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Cancer Genomics & Proteomics 2023Angioleiomyoma is a benign tumor, occurs at any age, and arises most frequently in the lower extremities. Genetic information on angioleiomyomas is restricted to six...
BACKGROUND/AIM
Angioleiomyoma is a benign tumor, occurs at any age, and arises most frequently in the lower extremities. Genetic information on angioleiomyomas is restricted to six reported abnormal karyotypes, losses in chromosome 22 and gains in Xq found by comparative genomic hybridization, and mutation analysis of notch receptor 2 (NOTCH2), NOTCH3, platelet-derived growth factor receptor beta (PDGFRB), and mediator complex subunit 12 (MED12) in a few tumors. Herein, we report the genetic findings in another three angioleiomyomas.
MATERIALS AND METHODS
The tumors were examined using G-banding and karyotyping, RNA sequencing, reverse transcription-polymerase chain reaction, Sanger sequencing, and expression analysis.
RESULTS
The first tumor carried a t(4;5)(p12;q32) translocation resulting in fusion of the cardiac mesoderm enhancer-associated non-coding RNA (CARMN in 5q32) with the TXK tyrosine kinase gene (TXK in 4p12) leading to overexpression of TXK. To our knowledge, this is the first time that a recurrent chromosome translocation and its resulting fusion gene have been described in angioleiomyomas. The second tumor carried a four-way translocation, t(X;3;4;16)(q22;p11;q11;p13) which fused the myosin heavy chain 11 gene (MYH11 in 16p13) with intergenic sequences from Xq22 that mapped a few kilobase pairs distal to the insulin receptor substrate 4 gene (IRS4), resulting in enhanced IRS4 expression. The third angioleiomyoma carried another rearrangement of chromosome band Xq22, t(X;9)(q22;q32), as the sole cytogenetic aberration, but no material was available for further molecular investigation.
CONCLUSION
Our data, together with previously reported abnormal karyotypes in angioleiomyomas, show the presence of two recurrent genetic pathways in this tumor type: The first is characterized by presence of the translocation t(4;5)(p12;q32), which generates a CARMN::TXK chimera. The second is recurrent rearrangement of Xq22 resulting in overexpression of IRS4.
Topics: Humans; Angiomyoma; Comparative Genomic Hybridization; Chromosome Aberrations; Translocation, Genetic; Transcription Factors; Abnormal Karyotype
PubMed: 37889065
DOI: 10.21873/cgp.20405 -
Comparative Cytogenetics 2023An account is given of my development of techniques to obtain well-spread Giemsa-stained banded chromosome preparations. Apparent G-banding could be obtained following...
An account is given of my development of techniques to obtain well-spread Giemsa-stained banded chromosome preparations. Apparent G-banding could be obtained following very slight trypsin treatment of freshly prepared slides, but this banding was very fine (close-grained) and possibly not a reflection of chromosome structure. However, treatment of developing embryos with 5-fluorouridine produced a similar chromomere banding, which is therefore regarded as genuine. Steady accumulation of Fabricius, 1775 karyotypes has resulted in the production of an Atlas covering 62 of the 170 species known to occur in the Palaearctic. Chromosome polymorphisms involving pericentric inversions and addition of extra C-banding regions have been found, as well as small B-chromosomes in a few species. In general, karyotypes have proved very useful in establishing the limits of individual species. Parthenogenesis involving triploidy has been found in two species. Karyotypes of experimentally produced hybrids have revealed irregularities in chromosome condensation.
PubMed: 38284104
DOI: 10.3897/compcytogen.17.112831 -
Plants (Basel, Switzerland) Jul 2023The genus Medik. (Subfamily: Scilloideae) has a narrow distribution in India and several overlapping morphological traits make the genus taxonomically challenging at...
The genus Medik. (Subfamily: Scilloideae) has a narrow distribution in India and several overlapping morphological traits make the genus taxonomically challenging at the species level. Cytogenetic characterization can provide additional taxonomic data and can be used to evaluate genetic diversity at the species level. We have accomplished comparative karyotype analysis and fluorescence banding patterns using 4'-6-Diamidino-2-phenylindole (DAPI) and Chromomycin A (CMA) in five Indian species for the first time. The karyotypes of and exhibited similar fluorochrome banding profiles. However, , differ distinctly in their karyotypes. In all taxa, CMA/DAPI or DAPI (GC-rich) constitutive heterochromatin was located at the constriction region or terminal satellite of the nucleolar chromosome. DAPI/CMA or CMA (AT-rich) heterochromatin dominates in . However, shows a distinct variation in fluorochrome banding pattern from all other species. The distribution of CMA and DAPI bands is a reflection of heterochromatin composition and variations acquired by different species. This characterization can be used to assess phylogenetic relationships in the understudied genus and may serve as a basis for other genomic analyses and evolutionary studies.
PubMed: 37447096
DOI: 10.3390/plants12132534 -
Animals : An Open Access Journal From... Sep 2023This study presents a novel approach that combines next-generation sequencing (NGS) and cytogenetic technologies for identifying chromosomes involved in chromosomal...
This study presents a novel approach that combines next-generation sequencing (NGS) and cytogenetic technologies for identifying chromosomes involved in chromosomal anomalies. This research focuses on a chromosome anomaly discovered in male Alpine Grey cattle, as well as two previously reported cases of reciprocal translocations (rcps), namely rcp(9;11) and rcp(4;7). Abnormal chromosomes from Alpine Grey cattle were microdissected from conventional preparations, and the amplified products were sequenced using NGS. The sequencing reads were then mapped to the reference genome, and the leverage effect was calculated to identify abnormal reads/Mb values. The result revealed the presence of rob(26;29), which was further confirmed through traditional cytogenetic analyses such as Giemsa staining, CBA-banding, RBA-banding, and FISH techniques. Furthermore, the feasibility of this approach on preserved metaphases was demonstrated through analysis of old slides from previously characterized cases. The study highlights the challenges involved in identifying and characterizing chromosomal aberrations in bovine species and offers a potential solution for analyzing historical anomalies when fresh blood material is unavailable. The combination of NGS and cytogenetic techniques provides a cost-effective and reliable approach for characterizing chromosomal anomalies in various species, including those identified before the availability of modern banding technologies and FISH mapping using specific molecular markers.
PubMed: 37835624
DOI: 10.3390/ani13193018 -
Pathology Oncology Research : POR 2024Intramuscular myxomas are benign tumors that are challenging to diagnose, especially on core needle biopsies. Acquired chromosomal aberrations and pathogenic variants...
Intramuscular myxomas are benign tumors that are challenging to diagnose, especially on core needle biopsies. Acquired chromosomal aberrations and pathogenic variants in codon 201 or codon 227 in GNAS complex locus gene () have been reported in these tumors. Here we present our genetic findings in a series of 22 intramuscular myxomas. The tumors were investigated for the presence of acquired chromosomal aberrations using G-banding and karyotyping. Pathogenic variants in codon 201 or codon 227 of were assessed using direct cycle Sanger sequencing and Ion AmpliSeq Cancer Hotspot Panel v2 methodologies. Eleven tumors carried chromosomal abnormalities. Six tumors had numerical, four had structural, and one had both numerical and structural chromosomal aberrations. Gains of chromosomes 7 and 8 were the most common abnormalities being found in five and four tumors respectively. Pathogenic variants in were detected in 19 myxomas (86%) with both methodologies. The detected pathogenic variants were p.R201H in nine cases (seven with abnormal and two with normal karyotypes), p.R201C in five cases, all with normal karyotypes, p.R201S in three cases (two with abnormal and one with normal karyotype), p.R201G in one case with a normal karyotype, and p.Q227E in one case with a normal karyotype. Firstly, our data indicate a possible association between chromosomal abnormalities and pathogenic variants in intramuscular myxomas. Secondly, the presence of the rare pathogenic variants R201S, p.R201G and p.Q227E in 26% (5 out of 19) of myxomas with pathogenic variants shows that methodologies designed to detect only the common "hotspot" of p.R201C and p.R201H will give false negative results. Finally, a comparison between Ion AmpliSeq Cancer Hotspot Panel v2 and direct cycle Sanger sequencing showed that direct cycle Sanger sequencing provides a quick, reliable, and relatively cheap method to detect pathogenic variants, matching even the most cutting-edge sequencing methods.
Topics: Humans; Mutation; Chromosome Aberrations; Muscle Neoplasms; Codon; Myxoma
PubMed: 38317844
DOI: 10.3389/pore.2024.1611553 -
Blood Research Feb 2024Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the... (Review)
Review
Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diagnostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limitations, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research. This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.
PubMed: 38485792
DOI: 10.1007/s44313-024-00001-1 -
Animals : An Open Access Journal From... Jun 2023We performed a molecular and phylogenetic analysis and a comparative cytogenetic study with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding +...
We performed a molecular and phylogenetic analysis and a comparative cytogenetic study with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, + fluorochromes on several samples. The phylogenetic inference retrieved two main clades, the first comprises , and , while the second includes , and . The available samples of form two different clades (here named clade A and clade B), which probably deserve a taxonomic re-evaluation. We found a karyological variability in in terms of chromosome number (2n = 40-42), morphology, location of NORs, and heterochromatin distribution pattern. and clade A and B showed a karyotype of 2n = 40 mostly telocentric chromosomes. Pairs 1 and 6 were metacentric in clade A and B, while pair 1 was composed of subtelocentric/submetacentric elements in In contrast, displayed a karyotype with 2n = 42 only telocentric chromosomes. NORs were on the first chromosome pair in , and on the second pair in . Adding our data to those available from the literature on evolutionarily related species, we highlight that the chromosome diversification in the genus probably proceeded towards a progressive reduction in the chromosome number and the formation of metacentric elements.
PubMed: 37443866
DOI: 10.3390/ani13132068 -
Vavilovskii Zhurnal Genetiki I Selektsii Oct 2023Introgressive hybridization is the main method of broadening the genetic diversity of bread wheat. Wild barley Hordeum marinum ssp. gussoneanum Hudson (2n = 4x = 28) has...
Development and characterization of a line with substitution of chromosome 4B of wheat Triticum aestivum L. on chromosome 4Hmar of wild barley Hordeum marinum ssp. gussoneanum (4x).
Introgressive hybridization is the main method of broadening the genetic diversity of bread wheat. Wild barley Hordeum marinum ssp. gussoneanum Hudson (2n = 4x = 28) has useful agronomical traits, such as high resistance to stress factors, that could be a potential source of new genes for bread wheat improvement. This study aimed to evaluate the possibility of introgression of H. marinum chromosomes into the genome of bread wheat using an incomplete amphiploid H. marinum ssp. gussoneanum (4x)-T. aestivum (Pyrotrix 28) (2n = 54) carrying the cytoplasm of wild barley. For this purpose, we crossed the line of bread wheat variety Pyrotrix 28 with an incomplete amphiploid, and then selected cytogenetically stable 42-chromosome plants with a high level of fertility in hybrid progeny. Genomic in situ hybridization (GISH) revealed a pair of H. marinum chromosomes in the genome of these plants. C- banding analysis confirmed that bread wheat chromosome 4B was replaced by wild barley chromosome 4Hmar. SSR markers Xgwm368 and Xgwm6 confirmed the absence of chromosome 4B, and EST markers BAWU808 and BAW112 identified chromosome 4Hmar in the genome of the isolated disomic wheat-barley substitution line. The study of this line showed that the substitution of chromosome 4B with chromosome 4Hmar resulted in a change of some morphological traits. It included intense anthocyanin coleoptile coloration, specific for H. marinum, as well as a lack of purple coloration of the ears in the leaf sheath, specific for Pyrotrix 28. Line 4Hmar(4B) showed increased performance for several traits, including plant height, number of spikes and tillers per plant, spikelet and grain number in the main spike, grain number per plant, but it had decreased values of 1000-grain weight compared to wheat. Cytogenetic stability and fertility of line 4Hmar(4B) indicated a high compensation ability of barley 4Hmar for wheat chromosome 4B and confirmed their homeology.
PubMed: 38213465
DOI: 10.18699/VJGB-23-66