46,XY,tetrac r(13;13;13;13)[1]. FISH analysis supported the findings of the cytogenetic analysis. Y microdeletion analysis showed that the AZF region was intact. On aCGH analysis, we detected a 1.5 megabase deletion at the end of chromosome 13, including the CHAMP1 gene. The loss of the CHAMP1 gene, in particular, may explain our patient's MID, and the other deleted genes at 13q34 may explain our patient's infertility.

Association of clusterin with the BRI2-derived amyloid molecules ABri and ADan.

Familial British and Danish dementias (FBD and FDD) share striking neuropathological similarities with Alzheimer's disease (AD), including intraneuronal neurofibrillary tangles as well as parenchymal and vascular amyloid deposits. Multiple amyloid associated proteins with still controversial role in amyloidogenesis colocalize with the structurally different amyloid peptides ABri in FBD, ADan in FDD, and Aß in AD. Genetic variants and plasma levels of one of these associated proteins, clusterin, have been identified as risk factors for AD. Clusterin is known to bind soluble Aß in biological fluids, facilitate its brain clearance, and prevent its aggregation. The current work identifies clusterin as the major ABri- and ADan-binding protein and provides insight into the biochemical mechanisms leading to the association of clusterin with ABri and ADan deposits. Mirroring findings in AD, the studies corroborate clusterin co-localization with cerebral parenchymal and vascular amyloid deposits in both disorders. Ligand affinity chromatography with downstream Western blot and amino acid sequence analyses unequivocally identified clusterin as the major ABri- and ADan-binding plasma protein. ELISA highlighted a specific saturable binding of clusterin to ABri and ADan with low nanomolar Kd values within the same range as those previously demonstrated for the clusterin-Aß interaction. Consistent with its chaperone activity, thioflavin T binding assays clearly showed a modulatory effect of clusterin on ABri and ADan aggregation/fibrillization properties. Our findings, together with the known multifunctional activity of clusterin and its modulatory activity on the complex cellular pathways leading to oxidative stress, mitochondrial dysfunction, and the induction of cell death mechanisms - all known pathogenic features of these protein folding disorders - suggests the likelihood of a more complex role and a translational potential for the apolipoprotein in the amelioration/prevention of these pathogenic mechanisms.

Reduced anogenital distance, hematuria and left renal hypoplasia in a patient with 13q33.1-34 deletion: case report and literature review.

BACKGROUND: 13q33-q34 microdeletions are rare chromosomal aberrations associated with a high risk of developmental disability, facial dysmorphism, cardiac defects and other malformation of organs. It is necessary to collect and report evidence of this rare chromosome mutation to improve the prognosis of this rare disease. CASE PRESENTATION: We report a patient harboring an 11.56 Mb microdeletion at 13q33.1-34 region, which contains about 30 OMIM genes. Besides the common clinical manifestations such as facial dysmorphism, developmental delay, intellectual disability, epilepsy, and congenital heart disease, she also suffered from a reduced anogenital distance, hematuria and left renal hypoplasia. Most related cases were characterized by facial deformity and heart defects, but there were few reports on renal malformation, especially regarding renal hypoplasia with hematuria. CONCLUSION: We have reported a patient suffering from a reduced anogenital distance, hematuria and left renal hypoplasia. A de novo 11.56 Mb deletion ranging from 13q33.1 to 13q34 (Chr13:103542220-115,106,996) was found by SNP-array analysis. It might be the first time for hematuria and renal hypoplasia to be reported as symptoms of 13q33-q34 deletion syndrome Neurodevelopmental disability, heart defects and urogenital/anorectal anomalies may be resulted from common or overlapping regions of deletion in chromosome bands 13q33.1-q34 and may share a common molecular mechanism.

Robust Sampling of Defective Pathways in Multiple Myeloma.

We present the analysis of defective pathways in multiple myeloma (MM) using two recently developed sampling algorithms of the biological pathways: The Fisher's ratio sampler, and the holdout sampler. We performed the retrospective analyses of different gene expression datasets concerning different aspects of the disease, such as the existing difference between bone marrow stromal cells in MM and healthy controls (HC), the gene expression profiling of CD34+ cells in MM and HC, the difference between hyperdiploid and non-hyperdiploid myelomas, and the prediction of the chromosome 13 deletion, to provide a deeper insight into the molecular mechanisms involved in the disease. Our analysis has shown the importance of different altered pathways related to glycosylation, infectious disease, immune system response, different aspects of metabolism, DNA repair, protein recycling and regulation of the transcription of genes involved in the differentiation of myeloid cells. The main difference in genetic pathways between hyperdiploid and non-hyperdiploid myelomas are related to infectious disease, immune system response and protein recycling. Our work provides new insights on the genetic pathways involved in this complex disease and proposes novel targets for future therapies.

Biallelic mutations in NALCN: Expanding the genotypic and phenotypic spectra of IHPRF1.

Loss-of function mutations in NALCN on chromosome 13q, a sodium leak channel that maintains baseline neuronal excitability, cause infantile hypotonia with psychomotor retardation and characteristic faces 1 (IHPRF1, OMIM #615419). Here, we document two individuals with early onset hypotonia with poor feeding and intellectual disability who were compatible with a diagnosis of IHPRF1. The two patients had bi-allelic mutations in NALCN through two different genetic mechanisms: Patient 1 had bi-allelic splice site mutations, that is c.1267-2A>G, derived from heterozygous parents, while Patient 2 had a partial maternal uniparental isodisomy that harbored a frameshift mutation, that is c.2022_2023delAT, in chromosome 13 that was detected through a dedicated algorithm for homozygosity data mapping in whole exome sequencing. The delineation of the exact pattern of inheritance provided vital information regarding the risk of recurrence. In animal models with Nalcn mutations, two behavioral phenotypes, that are, postnatal dyspnea and sleep disturbance, have been reported. Our observations of the two patients with postnatal dyspnea and one patient with sleep disturbance support an association between these two behavioral phenotypes and NALCN mutations in humans. The routine use of a detection algorithm for homozygosity data mapping might improve the diagnostic yields of next-generation sequencing.

Two Cases with Ring Chromosome 13 at either End of the Phenotypic Spectrum.

Ring chromosome 13 is a rare genetic condition with an incidence of 1/58,000 in live births. Major clinical features of patients with ring chromosome 13 include growth and developmental retardation, microcephaly, facial dysmorphism, ambiguous genitalia, anal atresia, eye malformations, retinoblastoma, and hand, foot, and toe abnormalities. The severity of the phenotype depends on the amount of genetic material lost during ring chromosome formation. Here, we report 2 cases with ring chromosome 13 at either end of the phenotypic spectrum.

Recurrent increased nuchal translucency: a first trimester presentation of familial 13p satellite deletion.

Chromosome 13 is one of the acrocentric chromosomes of the human karyotype. Acrocentric chromosomes are the most variable chromosomes in the human karyotype and these variations appear to have no clinical consequences. To the best of our knowledge, this is the first reported case of a first trimester presentation of a 13 short arm satellite deletion with markedly increased nuchal translucency (NT). In this case, the 13p short arm satellite deletion was associated with increased NT in two pregnancies from the same couple.

De Novo interstitial deletion 13q33.3q34 in a male patient with double outlet right ventricle, microcephaly, dysmorphic craniofacial findings, and motor and developmental delay.

We describe a 6-year-old male, diagnosed at birth with double outlet right ventricle (DORV), anterior aorta, multiple ventricular septal defects, pulmonary stenosis, microcephaly and mildly dysmorphic craniofacial findings. Chromosomal analysis showed a normal male karyotype but on subsequent array comparative genomic hybridization (array CGH) analysis a de novo 2.5 Mb loss in chromosome 13q at 13q33.3q34, together with an inherited gain at 4p12, were detected. The propositus underwent placement of a Blalock Taussig shunt and subsequently a Glenn and Fontan operation was performed. In this report we propose that COL4A1 and COL4A2 may be candidate genes for congenital heart disease (CHD) in individuals with a deletion in 13q within the 6Mb critical region for cardiac development proposed by Huang et al., [2012].

Congenital combined deficiency of coagulation factors VII and X--different genetic mechanisms.

Combined coagulation factor VII (FVII) and factor X (FX) deficiency (combined FVII/FX deficiency) belongs to the group of bleeding disorders in which both factors show reduced plasma activity. It may arise from coincidental inheritance of separate coagulation factor deficiencies or a common cause as large deletions comprising both gene loci. The F7 and F10 genes are located on the long arm of chromosome 13. Here, we describe 10 cases with combined FVII/FX deficiency representing both genetic mechanisms of occurrence. Genetic analyses included direct sequencing of the F7 and F10 genes and MLPA (multiplex ligation-dependent probe amplification) for detection of heterozygous large deletions. In four patients, the combined deficiency was due to a large deletion within the terminal end of chromosome 13. In the remaining six cases the deficiency resulted from coincidental inheritance of different genetic alterations affecting both genes independently. In most cases, the genetic defects were heterozygous, presenting with prolonged PT, normal aPTT and mild or no bleeding symptoms. Only in one case compound heterozygous mutations were detected in the F10, resulting in prolonged aPTT and a more severe bleeding phenotype. To avoid a misdiagnosis of combined FVII/FX deficiency, analyses of single factor activities have to be performed in all cases with prolonged PT even if aPTT is normal. Genetic analyses are substantial for correct prediction of an inheritance pattern and a proper genetic counselling.

Hexasomy 13q31.3q34 due to two marker chromosomes with inverted duplication in a fetus with increased nuchal translucency.

BACKGROUND: Small supernumerary marker chromosomes are structurally rearranged chromosomes that can be formed from different chromosomal fragments and cannot be identified using chromosomal banding analysis. Their examination has to be complemented by additional analyses like fluorescent in situ hybridization or array comparative genomic hybridization. METHODS: We report on partial hexasomy of chromosome 13q in a fetus of a pregnant woman referred to genetic counseling because of increased fetal nuchal translucency and increased risk of trisomy 21 and trisomy 18 in first-trimester combined prenatal screening. Using chromosome banding analysis, in situ hybridization and array comparative hybridization we revealed the presence of two marker chromosomes with inverted duplication resulting in hexasomy of a 22.6 Mbp fragment in chromosomal region 13q31.3-13q34 with the lack of chromosome 13 centromere. RESULTS: The fetus presented dysmorphic facial features, head and body disproportion, wide neck, ambiguous genitalia, incorrect position of the anus, and symmetrical shortening of the long bones were present in our described case. Some of these features were in accordance with other published cases. Other most often described features in tetrasomy were: microphtalmia or other major eye defects, ear abnormalities and deafness, hemangiomata, hypotelorism, severe learning disability and seizures. Despite a low risk of recurrence for small supernumerary marker chromosomes the possibility of germ line mosaicism exists, thus genetic counseling was offered to the examined family. CONCLUSION: A full characterization of small supernumerary marker chromosomes in fetal karyotype is necessary for pregnancy prognosis and genetic counseling.

De novo LINE-1 retrotransposition in HepG2 cells preferentially targets gene poor regions of chromosome 13.

Long interspersed nuclear elements (Line-1 or L1s) account for ~17% of the human genome. While the majority of human L1s are inactive, ~80-100 elements remain retrotransposition competent and mobilize through RNA intermediates to different locations within the genome. De novo insertions of L1s account for polymorphic variation of the human genome and disruption of target loci at their new location. In the present study, fluorescence in situ hybridization and DNA sequencing were used to characterize retrotransposition profiles of L1(RP) in cultured human HepG2 cells. While expression of synthetic L1(RP) was associated with full-length and truncated insertions throughout the entire genome, a strong preference for gene-poor regions, such as those found in chromosome 13 was observed for full-length insertions. These findings shed light into L1 targeting mechanisms within the human genome and question the putative randomness of L1 retrotransposition.

Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats.

The goal of the present study was to narrow a region of chromosome 13 to only several genes and then apply unbiased statistical approaches to identify molecular networks and biological pathways relevant to blood-pressure salt sensitivity in Dahl salt-sensitive (SS) rats. The analysis of 13 overlapping subcongenic strains identified a 1.37 Mbp region on chromosome 13 that influenced the mean arterial blood pressure by at least 25 mmHg in SS rats fed a high-salt diet. DNA sequencing and analysis filled genomic gaps and provided identification of five genes in this region, Rfwd2, Fam5b, Astn1, Pappa2, and Tnr. A cross-platform normalization of transcriptome data sets obtained from our previously published Affymetrix GeneChip dataset and newly acquired RNA-seq data from renal outer medullary tissue provided 90 observations for each gene. Two Bayesian methods were used to analyze the data: 1) a linear model analysis to assess 243 biological pathways for their likelihood to discriminate blood pressure levels across experimental groups and 2) a Bayesian graphical modeling of pathways to discover genes with potential relationships to the candidate genes in this region. As none of these five genes are known to be involved in hypertension, this unbiased approach has provided useful clues to be experimentally explored. Of these five genes, Rfwd2, the gene most strongly expressed in the renal outer medulla, was notably associated with pathways that can affect blood pressure via renal transcellular Na(+) and K(+) electrochemical gradients and tubular Na(+) transport, mitochondrial TCA cycle and cell energetics, and circadian rhythms.

Hepatoblastoma in a 15-month-old female with trisomy 13.

Trisomy 13 (T13) is a rare autosomal aneuploidy. Greater than 90% of patients die during the first year of life. Malignancies reported in association with T13 include two cases of Wilms tumor and one case of pilocytic astrocytoma. There is no previous report of hepatoblastoma in patients with T13. We report a unique case of hepatoblastoma in a 15-month-old female with constitutional T13. Our patient was born at 38 weeks gestation and was noted to have phenotypic features consistent with T13. Genetic testing confirmed an abnormal karyotype of 47,XX,+13 in all cells. At fifteen months of age she was noted to have a right hepatic lobe mass on a routine follow-up renal ultrasound for hydronephrosis. Serum alpha-fetoprotein level was 55,300 ng/ml. Staging work-up revealed the absence of metastases. She underwent a complete surgical resection with right hepatic lobectomy. Histopathology was consistent with hepatoblastoma, mixed epithelial and mesenchymal type. She had a protracted postoperative course complicated by Enterobacter aerogenes urosepsis, a significant biloma, chronic pancreatitis, and apneic episodes of uncertain etiology. She received four courses of doxorubicin monotherapy without any severe or unexpected toxicity. She continues to be in remission 8 months following diagnosis. This is the first reported case of hepatoblastoma in a child with constitutional T13. This may represent a non-random association, as somatic trisomy of chromosome 13 in hepatoblastoma tumors has been previously described in the literature. Prolonged survival may have allowed for hepatoblastoma to present in our patient.

Possible involvement of Hcn1 ion channel in learning and memory dysfunction in SAMP8 mice.

The senescence-accelerated mouse prone 8 (SAMP8) strain exhibits age-related learning and memory deficits (LMD) at 2 months of age. Combined linkage analysis of 264 F2 intercross SAMP8 × JF1 mice and RNA-seq analysis identified Hcn1 gene out of 29 genes in the LMD region on chromosome 13. Hcn1 in SAMP8 strain showed 15 times less polyglutamine repetition compared to Japanese fancy mouse 1 (JF1). Whole cell patch clamp analysis showed that Hcn1 ion conductivity was significantly lower in SAMP8 compared to that of JF1, which may be associated with learning and memory deficiency.

De novo 13q deletions in two patients with mild anorectal malformations as part of VATER/VACTERL and VATER/VACTERL-like association and analysis of EFNB2 in patients with anorectal malformations.

Anorectal malformations (ARMs) comprise a broad spectrum of conditions ranging from mild anal anomalies to complex cloacal malformations. In 40-50% of cases, ARM occurs within the context of defined genetic syndromes or complex multiple congenital anomalies, such as VATER/VACTERL (vertebral defects [V], ARMs [A], cardiac defects [C], tracheoesophageal fistula with or without esophageal atresia [TE], renal malformations [R], and limb defects [L]) association. Here, we report the identification of deletions at chromosome 13q using single nucleotide polymorphism-based array analysis in two patients with mild ARM as part of VATER/VACTERL and VATER/VACTERL-like associations. Both deletions overlap the previously defined critical region for ARM. Heterozygous Efnb2 murine knockout models presenting with mild ARM suggest EFNB2 as an excellent candidate gene in this region. Our patients showed a mild ARM phenotype, closely resembling that of the mouse. We performed a comprehensive mutation analysis of the EFNB2 gene in 331 patients with isolated ARM, or ARM as part of VATER/VACTERL or VATER/VACTERL-like associations. However, we did not identify any disease-causing mutations. Given the convincing argument for EFNB2 as a candidate gene for ARM, analyses of larger samples and screening of functionally relevant non-coding regions of EFNB2 are warranted. In conclusion, our report underlines the association of chromosome 13q deletions with ARM, suggesting that routine molecular diagnostic workup should include the search for these deletions. Despite the negative results of our mutation screening, we still consider EFNB2 an excellent candidate gene for contributing to the development of ARM in humans.

Recessive mutation on mouse chromosome 13 associated with abnormal hair texture and cardiomyopathy.

An autosomal recessive mutation (aht) associated with abnormal hair texture and cardiomyopathy spontaneously arose in the Y-chromosome consomic mouse strain DH-Chr YSS . The aht/aht mouse phenotypes closely resembled those of rul/rul mice, which were caused by a mutation in desmoplakin (Dsp) on chromosome 13. Quantitative trait locus (QTL) mapping using (DDD/Sgn × DH-Chr YSS -aht heterozygotes) F2 mice demonstrated that aht is contiguous with Dsp on chromosome 13. However, no nucleotide changes were identified in the coding region of Dsp in aht/aht mice by whole-exome sequencing. Therefore, the molecular nature of the aht mutation remains unclear. Nevertheless, aht/aht mice may serve as a new model for human diseases that are accompanied by abnormalities in the integumental and cardiovascular systems, including Carvajal-Huerta syndrome.

Prenatal Sonographic Features of Rare Chromosome 13 Aberrations.

Objective: Trisomy 13 is one of the most common chromosome aberrations diagnosed in the prenatal period, and is associated with some specific dysmorphic features. Rare chromosome 13 aberrations other than trisomy 13 may cause other fetal abnormalities. The aim of the study was to analyze cases with those rare chromosome 13 aberrations. Methods: We analyzed all prenatal tests performed in the Department of Clinical Genetics of the Medical University of Lodz from 2016 to 2021 to find all chromosome 13 aberrations. Results: The most common aberration of chromosome 13 was a simple trisomy 13 (n = 16). We found five rare chromosome 13 aberrations other than simple chromosome 13 trisomy: mosaic trisomy 13 mos 47,XX,+13[11]/46,XX[10], mosaic monosomy 13 mos 46,XY,-13,+mar[9]/46,XY[31], duplication 13q21.1-q31, deletion 13q34 and deletion 13q31.1-q34. The deletion 13q31.1-q34 occurred in monochorionic diamniotic twin pregnancy. Conclusion: Rare aberrations accounted for 24% of all chromosome 13 aberrations. Cases with mosaic monosomy of chromosome 13 and microdeletion 13q had similar abnormalities of the external genitalia and facial dysmorphia. The case with duplication 13q was very similar to the clinical features of chromosome 13 trisomy. Mosaic trisomy 13 can occur without any accompanying anatomical defects.