Mandibular hypoplasia, Deafness and Progeroid features with concomitant Lipodystrophy is a rare, genetic, premature aging disease named MDPL Syndrome, due to almost always a
variant in
gene, encoding ...the DNA polymerase δ. In previous
studies, we have already described several hallmarks of aging, including genetic damage, telomere shortening, cell senescence and proliferation defects. Since a clear connection has been reported between telomere shortening and mitochondria malfunction to initiate the aging process, we explored the role that mitochondrial metabolism and activity play in pathogenesis of MDPL Syndrome, an aspect that has not been addressed yet. We thus evaluated mtDNA copy number, assessing a significant decrease in mutated cells. The expression level of genes related to mitochondrial biogenesis and activity also revealed a significant reduction, highlighting a mitochondrial dysfunction in MDPL cells. Even the expression levels of mitochondrial marker SOD2, as assessed by immunofluorescence, were reduced. The decrease in this antioxidant enzyme correlated with increased production of mitochondrial ROS in MDPL cells, compared to WT. Consistent with these data, Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) analysis revealed in MDPL cells fewer mitochondria, which also displayed morphological abnormalities. Accordingly, we detected autophagic vacuoles containing partially digested mitochondria. Overall, our results demonstrate a dramatic impairment of mitochondrial biogenesis and activity in MDPL Syndrome. Administration of Metformin, though unable to restore mitochondrial impairment, proved efficient in rescuing nuclear abnormalities, suggesting its use to specifically ameliorate the premature aging phenotype.
The automatic discovery of functional dependencies (FDs) has been widely studied as one of the hardest problems in data profiling. Existing approaches have focused on making the FD computation ...efficient while inspecting single relations at a time. In this paper, for the first time we address the problem of inferring FDs for multiple relations as they occur in integrated views by solely using the functional dependencies of the base relations of the view itself. To this purpose, we leverage logical inference and selective mining and show that we can discover most of the exact FDs from the base relations and avoid the full computation of the FDs for the integrated view itself, while at the same time preserving the lineage of FDs of base relations. We propose algorithms to speedup the inferred FD discovery process and mine FDs on-the-fly only from necessary data partitions. We present InFine (INferred FunctIoNal dEpendency), an end-to-end solution to discover inferred FDs on integrated views by leveraging provenance information of base relations. Our experiments on a range of real-world and synthetic datasets demonstrate the benefits of our method over existing FD discovery methods that need to rerun the discovery process on the view from scratch and cannot exploit lineage information on the FDs. We show that InFine outperforms traditional methods necessitating the full integrated view computation by one to two order of magnitude in terms of runtime. It is also the most memory efficient method while preserving FD provenance information using mainly inference from base table with negligible execution time.
Congenital disorders of glycosylation (CDG) are genetic diseases characterized by deficient synthesis (CDG type I) and/or abnormal processing (CDG type II) of glycan moieties linked to protein and ...lipids. The impact of the molecular defects on protein glycosylation and in turn on the clinical phenotypes of patients with CDG is not yet understood. ALG12-CDG is due to deficiency of ALG12 α1,6-mannosyltransferase that adds the eighth mannose residue on the dolichol-PP-oligosaccharide precursor in the endoplasmic reticulum. ALG12-CDG is a severe multisystem disease associated with low to deficient serum immunoglobulins and recurrent infections. We thoroughly investigated the glycophenotype in a patient with novel
ALG12
variants and immunodeficiency. We analyzed serum native transferrin, as first line test for CDG and we profiled serum IgG and total serum N-glycans by a combination of consolidated (N-glycan analysis by MALDI MS) and innovative mass spectrometry-based protocols, such as GlycoWorks
Rapi
Fluor N-glycan analysis coupled with LC-ESI MS. Intact serum transferrin showed, as expected for a CDG type I defect, underoccupancy of N-glycosylation sites. Surprisingly, total serum proteins and IgG N-glycans showed some specific changes, consisting in accumulating amounts of definite high-mannose and hybrid structures. As a whole, ALG12-CDG behaves as a dual CDG (CDG-I and II defects) and it is associated with distinct, abnormal glycosylation of total serum and IgG N-glycans. Glycan profiling of target glycoproteins may endorse the molecular defect unraveling the complex clinical phenotype of CDG patients.
BAP1 is a novel regulator of HIF-1α Bononi, Angela; Wang, Qian; Zolondick, Alicia A ...
Proceedings of the National Academy of Sciences - PNAS,
01/2023, Letnik:
120, Številka:
4
Journal Article
Recenzirano
Odprti dostop
is a powerful tumor suppressor gene characterized by haplo insufficiency. Individuals carrying germline
mutations often develop mesothelioma, an aggressive malignancy of the serosal layers covering ...the lungs, pericardium, and abdominal cavity. Intriguingly, mesotheliomas developing in carriers of germline
mutations are less aggressive, and these patients have significantly improved survival. We investigated the apparent paradox of a tumor suppressor gene that, when mutated, causes less aggressive mesotheliomas. We discovered that mesothelioma biopsies with biallelic
mutations showed loss of nuclear HIF-1α staining. We demonstrated that during hypoxia,
binds, deubiquitylates, and stabilizes HIF-1α, the master regulator of the hypoxia response and tumor cell invasion. Moreover, primary cells from individuals carrying germline
mutations and primary cells in which
was silenced using siRNA had reduced HIF-1α protein levels in hypoxia. Computational modeling and co-immunoprecipitation experiments revealed that mutations of
residues I675, F678, I679, and L691 -encompassing the C-terminal domain-nuclear localization signal- to A, abolished the interaction with HIF-1α. We found that
binds to the N-terminal region of HIF-1α, where HIF-1α binds DNA and dimerizes with HIF-1β forming the heterodimeric transactivating complex HIF. Our data identify
as a key positive regulator of HIF-1α in hypoxia. We propose that the significant reduction of HIF-1α activity in mesothelioma cells carrying biallelic
mutations, accompanied by the significant reduction of HIF-1α activity in hypoxic tissues containing germline
mutations, contributes to the reduced aggressiveness and improved survival of mesotheliomas developing in carriers of germline
mutations.
Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating ...predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements. The assessment of chromosomal fragility after exposure to DNA cross-linking agents is generally required to definitively confirm diagnosis. We assessed peripheral blood genome-wide DNA methylation (DNAm) profiles in 25 subjects with molecularly confirmed clinical diagnosis of FA (FANCA complementation group) using Illumina’s Infinium EPIC array. We identified 82 differentially methylated CpG sites that allow to distinguish subjects with FA from healthy individuals and subjects with other genetic disorders, defining an FA-specific DNAm signature. The episignature was validated using a second cohort of subjects with FA involving different complementation groups, documenting broader genetic sensitivity and demonstrating its specificity using the EpiSign Knowledge Database. The episignature properly classified DNA samples obtained from bone marrow aspirates, demonstrating robustness. Using the selected probes, we trained a machine-learning model able to classify EPIC DNAm profiles in molecularly unsolved cases. Finally, we show that the generated episignature includes CpG sites that do not undergo functional selective pressure, allowing diagnosis of FA in individuals with reverted phenotype due to gene conversion. These findings provide a tool to accelerate diagnostic testing in FA and broaden the clinical utility of DNAm profiling in the diagnostic setting.
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Fanconi anemia (FA) is the most common bone marrow failure syndrome. Molecular diagnosis is challenging due to its genetic heterogeneity and wide mutation spectrum. We identify an FA-specific DNA methylation signature that aids in classification of variants and establishing/refuting a clinical diagnosis in molecularly uninformative and revertant cases.
Abstract BACKGROUND Optical Genome Mapping (OGM) is a recent platform which enables the detection of genome-wide balanced and unbalanced structural rearrangements (SR), providing a genome complexity ...overview. METHODS This study explores OGM implementation in the context of paediatric central nervous system (CNS) tumours by analyzing a series of 26 cases. RESULTS OGM equaled Chromosomal Microarray Analysis in detecting aneuploidies and copy number alterations (CNA), and, although less sensitive than RNAseq in identifying gene-fusions (15/19), enabled the definition of their causative mechanism. The assessment of SR and CNA allowed the distinction of different groups. Amount and distribution of SR identified 4 groups: HIGH_SR with >10 breakpoints (BP) distributed in ≥5 chromosomes (8 cases), SR_CHROMOTHRIPSIS with ≥10BP in <5 chromosomes with the most affected chromosome presenting with >10 BP (9 cases), and LOW_SR with <10BP (9 cases). CNA non-associated with chromothripsis (nCthCNA) stratified the series in NO_nCthCNA, LOW_nCthCNA, INT_nCthCNA, HIGH_nCthCNA group, where the alterations were absent (9 cases), <10 (9 cases), 10-49 (2 cases) and ≥50 (6 cases), respectively. nCthCNA directly correlated with the mean number of chromosomes harboring SR, i.e. 10.2 in HIGH_/INT_nCthCNA vs 2.5 in NO_/LOW_nCthCNA (p=0.001), and inversely with chromothripsis (9/18 in NO_/LOW_nCthCNA vs 0/8 in HIGH_/INT_nCthCNA, p=0.015). CONCLUSIONS High complexity groups associated with biological aggressiveness, with HIGH_nCthCNA including only high-grade tumours (p=0.004) and disease progression mostly occurring in HIGH_SR (6/7 cases vs 1/17, p<0.001) and HIGH_nCthCNA (4/5 vs 2/12 cases, p=0.013). Low-complexity groups were enriched of low/intermediate-grade tumours (13/15 in NO_/LOW_nCthCNA vs 5/11 in INT_/HIGH_nCthCNA, p=0.024). SR_CHROMOTHRIPSIS cases were all low/intermediate-grade fusion-driven tumours, did not harbour TP53 mutations or high-impact CNA (0/9 vs 7/17, p=0.030), and did not progress (0/9 vs 7/16, p=0.030). This study suggests a possible value of OGM assessment of genome complexity in prognostication of paediatric CNS tumours.
Colorectal carcinomas develop according to particular genetic pathways, including the chromosomal instability (CIN+), microsatellite instability (MSI+) and MSI- CIN- routes. We have determined the ...genetic pathway in patients with MYH-associated polyposis (MAP), a syndrome of colorectal adenomas and cancer that results from defective base excision repair (BER). As in previous studies, MAP tumors showed a high frequency of G>T mutations in APC, in accordance with defective BER. We found that K-ras mutations were common in MAP tumors, all of the changes comprising conversion of the first guanine residue of codon 12 to thymidine (G12C, GGT>TGT). We found no BRAF mutations at the codon 599 hotspot or elsewhere in exon 14. Almost all of the MAP cancers were near-diploid (CIN-), and none was MSI+. A few p53 mutations were found, but these were not predominantly G>T changes. p53 overexpression was, however, frequent. No SMAD4 or TGFBIIR mutations were found. MAP tumors appear to follow a distinct genetic pathway, with some features of both the CIN and MSI pathways. BER deficiency is rarely accompanied by CIN or MSI. The spectrum of somatic mutations in MAP tumors reflects both selection and hypermutation to which certain guanine residues are particularly prone.
Bi‐allelic inactivation of XPD protein, a nucleotide excision repair (NER) signaling pathway component encoded by ERCC2 gene, has been associated with several defective DNA repair phenotypes, ...including xeroderma pigmentosum, photosensitive trichothiodystrophy, and cerebro‐oculo‐facio‐skeletal syndrome. We report a pediatric patient harboring two compound heterozygous variants in ERCC2 gene, c.361‐1G>A and c.2125A>C (p.Thr709Pro), affected by severe postnatal growth deficiency, microcephaly, facial dysmorphisms and pilocytic astrocytoma of the brainstem. Some of these features point to a DNA repair syndrome, and altogether delineate a phenotype differentiating from disorders known to be associated with ERCC2 mutations. The DNA repair efficiency following UV irradiation in the proband's skin fibroblasts was defective indicating that the new set of ERCC2 alleles impacts on NER efficiency. Sequencing analysis on tumor DNA did not reveal any somatic deleterious point variant in cancer‐related genes, while SNP‐array analysis disclosed a 2 Mb microduplication involving the 7q34 region, spanning from KIAA1549 to BRAF, and resulting in the KIAA1549:BRAF fusion protein, a marker of pilocytic astrocytoma. In conclusion, this report expands the clinical and mutational spectrum of ERCC2‐related disorders.
We describe a patient harboring two compound heterozygous variants in ERCC2 gene, affected by severe postnatal growth deficiency, microcephaly, facial dysmorphisms and pilocytic astrocytoma of the brainstem. The present report expands the clinical and mutational spectrum of ERCC2‐related disorders.
PATZ1-rearranged sarcomas are well-recognized tumors as part of the family of round cell sarcoma with EWSR1-non-ETS fusions. Whether PATZ1-rearranged central nervous system (CNS) tumors are a ...distinct tumor type is debatable. We thoroughly characterized a pediatric series of PATZ1-rearranged CNS tumors by chromosome microarray analysis (CMA), DNA methylation analysis, gene expression profiling and, when frozen tissue is available, optical genome mapping (OGM). The series consisted of 7 cases (M:F=1.3:1, 1-17 years, median 12). On MRI, the tumors were supratentorial in close relation to the lateral ventricles (intraventricular or iuxtaventricular), preferentially located in the occipital lobe. Two major histologic groups were identified: one (4 cases) with an overall glial appearance, indicated as "neuroepithelial" (NET) by analogy with the corresponding methylation class (MC); the other (3 cases) with a predominant spindle cell sarcoma morphology, indicated as "sarcomatous" (SM). A single distinct methylation cluster encompassing both groups was identified by multidimensional scaling analysis. Despite the epigenetic homogeneity, unsupervised clustering analysis of gene expression profiles revealed 2 distinct transcriptional subgroups correlating with the histologic phenotypes. Interestingly, genes implicated in epithelial-mesenchymal transition and extracellular matrix composition were enriched in the subgroup associated to the SM phenotype. The combined use of CMA and OGM enabled the identification of chromosome 22 chromothripsis in all cases suitable for the analyses, explaining the physical association of PATZ1 to EWSR1 or MN1. Six patients are currently disease-free (median follow-up 30 months, range 12-92). One patient of the SM group developed spinal metastases at 26 months from diagnosis and is currently receiving multimodal therapy (42 months). Our data suggest that PATZ1-CNS tumors are defined by chromosome 22 chromothripsis as causative of PATZ1 fusion, show peculiar MRI features (eg, relation to lateral ventricles, supratentorial frequently posterior site), and, although epigenetically homogenous, encompass 2 distinct histologic and transcriptional subgroups.
hMena (ENAH), a cytoskeleton regulatory protein involved in the regulation of cell motility and adhesion, is overexpressed in breast cancer. The aim of this study was to define at what stage of ...breast carcinogenesis hMena is overexpressed and to correlate hMena overexpression with established prognostic factors in breast cancer, focusing on human epidermal growth factor receptor-2 (HER-2).
hMena expression was assessed immunohistochemically in a prospective cohort of cases (n = 360) encompassing a highly representative spectrum of benign breast diseases associated with different risk of transformation, in situ, invasive, and metastatic tumors. Correlations with conventional pathologic and prognostic variables, such as proliferation index, hormonal receptor status, and HER-2 overexpression, were also evaluated. In vitro experiments were done to study the effect of neuregulin-1 and Herceptin treatments on hMena expression.
hMena protein is undetectable in normal breast and is weakly expressed in a small percentage of low-risk benign diseases (9%), but displays a progressive and significant increase of positivity in benign lesions at higher risk of transformation (slightly increased risk 43%; moderate increased risk 67%), in in situ (72%), invasive (93%), and metastatic breast cancer (91%). A significant direct correlation with tumor size (P = 0.04), proliferation index (P < 0.0001), and HER-2 overexpression (P < 0.0001) and an inverse relationship with estrogen (P = 0.036) and progesterone receptors (P = 0.001) are found in invasive carcinomas. In vitro experiments show that neuregulin-1 up-regulates, whereas Herceptin down-regulates, hMena expression.
Our data provide new insights into the relevance of actin-binding proteins in human breast carcinogenesis and indicate hMena overexpression as a surrogate indicator in breast disease management.
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