Acute promyelocytic leukemia (APL) with atypical breakpoints in the promyelocytic leukemia (PML) and retinoic acid receptor-alpha (RARA) genes represents a rare leukemic event, which occurs preferentially in patients with variant types of the PML/RARA fusion gene. Here we report on a patient with APL with a unique PML/RARA fusion transcript that harbors a short type of this fusion gene, exhibiting unexpected results of standard PCR diagnostics. The detected transcript originates from fusion of PML exon 4 and a truncated form of transcription variant 2 of the RARA gene, with an additional 9 bp insertion. According to our knowledge, this differs from all previously described fusion transcripts.

• MeSH
• Electrophoresis, Agar Gel MeSH
• Oncogene Proteins, Fusion genetics   MeSH
• Transcription, Genetic MeSH
• Middle Aged MeSH
• Humans MeSH
• RNA, Messenger genetics   metabolism   MeSH
• Molecular Sequence Data MeSH
• Protein Isoforms genetics   MeSH
• Receptors, Retinoic Acid genetics   MeSH
• Base Sequence MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND: Variants in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been reported as being etiologically associated with early infantile epileptic encephalopathy type 2 (EIEE2). We report on two patients, a boy and a girl, with EIEE2 that present with early onset epilepsy, hypotonia, severe intellectual disability, and poor eye contact. METHODS: Massively parallel sequencing (MPS) of a custom-designed gene panel for epilepsy and epileptic encephalopathy containing 112 epilepsy-related genes was performed. Sanger sequencing was used to confirm the novel variants. For confirmation of the functional consequence of an intronic CDKL5 variant in patient 2, an RNA study was done. RESULTS: DNA sequencing revealed de novo variants in CDKL5, a c.2578C>T (p. Gln860*) present in a hemizygous state in a 3-year-old boy, and a potential splice site variant c.463+5G>A in heterozygous state in a 5-year-old girl. Multiple in silico splicing algorithms predicted a highly reduced splice site score for c.463+5G>A. A subsequent mRNA study confirmed an aberrant shorter transcript lacking exon 7. CONCLUSIONS: Our data confirmed that variants in the CDKL5 are associated with EIEE2. There is credible evidence that the novel identified variants are pathogenic and, therefore, are likely the cause of the disease in the presented patients. In one of the patients a stop codon variant is predicted to produce a truncated protein, and in the other patient an intronic variant results in aberrant splicing.

• MeSH
• Epilepsy genetics   MeSH
• Exons MeSH
• Genetic Variation genetics   MeSH
• Spasms, Infantile genetics   MeSH
• Humans MeSH
• Mutation MeSH
• Child, Preschool MeSH
• Protein Serine-Threonine Kinases genetics   metabolism   MeSH
• Rett Syndrome genetics   MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Child, Preschool MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH

We report cytogenetic and molecular genetic analysis of a pediatric tumor positive for the CIC-DUX4 fusion. The tumor belongs to a rare, diagnostically challenging subgroup of undifferentiated small round cell sarcomas. A balanced t(4;19)(q35;q13.1-2) was identified by G-banding, as a sole cytogenetic finding. The translocation was also identified by the M-FISH technique. After RT-PCR, the tumor sample was positive for the CIC-DUX4 fusion. The PCR product contains a novel, so far unreported variant of the CIC-DUX4 fusion transcript, with a fusion of the exon 20 from the CIC gene and the exon 1 from the DUX4 gene.

• MeSH
• Fatal Outcome MeSH
• Oncogene Proteins, Fusion genetics   MeSH
• Humans MeSH
• Adolescent MeSH
• Soft Tissue Neoplasms genetics   pathology   MeSH
• Sarcoma genetics   pathology   MeSH
• Translocation, Genetic * MeSH
• Check Tag
• Humans MeSH
• Adolescent MeSH
• Male MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH

BACKGROUND: Apoptosis plays a critical role in cancer cell survival and tumor development. We provide a hypothesis-generating screen for further research by exploring the expression profile and genetic variability of caspases (2, 3, 7, 8, 9, and 10) in breast carcinoma patients. This study addressed isoform-specific caspase transcript expression and genetic variability in regulatory sequences of caspases 2 and 9. METHODS: Gene expression profiling was performed by quantitative real-time PCR in tumor and paired non-malignant tissues of two independent groups of patients. Genetic variability was determined by high resolution melting, allelic discrimination, and sequencing analysis in tumor and peripheral blood lymphocyte DNA of the patients. RESULTS: CASP3 A+B and S isoforms were over-expressed in tumors of both patient groups. The CASP9 transcript was down-regulated in tumors of both groups of patients and significantly associated with expression of hormonal receptors and with the presence of rs4645978-rs2020903-rs4646034 haplotype in the CASP9 gene. Patients with a low intratumoral CASP9A/B isoform expression ratio (predicted to shift equilibrium towards anti-apoptotic isoform) subsequently treated with adjuvant chemotherapy had a significantly shorter disease-free survival than those with the high ratio (p=0.04). Inheritance of CC genotype of rs2020903 in CASP9 was associated with progesterone receptor expression in tumors (p=0.003). CONCLUSIONS: Genetic variability in CASP9 and expression of its splicing variants present targets for further study.

• MeSH
• Molecular Targeted Therapy * MeSH
• Transcription, Genetic * MeSH
• Genetic Variation * genetics   MeSH
• Caspase 9 genetics   metabolism   MeSH
• Caspases * genetics   metabolism   MeSH
• Middle Aged MeSH
• Humans MeSH
• Breast Neoplasms * enzymology   genetics   MeSH
• Gene Expression Regulation, Neoplastic * MeSH
• Gene Expression Profiling MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Female MeSH

SUMOylation is a post-translational modification that positively regulates monoallelic expression of the trypanosome variant surface glycoprotein (VSG). The presence of a highly SUMOylated focus associated with the nuclear body, where the VSG gene is transcribed, further suggests an important role of SUMOylation in regulating VSG expression. Here, we show that SNF2PH, a SUMOylated plant homeodomain (PH)-transcription factor, is upregulated in the bloodstream form of the parasite and enriched at the active VSG telomere. SUMOylation promotes the recruitment of SNF2PH to the VSG promoter, where it is required to maintain RNA polymerase I and thus to regulate VSG transcript levels. Further, ectopic overexpression of SNF2PH in insect forms, but not of a mutant lacking the PH domain, induces the expression of bloodstream stage-specific surface proteins. These data suggest that SNF2PH SUMOylation positively regulates VSG monoallelic transcription, while the PH domain is required for the expression of bloodstream-specific surface proteins. Thus, SNF2PH functions as a positive activator, linking expression of infective form surface proteins and VSG regulation, thereby acting as a major regulator of pathogenicity.

• MeSH
• Epigenesis, Genetic MeSH
• Glycoproteins genetics   metabolism   MeSH
• Protozoan Proteins genetics   metabolism   MeSH
• Chromatin Assembly and Disassembly MeSH
• RNA Polymerase I metabolism   MeSH
• Sumoylation * MeSH
• Transcription Factors genetics   metabolism   MeSH
• Trypanosoma brucei brucei genetics   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Prevence vzniku nádorů u nosičů dědičných alterací nádorových predispozičních genů vyžaduje jasnou identifikaci zodpovědných patogenních mutací. Při analýze nádorové predispozice je odhalena řada variant s nejasným významem (VUS) komplikujících klinickou interpretaci výsledků. Pokud VUS postihují proces sestřihu transkriptu příslušného genu, lze je považovat za patogenní. V projektu se zaměříme na vyhodnocení změn sestřihového vzorce mRNA transkriptů u nosičů dědičných variant genů predisponujících ke vzniku dědičné formy karcinomu (ca) prsu a ovarií (CHEK2, PALB2, NBN, TP53, RAD51C/D, MLH1, MSH2/6, BRIP1). Nejprve provedeme identifikaci jejich sestřihových variant v normálních tkáních (leukocyty, mamární a tuková tkáň) zdravých osob bez přítomnosti dědičných variant pomocí multiplexní PCR (mPCR) umožňující amplifikaci všech sestřihových oblastí s následnou charakterizací sekvenovánín nové generace (NGS). Vyšetření RNA od nosičů VUS umožní kvalitativně (fragmentační a mPCR/NGS analýza) i kvantitativně (qPCR) identifikovat VUS způsobující změny sestřihového vzorce příslušného genu.; Clinical management that enables efficient cancer prevention in carriers of germ-line alterations in cancer susceptibility genes requires and unequivocal characterization of the pathogenic mutation. Current cancer predisposition analyses reveal many variants of unknown clinical significance (VUS) which complicate the clinical interpretation of results. The VUS that change splicing of corresponding gene product may be considered as pathogenic. Our project aims to identify splicing alterations in carriers of VUS in genes predisposing to breast and ovarian cancer (CHEK2, PALB2, NBN, TP53, RAD51C/D, MLH1, MSH2/6, BRIP1). First, we aim to perform a comprehensive characterization of naturally occurring splicing variants of analyzed genes in normal lymphocytes, mammary and adipose tissues from non-cancer individuals using multiplex (m)PCR/next generation sequencing (NGS) analysis. Subsequently, the analyses of RNA from carriers of VUS will enable to characterize the qualitative (fragment analysis, mPCR/NGS) and quantitative (qPCR) changes in splicing pattern of corresponding genes.

• MeSH
• Hereditary Breast and Ovarian Cancer Syndrome genetics   classification   MeSH
• Genetic Predisposition to Disease genetics   classification   MeSH
• Genes, Neoplasm genetics   MeSH
• RNA Precursors MeSH
• RNA Splicing genetics   MeSH
• RNA Splicing Factors MeSH
• High-Throughput Nucleotide Sequencing MeSH

• Conspectus
• Patologie. Klinická medicína
• NML Fields
• onkologie
• genetika, lékařská genetika
• gynekologie a porodnictví
• NML Publication type
• závěrečné zprávy o řešení grantu AZV MZ ČR

Cílem projektu je identifikace tkáňové specifičnosti sestřihových forem genu BRCA1 s ohledem na jejich význam jako prognostických a prediktivních ukazatelů karcinomu prsu. Vzorky RNA izolované z peroperačně získané mamární tkáně pacientek s ca prsu a ženbez nádoru podstupujících mamoplastiku a izolované z periferní krve budou sloužit pro syntézu cDNA. Sestřihové varianty BRCA1 mRNA budou z cDNA amplifikovány s primery zasahujícími 5' a 3' UTR sekvece BRCA1 a analyzovány fragmentační gelovou elektroforézou (Agilent 2100). Alternativní sestřihové varianty budou zaklonovány pomocí TA-klonování do vektorů a sekvenačně charakterizovány ze získaných plasmidů. Tkáňová exprese jednotlivých variant BRCA1 bude kvantifikována pomocí qPCR. Statisticky budou vyhodnoceny rozdíly v sestřihovém vzorci buněk periferní krve a mamy a mezi pacientkami s ca prsu a nenádorovou populací, u pacientek s ca prsu budou vyhodnoceny sestřihové vzorce BRCA1 mRNA ve vztahu k průběhu a léčbě onemocnění.; The aim of the project is identification of BRCA1 splicing variants specificity regarding their significance as a prognostic factors and predictive markers of breast cancer. cDNA will be synthesized from RNA isolated from mammary tissue samples receivedfrom breast cancer patients and from women without breast cancer and from their peripheral blood. BRCA1 mRNA splicing variants will be identified using cDNA as a template for PCR amplification with primers localized in 5´ and 3´ BRCA1 UTR and subsequently analyzed by fragmentation gel electrophoresis (Agilent 2100). Detected BRCA1 splicing variants will be cloned into TA ? cloning vector and sequenced. Tissue specific expression of particular variants will be quantified by qPCR. Differences between splicing patterns of lymphocytes and mammary tissue within patients with breast cancer and controls will be statistically evaluated. BRCA1 splicing variants within breast cancer patients will be evaluated in relation to disease course and treatment.

• MeSH
• Alternative Splicing MeSH
• Hereditary Breast and Ovarian Cancer Syndrome MeSH
• Genetic Predisposition to Disease MeSH
• Genes, BRCA1 MeSH
• Breast Neoplasms MeSH
• Predictive Value of Tests MeSH

• Conspectus
• Gynekologie. Porodnictví
• NML Fields
• gynekologie a porodnictví
• onkologie
• NML Publication type
• závěrečné zprávy o řešení grantu IGA MZ ČR

• MeSH
• Fusion Proteins, bcr-abl genetics   MeSH
• Leukemia, Myelogenous, Chronic, BCR-ABL Positive diagnosis   drug therapy   genetics   MeSH
• Cytogenetic Analysis methods   MeSH
• Adult MeSH
• Exons MeSH
• Genetic Variation MeSH
• Remission Induction methods   MeSH
• Humans MeSH
• Piperazines therapeutic use   MeSH
• Reverse Transcriptase Polymerase Chain Reaction methods   MeSH
• Pyrimidines therapeutic use   MeSH
• Check Tag
• Adult MeSH
• Humans MeSH
• Male MeSH
• Publication type
• Letter MeSH
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH

Intragenic rearrangements and sequence variants in the calmodulin-binding transcription activator 1 gene (CAMTA1) can result in a spectrum of clinical presentations, most notably congenital ataxia with or without intellectual disability. We describe for the first time a myoclonic dystonia-predominant phenotype associated with a novel CAMTA1 sequence variant. Furthermore, by identifying an additional, recurrent CAMTA1 sequence variant in an individual with a more typical neurodevelopmental disease manifestation, we contribute to the elucidation of phenotypic variability associated with CAMTA1 gene mutations.

• MeSH
• Adult MeSH
• Dystonic Disorders genetics   MeSH
• Phenotype MeSH
• Genetic Association Studies MeSH
• Humans MeSH
• Intellectual Disability genetics   MeSH
• Hearing Loss genetics   MeSH
• Codon, Nonsense * MeSH
• Vision Disorders genetics   MeSH
• Frameshift Mutation * MeSH
• Child, Preschool MeSH
• Calcium-Binding Proteins genetics   MeSH
• Pedigree MeSH
• Sequence Deletion * MeSH
• Exome Sequencing MeSH
• Trans-Activators genetics   MeSH
• Check Tag
• Adult MeSH
• Humans MeSH
• Male MeSH
• Child, Preschool MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH

The nine-amino-acid transactivation domains (9aaTAD) was identified in numerous transcription factors including Gal4, p53, E2A, MLL, c-Myc, N-Myc, and also in SP, KLF, and SOX families. Most of the 9aaTAD domains interact with the KIX domain of transcription mediators MED15 and CBP to activate transcription. The NFkB activation domain occupied the same position on the KIX domain as the 9aaTADs of MLL, E2A, and p53. Binding of the KIX domain is established by the two-point interaction involving 9aaTAD positions p3-4 and p6-7. The NFkB primary binding region (positions p3-4) is almost identical with MLL and E2A, but secondary NFkB binding region differs by the position and engages the distal NFkB region p10-11. Thus, the NFkB activation domain is five amino acids longer than the other 9aaTADs. The NFkB activation domain includes an additional region, which we called the Omichinski Insert extending activation domain length to 14 amino acids. By deletion, we demonstrated that Omichinski Insert is an entirely non-essential part of NFkB activation domain. In summary, we recognized the NFkB activation domain as prolonged 9aaTAD conserved in evolution from humans to amphibians.

• MeSH
• Transcriptional Activation MeSH
• Amino Acids * metabolism   MeSH
• Humans MeSH
• Tumor Suppressor Protein p53 * metabolism   MeSH
• NF-kappa B metabolism   MeSH
• Amino Acid Sequence MeSH
• Transcription Factors metabolism   MeSH
• Protein Binding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH