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Moysset I, Castrejon N, Garcia-Herrera A, Castillo P, Marginet M, Teixido C, Podlipnik S, Albero-Gonzalez R, Montironi C, Navarro J, Rovira C, Puig S, Carrera C, Alos L. Restrospective reappraisal of the prognostic classification of spitzoid melanocytic neoplasms after BRAF and NRAS mutation characterisation: a single institution experience. Histopathology 2024; 84:1154-1166. [PMID: 38409889 DOI: 10.1111/his.15160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
AIMS The current WHO classification of melanocytic tumours excludes neoplasms showing BRAF or NRAS mutations from the Spitz category. This study aimed to review and reclassify atypical melanocytic tumours with spitzoid morphological features diagnosed between 2009 and 2021 in our hospital after expanding the molecular profile, including BRAF and NRAS mutations in all cases. METHODS AND RESULTS A total of 71 neoplasms showing spitzoid features (Spitz-like) and atypia were included. The risk of progression of tumours was first studied by integrating the morphology, immunohistochemistry (p16, Ki67, HMB45 and PRAME) and fluorescence in-situ hybridisation (FISH) results (melanoma multiprobe and 9p21). In a second step, after expanding the molecular study, including BRAF and NRAS mutational status, the neoplasms were finally classified into four subgroups: atypical Spitz tumour (AST, n = 45); BRAF-mutated naevus/low-grade melanocytoma with spitzoid morphology (BAMS, n = 2); Spitz melanoma (SM, n = 14); and BRAF or NRAS mutated melanoma with spitzoid features (MSF, n = 10). Follow-up of patients revealed uneventful results for AST and BAMS. Only one SM presented lymph node metastasis after 134 months. Conversely, patients with MSF showed an unfavourable outcome: three developed lymph node metastases after a mean time of 22 months, with one patient presenting distant metastasis and dying of the disease 64 months from diagnosis. The progression-free survival showed significant differences between the four groups of spitzoid tumours (P < 0.001) and between both melanoma subtypes (P = 0.012). CONCLUSIONS The classification and prognostication of atypical neoplasms with spitzoid features requires the integration of histomorphology with the molecular investigation of tumours, which should include BRAF and NRAS mutational status.
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Affiliation(s)
- Irene Moysset
- Department of Pathology, Consorci Sanitari Integral, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Natalia Castrejon
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Adriana Garcia-Herrera
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Paola Castillo
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Marta Marginet
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Molecular Biology Core, Hospital Clinic Barcelona, Barcelona, Spain
| | | | - Raquel Albero-Gonzalez
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Carla Montironi
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- Molecular Biology Core, Hospital Clinic Barcelona, Barcelona, Spain
| | - Judit Navarro
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Carlota Rovira
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Susana Puig
- University of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- University of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Llucia Alos
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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Dashti NK, Jebastin Thangaiah J, Gliem T, Knutson D, Kloft-Nelson S, Armstrong SM, Bakhshwin A, Greipp P, Fritchie KJ. MDM2 Amplification Status in a Cohort of Well-Characterized Myxofibrosarcoma: A Clinicopathologic Analysis of 22 Tumors. Int J Surg Pathol 2024; 32:478-485. [PMID: 37501528 DOI: 10.1177/10668969231186930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Myxofibrosarcomas (MFS) present as slowly enlarging superficial masses in elderly patients. Even though these tumors fail to exhibit a distinct immunophenotype, diagnosis is straightforward when they present in subcutaneous tissue. Intramuscular MFS, however, are more challenging to diagnose as the differential also includes dedifferentiated liposarcoma with myxoid features. The vast majority of dedifferentiated liposarcomas show MDM2 amplification, whereas limited data exists as to the MDM2 status of MFS. We sought to explore the rate of MDM2 amplification in cases of classic MFS. Our archives were searched for MFS; only subcutaneous well-sampled resections were included. FISH for MDM2 amplification was performed on each tumor. A cohort of myxoid dedifferentiated liposarcoma resections was studied for comparison. Twenty-two MFS arose in patients aged 44 to 85 years. All tumors contained an infiltrative population of atypical cells embedded in a myxoid stroma with curvilinear blood vessels. MDM2 amplification by FISH was identified in 3 (of 22; 14%) tumors. Available follow up on 17 patients (range 1-96 months; median 13 months) revealed 6 patients with local recurrence and 1 with distant metastasis. Of 3 patients with MDM2- amplified MFS, 1 experienced recurrence and died of unrelated causes, while the second was alive without disease 12 months after diagnosis. Even though the rate of MDM2 amplification by FISH in MFS appears to be low, a subset of cases may show this genetic alteration, which pathologists should be aware of to avoid misclassification as myxoid dedifferentiated liposarcomas. Further studies are necessary to determine if amplification status adds prognostic value.
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Affiliation(s)
- Nooshin K Dashti
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Troy Gliem
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Darlene Knutson
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Sara Kloft-Nelson
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Susan M Armstrong
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ahmed Bakhshwin
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patricia Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Karen J Fritchie
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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3
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Bernegossi AM, Galindo DJ, Peres PHF, Vozdova M, Cernohorska H, Kubickova S, Kadlcikova D, Rubes J, Duarte JMB. Comparative karyotype analysis of the red brocket deer (M. americana sensu lato and M. rufa) complex: evidence of drastic chromosomal evolution and implications on speciation process. J Appl Genet 2024:10.1007/s13353-024-00861-4. [PMID: 38662189 DOI: 10.1007/s13353-024-00861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Chromosomal rearrangements are often associated with playing a role in the speciation process. However, the underlying mechanism that favors the genetic isolation associated with chromosomal changes remains elusive. In this sense, the genus Mazama is recognized by its high level of karyotype diversity among species with similar morphology. A cryptic species complex has been identified within the genus, with the red brocket deer (Mazama americana and Mazama rufa) being the most impressive example. The chromosome variation was clustered in cytotypes with diploid numbers ranging from 42 to 53 and was correlated with geographical location. We conducted an analysis of chromosome evolution of the red brocket deer complex using comparative chromosome painting and Bacterial Artificial Chromosome (BAC) clones among different cytotypes. The aim was to deepen our understanding of the karyotypic relationships within the red brocket, thereby elucidating the significant chromosome variation among closely related species. This underscores the significance of chromosome changes as a key evolutionary process shaping their genomes. The results revealed the presence of three distinct cytogenetic lineages characterized by significant karyotypic divergence, suggesting the existence of efficient post-zygotic barriers. Tandem fusions constitute the main mechanism driving karyotype evolution, following a few centric fusions, inversion X-autosomal fusions. The BAC mapping has improved our comprehension of the karyotypic relationships within the red brocket deer complex, prompting questions regarding the role of these changes in the speciation process. We propose the red brocket as a model group to investigate how chromosomal changes contribute to isolation and explore the implications of these changes in taxonomy and conservation.
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Affiliation(s)
- Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - David Javier Galindo
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
- Laboratory of Animal Reproduction, Faculty of Veterinary Medicine, National University of San Marcos, San Borja, 15021, Lima, Peru.
| | - Pedro Henrique Faria Peres
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Dita Kadlcikova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - José Maurício Barbanti Duarte
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
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Cardoso PM, Hill LJ, Villela HDM, Vilela CLS, Assis JM, Rosado PM, Rosado JG, Chacon MA, Majzoub ME, Duarte GAS, Thomas T, Peixoto RS. Localization and symbiotic status of probiotics in the coral holobiont. mSystems 2024:e0026124. [PMID: 38606974 DOI: 10.1128/msystems.00261-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome. IMPORTANCE Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.
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Affiliation(s)
- P M Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - L J Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H D M Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - C L S Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J M Assis
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - P M Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - J G Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - M A Chacon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M E Majzoub
- Center for Marine Science and Innovation; School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - G A S Duarte
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - T Thomas
- Center for Marine Science and Innovation; School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - R S Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Biology Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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5
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Masui K, Onizuka H, Muragaki Y, Kawamata T, Kurata A, Komori T. Intratumoral heterogeneity of CDKN2A deletions in IDH-mutant astrocytoma. Brain Tumor Pathol 2024:10.1007/s10014-024-00484-x. [PMID: 38597998 DOI: 10.1007/s10014-024-00484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan.
| | - Hiromi Onizuka
- Department of Pathology, Kyorin University, Tokyo, Japan
| | - Yoshihiro Muragaki
- Center for Advanced Medical Engineering Research and Development, Kobe University, Hyogo, Japan
- Department of Neurosurgery, Tokyo Women's Medical University Hospital, Tokyo, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University Hospital, Tokyo, Japan
| | - Atsushi Kurata
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
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Sharma D, Wilson C, Kumar S, Ghose S, Sahoo R, Sharawat SK. Does presence of complex translocations involving BCR::ABL1 in chronic myeloid leukemia affect the response rate to tyrosine kinase inhibitors? A systematic review of the literature. Ann Diagn Pathol 2024; 71:152303. [PMID: 38636337 DOI: 10.1016/j.anndiagpath.2024.152303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/20/2024]
Abstract
Philadelphia (Ph) chromosome (9;22)(q34;q11) comprises 90-95 % of chronic myeloid leukemia (CML), while 5-10 % of CML have translocations involving three or more chromosomes. The outcome of treating patients harbouring complex Ph-positive cytogenetics with tyrosine kinase inhibitors (TKI) is unclear. In the present systematic review, we aim to summarise the response of patients with complex Ph-positive cytogenetics to treatment with TKI therapy. We collated all available literature from databases such as PubMed, Google Scholar, Web of Science database, Cochrane library, Scopus and Embase (up until January 31st, 2024), which describe cases of patients with CML, harbouring complex Ph-positive variations (three and four-way translocations), and summarised their response to TKI therapy. The studies were screened for the following criteria: documented TKI intervention and outcome (whether CR was achieved). Studies that did not report the same, were excluded. Additionally, we report a case from our center of a 55-year-old patient with CML, positive for the Ph-chromosome, harbouring a three-way translocation involving chromosome 15 i.e. 46XX, t(9;15;22) (q34;p11;q11). Identification of BCR::ABL and involvement of chromosome 15 was carried out using conventional cytogenetics, fluorescence in situ hybridization (FISH), and quantitative PCR (qPCR). Based on the inclusion criteria, a total of 15 studies were included from which a total of 87 cases were covered. Overall, we identified 38 unique complex three- and four-way translocations across 87 Ph-positive cases and found that 85 patients with complex Ph-positive cytogenetics achieved complete remission upon treatment and did not appear to have a lesser response to TKI therapy.
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Affiliation(s)
- Diwakar Sharma
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Christine Wilson
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sampa Ghose
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Sahoo
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India.
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Seiffer S, Brendler J, Schulz A, Ricken A. Reliable detection of RNA in hippocampus sections of mice by FISH up to a post-mortem delay of 24 h. Histochem Cell Biol 2024:10.1007/s00418-024-02277-x. [PMID: 38582805 DOI: 10.1007/s00418-024-02277-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Proteins can be successfully localized in post-mortem (PM) brain tissue sections if the time until PM tissue sampling is not too long. In this study, we show that this also applies to the localization of RNA and in particular to the RNA of microglia-specific receptor proteins using the probes and the RNAscope™ Multiplex Fluorescent Detection Kit v2 from Advanced Cell Diagnostics. Brains were removed from killed mice after different PM delays and processed into paraffin sections. In sections of brains from animals whose cadavers had been kept at room temperature (21 °C) before tissue removal, ubiquitously expressed RNAs of genes with low to high expression levels (Polr2a, PPIB, and UBC) were reliably detected in the brain sections even if tissue removal was delayed by up to 48 h. In addition, microglia-specific G protein-coupled receptor RNA (Gpr34, P2ry12) could be reliably assigned to microglia by simultaneous labeling of the microglia with microglia-specific antibodies (Iba1 or P2ry12). Only after a delay of 48 h until tissue removal were the receptor RNA signals significantly lower. The reduction in receptor RNA signals could be delayed if the animal cadavers were stored at 4 °C until the brains were removed. Tissue sections of PM brain samples allow the spatial and cellular localization of specific RNA, at least if the sampling takes place within the first 24 h of PM.
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Affiliation(s)
- Sophie Seiffer
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Jana Brendler
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Angela Schulz
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Albert Ricken
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany.
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Cheng D, Lu CF, Gong F, Du J, Yuan S, Luo KL, Tan YQ, Lu GX, Lin G. A case report of a normal fertile woman with 46,XX/46,XY somatic chimerism reveals a critical role for germ cells in sex determination. Hum Reprod 2024; 39:849-855. [PMID: 38420683 DOI: 10.1093/humrep/deae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
Individuals with 46,XX/XY chimerism can display a wide range of characteristics, varying from hermaphroditism to complete male or female, and can display sex chromosome chimerism in multiple tissues, including the gonads. The gonadal tissues of females contain both granulosa and germ cells. However, the specific sex chromosome composition of the granulosa and germ cells in 46,XX/XY chimeric female is currently unknown. Here, we reported a 30-year-old woman with secondary infertility who displayed a 46,XX/46,XY chimerism in the peripheral blood. FISH testing revealed varying degrees of XX/XY chimerism in multiple tissues of the female patient. Subsequently, the patient underwent preimplantation genetic testing (PGT) treatment, and 26 oocytes were retrieved. From the twenty-four biopsied mature oocytes, a total of 23 first polar bodies (PBs) and 10 second PBs were obtained. These PBs and two immature metaphase I (MI) oocytes only displayed X chromosome signals with no presence of the Y, suggesting that all oocytes in this chimeric female were of XX germ cell origin. On the other hand, granulosa cells obtained from individual follicles exhibited varied proportions of XX/XY cell types, and six follicles possessed 100% XX or XY granulosa cells. A total of 24 oocytes were successfully fertilized, and 12 developed into blastocysts, where 5 being XY and 5 were XX. Two blastocysts were transferred with one originating from an oocyte aspirated from a follicle containing 100% XY granulosa cells. This resulted in a twin pregnancy. Subsequent prenatal diagnosis confirmed normal male and female karyotypes. Ultimately, healthy boy-girl twins were delivered at full term. In summary, this 46,XX/XY chimerism with XX germ cells presented complete female, suggesting that germ cells may exert a significant influence on the sexual determination of an individual, which provide valuable insights into the intricate processes associated with sexual development and reproduction.
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Affiliation(s)
- Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Chang-Fu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Fei Gong
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Juan Du
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Shimin Yuan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Ke-Li Luo
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Yue-Qiu Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Guang-Xiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
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Gagnon MF, Bruehl FK, Sill DR, Meyer RG, Greipp PT, Hoppman NL, Xu X, Baughn LB, Peterson JF, McPhail ED, Ketterling RP, King RL. Cytogenetic and pathologic characterization of MYC-rearranged B-cell lymphomas in pediatric and young adult patients. J Hematop 2024:10.1007/s12308-024-00579-6. [PMID: 38561469 DOI: 10.1007/s12308-024-00579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
MYC-rearranged B-cell lymphoma (BCL) in the pediatric/young adult (YA) age group differs substantially in disease composition from adult cohorts. However, data regarding the partner genes, concurrent rearrangements, and ultimate diagnoses in these patients is scarce compared to that in adult cohorts. We aimed to characterize the spectrum of MYC-rearranged (MYC-R) mature, aggressive BCL in the pediatric/YA population. A retrospective study of morphologic, immunophenotypic, and fluorescence in situ hybridization (FISH) results of patients age ≤ 30 years with suspected Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL) or high-grade B-cell lymphoma (HGBCL), and a MYC-R by FISH between 2013-2022 was performed. Two-hundred fifty-eight cases (129 (50%) pediatric (< 18 years) and 129 (50%) YA (18-30 years)) were included. Most MYC-R BCL in pediatric (89%) and YA (66%) cases were BL. While double-hit (DH) cytogenetics (MYC with BCL2 and/or BCL6-R, HGBCL-DH) was rare in the pediatric population (2/129, 2%), HGBCL-DH increased with age and was identified in 17/129 (13%) of YA cases. Most HGBCL-DH had MYC and BCL6-R, while BCL2-R were rare in both groups (3/258, 1%). MYC-R without an IG partner was more common in the YA group (14/116 (12%) vs 2/128 (2%), p = 0.001). The pediatric to YA transition is characterized by decreasing frequency in BL and increasing genetic heterogeneity of MYC-R BCL, with emergence of DH-BCL with MYC and BCL6-R. FISH to evaluate for BCL2 and BCL6 rearrangements is likely not warranted in the pediatric population but should continue to be applied in YA BCL.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Frido K Bruehl
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel R Sill
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen D McPhail
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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10
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Conde E, Hernandez S, Rodriguez Carrillo JL, Martinez R, Alonso M, Curto D, Jimenez B, Caminoa A, Benito A, Garrido P, Clave S, Arriola E, Esteban-Rodriguez I, De Castro J, Sansano I, Felip E, Rojo F, Dómine M, Abdulkader I, Garcia-Gonzalez J, Teixido C, Reguart N, Compañ D, Insa A, Mancheño N, Palanca S, Juan-Vidal O, Baixeras N, Nadal E, Cebollero M, Calles A, Martin P, Salas C, Provencio M, Aranda I, Massuti B, Lopez-Vilaro L, Majem M, Paz-Ares L, Lopez-Rios F. RET Fusion Testing in Patients With NSCLC: The RETING Study. JTO Clin Res Rep 2024; 5:100653. [PMID: 38525319 PMCID: PMC10957499 DOI: 10.1016/j.jtocrr.2024.100653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction RET inhibitors with impressive overall response rates are now available for patients with NSCLC, yet the identification of RET fusions remains a difficult challenge. Most guidelines encourage the upfront use of next-generation sequencing (NGS), or alternatively, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) when NGS is not possible or available. Taken together, the suboptimal performance of single-analyte assays to detect RET fusions, although consistent with the notion of encouraging universal NGS, is currently widening some of the clinical practice gaps in the implementation of predictive biomarkers in patients with advanced NSCLC. Methods This situation prompted us to evaluate several RET assays in a large multicenter cohort of RET fusion-positive NSCLC (n = 38) to obtain real-world data. In addition to RNA-based NGS (the criterion standard method), all positive specimens underwent break-apart RET FISH with two different assays and were also tested by an RT-PCR assay. Results The most common RET partners were KIF5B (78.9%), followed by CCDC6 (15.8%). The two RET NGS-positive but FISH-negative samples contained a KIF5B(15)-RET(12) fusion. The three RET fusions not identified with RT-PCR were AKAP13(35)-RET(12), KIF5B(24)-RET(9) and KIF5B(24)-RET(11). All three false-negative RT-PCR cases were FISH-positive, exhibited a typical break-apart pattern, and contained a very high number of positive tumor cells with both FISH assays. Signet ring cells, psammoma bodies, and pleomorphic features were frequently observed (in 34.2%, 39.5%, and 39.5% of tumors, respectively). Conclusions In-depth knowledge of the advantages and disadvantages of the different RET testing methodologies could help clinical and molecular tumor boards implement and maintain sensible algorithms for the rapid and effective detection of RET fusions in patients with NSCLC. The likelihood of RET false-negative results with both FISH and RT-PCR reinforces the need for upfront NGS in patients with NSCLC.
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Affiliation(s)
- Esther Conde
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Susana Hernandez
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | | | - Marta Alonso
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Daniel Curto
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | | | - Pilar Garrido
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Sergi Clave
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | | | - Javier De Castro
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigacion Sanitaria del Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Irene Sansano
- Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | | | - Federico Rojo
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Manuel Dómine
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Ihab Abdulkader
- Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Cristina Teixido
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Noemi Reguart
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | | | - Amelia Insa
- Hospital Clinico Universitario, Valencia, Spain
| | - Nuria Mancheño
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sarai Palanca
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Nuria Baixeras
- Hospital Universitari de Bellvitge, L’Hospitalet, Barcelona, Spain
| | - Ernest Nadal
- Catalan Institute of Oncology, L’Hospitalet, Barcelona, Spain
| | - Maria Cebollero
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Antonio Calles
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Paloma Martin
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Clara Salas
- Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Ignacio Aranda
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Bartomeu Massuti
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | | | | | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Fernando Lopez-Rios
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
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11
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Cardinali I, Ceccarelli M. Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants. R Soc Open Sci 2024; 11:240035. [PMID: 38601032 PMCID: PMC11004676 DOI: 10.1098/rsos.240035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
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12
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Jedraszak G, Jobic F, Receveur A, Bilan F, Gilbert-Dussardier B, Tiffany B, Missirian C, Willems M, Odent S, Lucas J, Dubourg C, Schaefer E, Scheidecker S, Lespinasse J, Goldenberg A, Guerrot AM, Joly-Helas G, Chambon P, Le Caignec C, David A, Coutton C, Satre V, Vieville G, Amblard F, Harbuz R, Sanlaville D, Till M, Vincent-Delorme C, Colson C, Andrieux J, Naudion S, Toutain J, Rooryck C, de Fréminville B, Prieur F, Daire VC, Amram D, Kleinfinger P, Schulze MB, Raabe-Meyer G, Courage C, Lemke J, Stefanou EG, Loretta T, Emmanouil M, Tzeli SK, Sodowska H, Anderson J, Nandini A, Copin H, Garçon L, Liehr T, Morin G. Cat eye syndrome: Clinical, cytogenetics and familial findings in a large cohort of 43 patients highlighting the importance of congenital heart disease and inherited cases. Am J Med Genet A 2024; 194:e63476. [PMID: 37974505 DOI: 10.1002/ajmg.a.63476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023]
Abstract
Cat Eye Syndrome (CES) is a rare genetic disease caused by the presence of a small supernumerary marker chromosome derived from chromosome 22, which results in a partial tetrasomy of 22p-22q11.21. CES is classically defined by association of iris coloboma, anal atresia, and preauricular tags or pits, with high clinical and genetic heterogeneity. We conducted an international retrospective study of patients carrying genomic gain in the 22q11.21 chromosomal region upstream from LCR22-A identified using FISH, MLPA, and/or array-CGH. We report a cohort of 43 CES cases. We highlight that the clinical triad represents no more than 50% of cases. However, only 16% of CES patients presented with the three signs of the triad and 9% not present any of these three signs. We also highlight the importance of other impairments: cardiac anomalies are one of the major signs of CES (51% of cases), and high frequency of intellectual disability (47%). Ocular motility defects (45%), abdominal malformations (44%), ophthalmologic malformations (35%), and genitourinary tract defects (32%) are other frequent clinical features. We observed that sSMC is the most frequent chromosomal anomaly (91%) and we highlight the high prevalence of mosaic cases (40%) and the unexpectedly high prevalence of parental transmission of sSMC (23%). Most often, the transmitting parent has mild or absent features and carries the mosaic marker at a very low rate (<10%). These data allow us to better delineate the clinical phenotype associated with CES, which must be taken into account in the cytogenetic testing for this syndrome. These findings draw attention to the need for genetic counseling and the risk of recurrence.
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Affiliation(s)
- Guillaume Jedraszak
- Constitutional Genetics Laboratory, University Hospital of Amiens, Amiens, France
- UR4666, University of Picardy Jules Verne, Amiens, France
| | - Florence Jobic
- Clinical Genetics Unit, University Hospital of Amiens, Amiens, France
| | - Aline Receveur
- Constitutional Genetics Laboratory, University Hospital of Amiens, Amiens, France
| | - Frédéric Bilan
- Genetics Laboratory, University Hospital of Poitiers, Poitiers, France
| | | | - Busa Tiffany
- Medical Genetics Unit, University Hospital of Marseille, Marseille, France
| | - Chantal Missirian
- Cytogenetics Laboratory, University Hospital of Marseille, Marseille, France
| | - Marjolaine Willems
- Medical Genetics Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Sylvie Odent
- Medical Genetics Unit, University Hospital of Rennes, Rennes, France
| | - Josette Lucas
- Genetics Laboratory, University Hospital of Rennes, Rennes, France
| | | | - Elise Schaefer
- Clinical Genetics Unit, University Hospital of Strasbourg, Strasbourg, France
| | | | | | - Alice Goldenberg
- Clinical Genetics Unit, University Hospital of Rouen, Rouen, France
| | | | | | - Pascal Chambon
- Cytogenetics Laboratory, University Hospital of Rouen, Rouen, France
| | - Cédric Le Caignec
- Medical Gentics Unit, University Hospital of Toulouse, Toulouse, France
| | - Albert David
- Clinical Genetics Unit, University Hospital of Nantes, Nantes, France
| | - Charles Coutton
- Cytogenetics Laboratory, University Hospital of Grenoble & INSERM U1209 Institute for Advanced Biosciences, University of Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Cytogenetics Laboratory, University Hospital of Grenoble & INSERM U1209 Institute for Advanced Biosciences, University of Grenoble Alpes, Grenoble, France
| | - Gaëlle Vieville
- Cytogenetics Laboratory, University Hospital of Grenoble, Grenoble, France
| | - Florence Amblard
- Cytogenetics Laboratory, University Hospital of Grenoble, Grenoble, France
| | - Radu Harbuz
- Cytogenetics Laboratory, University Hospital of Grenoble, Grenoble, France
| | | | - Marianne Till
- Cytogenetics Laboratory, University Hospital of Lyon, Bron, France
| | - Catherine Vincent-Delorme
- Catherine Vincent Delorme, Clinical Genetics Unit Guy Fontaine, University Hospital of Lille, Lille, France
| | - Cindy Colson
- Catherine Vincent Delorme, Clinical Genetics Unit Guy Fontaine, University Hospital of Lille, Lille, France
| | - Joris Andrieux
- Molecular Genetics Institute, University hospital of Lille, Lille, France
| | - Sophie Naudion
- Clinical Genetics Unit, University Hospital of Bordeaux, Bordeaux, France
| | - Jérome Toutain
- Clinical Genetics Unit, University Hospital of Bordeaux, Bordeaux, France
| | - Caroline Rooryck
- Medical Genetics Laboratory, University Hospital of Bordeaux, Bordeaux, France
| | | | - Fabienne Prieur
- Medical Genetics Unit, University Hospital of Saint-Etienne, Saint Etienne, France
| | | | - Daniel Amram
- Clinicial Genetics Unit, University Hospital of Creteil, Creteil, France
| | | | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Johannes Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Eunice G Stefanou
- Cytogenetics Unit, Laboratory of Medical Genetics, University General Hospital of Patras, Patras, Greece
| | - Thomaidis Loretta
- Developmental Assessment Unit, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Sophia Kitsiou Tzeli
- Department of Medical Genetics, National and Kapodistrian University of Athens, Athens, Greece
| | - Henryka Sodowska
- Niepubliczny Zakład Opieki Zdrowotne "Genom", Ruda Slaska, Poland
| | - Jasen Anderson
- Cytogenetics Department, Sullivan and Nicolaides Pathology, Taringa, Queensland, Australia
| | - Adayapalam Nandini
- Department of Cytogenetics, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Henri Copin
- Constitutional Genetics Laboratory, University Hospital of Amiens, Amiens, France
| | - Loïc Garçon
- Constitutional Genetics Laboratory, University Hospital of Amiens, Amiens, France
- UR4666, University of Picardy Jules Verne, Amiens, France
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Gilles Morin
- Clinical Genetics Unit, University Hospital of Amiens, Amiens, France
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13
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Wu J, Cao CZ, Cui HL, Du G, Shi HZ, Liang J, Guo L, Wang YC, Zhang J, Zhou AP, Li CL, Zheng S, Shou JZ. Prognosis and Clinicopathological Characters of Adult TFEB-Altered Renal Cell Carcinoma: A Single Center Experience of 18 Cases. Clin Genitourin Cancer 2024; 22:261-268.e3. [PMID: 38104031 DOI: 10.1016/j.clgc.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023]
Abstract
INTRODUCTION TFEB-altered renal cell carcinoma (RCC) is a rare entity characterized by the rearrangement of the TFEB gene or TFEB amplified. The therapeutic implications and long-term survival of TFEB-altered RCC remain unclear, especially for metastatic cases. MATERIALS AND METHODS The current study initially enrolled 7604 consecutive RCC patients at our center and a total of 248 patients were selected for FISH and immunohistochemistry (IHC) analysis. Eventually, eighteen TFEB-altered RCC patients were identified. We then reported the clinical, morphological, IHC, and radiological features of these cases. RESULTS The median age at initial diagnosis was 45 years, ranging from 18 years to 66 years. The majority of the TFEB-altered RCC patients were male (61.1%), with localized disease (T1-2N0M0, 77.8%). The median split TFEB fluorescent signal was 24%, ranging from 15%-80%. The morphological characteristics of TFEB-altered RCC were variable, with acinar, papillary, solid, or nest patterns. IHC and magnetic resonance imaging features of TFEB-altered RCC were nonspecific. Nine patients with localized disease received partial nephrectomy and five patients with localized disease received radical nephrectomy. During the median follow-up of 67 months, no signs of recurrence or metastasis were found in these patients. Two patients had distant metastasis and received axitinib plus PD-1 immunotherapy. One of them died at 40-month follow-up and another still alive at 88-month follow-up. CONCLUSION TFEB-altered RCC is an extremely rare variant, exhibited mixed morphological characteristics. The radiological feature lack specificity, resembling clear cell RCC or papillary RCC. Genetic analyses including FISH analysis is crucial in the diagnosis of TFEB-altered RCC. For localized TFEB-altered RCC, both radical nephrectomy and partial nephrectomy conferred satisfactory prognosis. For metastatic TFEB-altered RCC, immunotherapy-based drug combinations could be a promising treatment strategy.
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Affiliation(s)
- Jie Wu
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chuan-Zhen Cao
- Department of Urology, China-Japan Friendship Hospital, Beijing, China
| | - Hong-Lei Cui
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gan Du
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong-Zhe Shi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Liang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Cheng Wang
- Department of Imaging, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jin Zhang
- Department of Imaging, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ai-Ping Zhou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chang-Ling Li
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shan Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jian-Zhong Shou
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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14
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Uro-Coste E. [Salivary gland tumours: When molecular biology resolves diagnostic dilemmas]. Ann Pathol 2024:S0242-6498(24)00047-6. [PMID: 38555271 DOI: 10.1016/j.annpat.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Affiliation(s)
- Emmanuelle Uro-Coste
- Service d'anatomie et cytologie pathologiques, institut universitaire du cancer-oncopole, 1, avenue Irène-Joliot-Curie, 31059 Toulouse cedex 9, France.
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15
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Pei D, Yu X, Fu W, Ma X, Fang J. The evolution and formation of centromeric repeats analysis in Vitis vinifera. Planta 2024; 259:99. [PMID: 38522063 DOI: 10.1007/s00425-024-04374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.
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Affiliation(s)
- Dan Pei
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Yu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weihong Fu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Ma
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
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Rangel N, Sánchez IL, Valbuena DS, Rondón-Lagos M. ZNF217 Gene Copy Number as a Marker of Response to Standard Therapy Drugs According to ERα Status in Breast Cancer. Breast Cancer (Dove Med Press) 2024; 16:127-139. [PMID: 38505863 PMCID: PMC10950081 DOI: 10.2147/bctt.s445753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024]
Abstract
Purpose The therapeutic decision for the management of breast cancer (BC) patients is based on the evaluation of prognostic factors alongside clinical and pathological parameters. Despite the use of standard biomarkers, response and resistance to therapy represent a challenge for clinicians. Among the new potential biomarkers for BC the ZNF217 gene have gained importance in recent years. However, while associations between ZNF217 gene copy number and clinicopathological characteristics have been established, its correlation with treatment response remains unclear. Patients and Methods This study aimed to evaluate the ZNF217 gene copy number and establish its associations with treatment response in estrogen receptor positive (ERα+) and ERα negative (ERα-) BC cell lines. In addition, a validation of the relationship between ZNF217 gene copy number and its prognostic value was performed using datasets of BC patients retrieved from the cBioPortal public database. Results Our data show that in ERα+ cells, ZNF217 gene copy number increase (amplification), while cell proliferation decreases in response to standard drug treatments. In contrast, both ZNF217 gene copy number (gain) and cell proliferation increases in response to standard drug treatments in ERα- cells. The results obtained align with findings from the cBioPortal database analysis, demonstrating that ERα+/HER2- low proliferation patients, exhibiting ZNF217 gene amplification or gain, have a significantly higher survival probability after treatment, compared to ERα-/HER2- and HER2+ patients. Conclusion Our results suggest that in ERα+ BC cells, ZNF217 gene amplification could be indicative of a favorable response, while in ERα- BC cells, ZNF217 gene gain could be postulated as a potential predictor of treatment resistance. A broader understanding of the role of ZNF217 gene in treatment response, together with prospective studies in BC patients, could contribute to confirming our data, as well as optimizing existing treatments and exploring novel approaches to improve overall cancer treatment outcomes.
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Affiliation(s)
- Nelson Rangel
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Iris Lorena Sánchez
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
| | - Duván Sebastián Valbuena
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
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Dias S, Souza RC, Vasconcelos EV, Vasconcelos S, da Silva Oliveira AR, do Vale Martins L, de Oliveira Bustamante F, da Costa VA, Souza G, da Costa AF, Benko-Iseppon AM, Knytl M, Brasileiro-Vidal AC. Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera. Protoplasma 2024:10.1007/s00709-024-01944-z. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Rosilda Cintra Souza
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | | | - Lívia do Vale Martins
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Campus Amilcar Ferreira Sobral, Universidade Federal Do Piauí, Floriano, PI, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Do Estado de Minas Gerais - Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Victor Alves da Costa
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
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Fornaini NR, Černohorská H, do Vale Martins L, Knytl M. Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution. Genome Biol Evol 2024; 16:evae028. [PMID: 38340334 DOI: 10.1093/gbe/evae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.
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Affiliation(s)
- Nicola R Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Halina Černohorská
- Genetics and Reproductive Biotechnologies, CEITEC-Veterinary Research Institute, Brno 62100, Czech Republic
| | | | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
- Department of Biology, McMaster University, Hamilton, Ontario L8S4K1, Canada
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Cocchi S, Gambarotti M, Gamberi G, Magagnoli G, Maioli M, Stevanin M, Samperi F, Righi A, Benini S. The utility of FISH analysis in the diagnosis of BCOR-rearranged sarcomas. Pathol Res Pract 2024; 255:155209. [PMID: 38422910 DOI: 10.1016/j.prp.2024.155209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/17/2024] [Accepted: 02/11/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND A BCL6 corepressor (BCOR) gene alteration is a genetic signature of rare subsets of sarcomas. The identification of this alteration has recently contributed to the definition of new entities in the current WHO (2020) classification of soft tissue and bone tumours. We retrospectively examined cases of BCOR-rearranged sarcoma (BRS) to assess the reliability of the BCOR FISH analysis using an IVD (in vitro diagnostic) probe. METHODS We investigated and compared the molecular diagnostic strategies and features by collecting 17 data from patients with a BCOR gene rearrangement detected using quantitative-Reverse Transcription-Polymerase Chain Reaction (qRTPCR), Next-Generation Sequencing (NGS) and Fluorescence in situ hybridization (FISH). RESULTS We describe fourteen BCOR::CCNB3 sarcomas, one spindle cell sarcoma with a novel BCOR::MAML1 fusion, one spindle cell sarcoma with a novel BCOR::AHR fusion, and one ossifying fibromyxoid tumour with a BCOR::ZC3H7B fusion. FISH analysis of all, except one, BCOR::CCNB3 sarcoma, showed a FISH break-apart pattern with mild signal separation. The MAML1::BCOR sarcoma showed large-space split signals, while in the two patients with AHR::BCOR and ZC3H7B::BCOR fusions, no BCOR rearrangement was observed using FISH. CONCLUSIONS Our study indicates that BCOR FISH analysis using an IVD probe, may be useful to detect the presence of a BCOR rearrangement, including both translocations and inversions; however, negative results, in some cases, can occur.
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Affiliation(s)
- Stefania Cocchi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Marco Gambarotti
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Gabriella Gamberi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Giovanna Magagnoli
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
| | - Margherita Maioli
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Monica Stevanin
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federica Samperi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Righi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefania Benini
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Takeda N, Makise N, Kageyama H, Takahashi T, Katoh H, Odaka A, Oikawa M, Sugiyama T, Kawana H, Araki A, Kinoshita H, Hagiwara Y, Kamoda H, Yonemoto T, Itami M. The diagnostic utility of cytology specimen in a case of EWSR1::NFATC2 sarcoma. Virchows Arch 2024; 484:533-538. [PMID: 38483612 DOI: 10.1007/s00428-024-03784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/26/2024] [Accepted: 03/10/2024] [Indexed: 04/17/2024]
Abstract
EWSR1::NFATC2 sarcoma, a rare round cell sarcoma constituting the majority of EWSR1::non-ETS sarcomas, has recently been defined in the latest WHO classification. To date, the cytological findings of EWSR1::NFATC2 sarcoma remain undocumented. We present the case of a 25-year-old man with a history of polyostotic fibrous dysplasia in the right leg, referred to our hospital with left thigh pain. Cytological findings included metachromasia, minimally pleomorphic round cells, and eosinophilic infiltration. There was no precursor fibrous dysplasia and the initial diagnosis was undifferentiated pleomorphic sarcoma. Following histologic review, we successfully performed immunocytochemistry and fluorescence in situ hybridization (FISH) on archival cytology specimens. The tumor cells were positive for NKX2-2, NKX3-1, and PAX7 and showed amplified 5' single signals of EWSR1 gene. Reverse transcriptase-polymerase chain reaction revealed an in-frame fusion of EWSR1 and NFATC2. This report describes the cytological features of EWSR1::NFATC2 sarcoma and highlights the diagnostic utility of archival cytology specimens.
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Affiliation(s)
- Naoki Takeda
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Naohiro Makise
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan.
| | - Hajime Kageyama
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Tsukasa Takahashi
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Hiroshi Katoh
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Akiko Odaka
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Mariko Oikawa
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Takahiro Sugiyama
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Hidetada Kawana
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | - Akinobu Araki
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
| | | | - Yoko Hagiwara
- Division of Orthopaedic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Hiroto Kamoda
- Division of Orthopaedic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Tsukasa Yonemoto
- Division of Orthopaedic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Makiko Itami
- Division of Surgical Pathology, Chiba Cancer Center, 666-2 Nitona-Cho, Chuo-Ku, Chiba-Shi, Chiba, 260-8717, Japan
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21
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Balini LC, Fernandes CA, Portela-Castro ALDB, Melo RFD, Zawadzki CH, Borin-Carvalho LA. Initial Steps of XY Sex Chromosome Differentiation in the Armored Cat fish Hypostomus albopunctatus (Siluriformes: Loricariidae) Revealed by Heterochromatin Accumulation. Zebrafish 2024. [PMID: 38386543 DOI: 10.1089/zeb.2023.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
In fish species, heterochromatinization is one process that could trigger sex chromosome differentiation. The present article describes a nascent XX/XY sex chromosome system evidenced by heterochromatin accumulation and microsatellite (GATA)8 in Hypostomus albopunctatus from two populations of the Paraná River basin. The specimens of H. albopunctatus from the Campo and Bossi Rivers share the same karyotype. The species exhibits 74 chromosomes (8m+14sm +16st +36a, fundamental number = 112). The C-banding technique suggests male heterogamety in H. albopunctatus, where the Y-chromosome is morphologically like the X-chromosome but differs from it for having long arms that are entirely heterochromatic. Double fluorescence in situ hybridization (FISH) with 18S and 5S rDNA probes confirmed the Ag-nucleolus organizer region sites in a single pair for both populations, and minor rDNA clusters showed interpopulational variation. FISH with the microsatellite (GATA)8 probe showed a dispersed pattern in the karyotype, accumulating these sequences of sex chromosomes of both populations. FISH with microsatellite (CGC)10 probe showed interpopulational variation. The absence of differentiated sex chromosomes in H. albopunctatus is described previously, and a new variant is documented herein where XY chromosomes can be seen in an early stage of differentiation.
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Affiliation(s)
- Ligia Carla Balini
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
| | - Carlos Alexandre Fernandes
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
| | - Ana Luiza de Brito Portela-Castro
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
| | - Rafael Fernando de Melo
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
| | - Cláudio Henrique Zawadzki
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
- Department of Biology, State University of Maringá, Maringá, Paraná, Brazil
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Eleonora P, Barbora A, Lukáš K, Michail R. Differentiated sex chromosomes, karyotype evolution and spontaneous triploidy in carphodactylid geckos. J Hered 2024:esae010. [PMID: 38366660 DOI: 10.1093/jhered/esae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Indexed: 02/18/2024] Open
Abstract
Geckos exhibit derived karyotypes without clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterised by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerged through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of bi-armed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.
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Affiliation(s)
- Pensabene Eleonora
- Department of Ecology, Faculty of Science, Charles University, Prague, 12844, Czech Republic
| | - Augstenová Barbora
- Department of Ecology, Faculty of Science, Charles University, Prague, 12844, Czech Republic
| | - Kratochvíl Lukáš
- Department of Ecology, Faculty of Science, Charles University, Prague, 12844, Czech Republic
| | - Rovatsos Michail
- Department of Ecology, Faculty of Science, Charles University, Prague, 12844, Czech Republic
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Su JW, Weng CD, Lin XC, Fang MM, Xiao X, Zhang YC, Zhang XC, Su J, Xu CR, Yan HH, Chen HJ, Wu YL, Yang JJ. Plasma ddPCR for the detection of MET amplification in advanced NSCLC patients: a comparative real-world study. Ther Adv Med Oncol 2024; 16:17588359241229435. [PMID: 38333112 PMCID: PMC10851729 DOI: 10.1177/17588359241229435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024] Open
Abstract
Background Mesenchymal-epithelial transition (MET) amplification is a crucial oncogenic driver and a resistance mechanism to epidermal growth factor receptor tyrosine kinase inhibitors (TKIs) of non-small-cell lung cancer (NSCLC). Fluorescence in situ hybridization (FISH) is the gold standard for MET amplification detection. However, it is inapplicable when tissue samples are unavailable. Objective This study assessed the performance of plasma droplet digital polymerase chain reaction (ddPCR) in MET amplification detection in NSCLC patients. Design and methods A total of 87 NSCLC patients were enrolled, and 94 paired tissue and plasma samples were analyzed for the concordance between FISH and plasma ddPCR/tissue next-generation sequencing (NGS) in detecting MET amplification. In addition, the efficacy of patients with MET amplification using different detection methods who were treated with MET-TKIs was evaluated. Results Plasma ddPCR showed substantial concordance with FISH (74.1% sensitivity, 92.5% specificity, and 87.2% accuracy with a kappa value of 0.68) and outperformed tissue NGS (kappa value of 0.64) in MET amplification detection. Combined plasma ddPCR and tissue NGS showed substantial concordance with FISH (92.3% sensitivity, 89.2% specificity, and an accuracy of 90.1% with a kappa value of 0.77). The efficacy is comparable in these NSCLC patients with MET amplification detected by FISH and plasma ddPCR who were treated with MET-TKIs. Conclusion Plasma ddPCR is a potentially reliable method for detecting MET amplification in advanced NSCLC patients. Combined plasma ddPCR and tissue NGS might be an alternative or complementary method to MET amplification detection.
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Affiliation(s)
- Jun-Wei Su
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Cheng-Di Weng
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xiao-Cheng Lin
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Mei-Mei Fang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xiao Xiao
- Shanghai Yuanqi Biomedical Technology Co., Ltd, Shanghai, China
| | - Yi-Chen Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jin-Ji Yang
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou 510080, China
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Guangzhou 510080, China
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Kushwaha S, Stinnett V, Zou YS, Murry JB. Live-born autosomal ring chromosomes at the Johns Hopkins Hospital Cytogenomics Laboratory: Case series-Spanning 52 years of experience in a single center. Am J Med Genet A 2024; 194:253-267. [PMID: 37807876 DOI: 10.1002/ajmg.a.63429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
Ring chromosomes (RCs) are a structural aberration that can be tolerated better in acrocentric or gonosomal chromosomes. Complete RCs arise from telomere-telomere fusions. Alternatively, genomic imbalances corresponding to the ends of the chromosomal arms can be seen with RC formation. RCs are unstable in mitosis, result in mosaicism, and are associated with a "ring syndrome," which presents with growth and development phenotypes and differs from those features more frequently observed with pure terminal copy number changes. Due to variability in mosaicism, size, and genomic content, clear genotype-phenotype correlations may not always be possible. Given the rarity of RCs, this historical data is invaluable. We performed a retrospective review of individuals bearing RCs to investigate the incidence in our laboratory. This work details the methods and features seen in association with twenty-three autosomal RCs. In decreasing order, the most frequently seen autosomal RCs were 18, 22, 4, 13, 17, and 9. The additional cases detail clinical and cytogenomic events similar to those reported in RCs. As methodologies advance, insights may be gleaned from following up on these cases to improve genotype-phenotype correlations and understand the cryptic differences or other predisposing factors that lead to ring formation and development.
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Affiliation(s)
- Shivani Kushwaha
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Victoria Stinnett
- Johns Hopkins Genomics, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cytogenetics Laboratory, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ying S Zou
- Johns Hopkins Genomics, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cytogenetics Laboratory, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Jaclyn B Murry
- Johns Hopkins Genomics, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cytogenetics Laboratory, Johns Hopkins Hospital, Baltimore, Maryland, USA
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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. Mol Breed 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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26
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Kubickova S, Kopecna O, Cernohorska H, Rubes J, Vozdova M. X Chromosome-Specific Repeats in Non-Domestic Bovidae. Genes (Basel) 2024; 15:159. [PMID: 38397149 PMCID: PMC10887555 DOI: 10.3390/genes15020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Repetitive sequences form a substantial and still enigmatic part of the mammalian genome. We isolated repetitive DNA blocks of the X chromosomes of three species of the family Bovidae: Kobus defassa (KDEXr sequence), Bos taurus (BTAXr sequence) and Antilope cervicapra (ACEXr sequence). The copy numbers of the isolated sequences were assessed using qPCR, and their chromosomal localisations were analysed using FISH in ten bovid tribes and in outgroup species. Besides their localisation on the X chromosome, their presence was also revealed on the Y chromosome and autosomes in several species. The KDEXr sequence abundant in most Bovidae species also occurs in distant taxa (Perissodactyla and Carnivora) and seems to be evolutionarily older than BTAXr and ACEXr. The ACEXr sequence, visible only in several Antilopini species using FISH, is probably the youngest, and arised in an ancestor common to Bovidae and Cervidae. All three repetitive sequences analysed in this study are interspersed among gene-rich regions on the X chromosomes, apparently preventing the crossing-over in their close vicinity. This study demonstrates that repetitive sequences on the X chromosomes have undergone a fast evolution, and their variation among related species can be beneficial for evolutionary studies.
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Affiliation(s)
| | | | | | | | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.R.)
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Bugrov A, Karamysheva T, Buleu O. New insights into the chromosomes of stoneflies: I. Karyotype, C-banding and localization of ribosomal and telomeric DNA markers in Skwalacompacta (McLachlan, 1872) (Polyneoptera, Plecoptera, Perlodidae) from Siberia. Comp Cytogenet 2024; 18:15-26. [PMID: 38313463 PMCID: PMC10835800 DOI: 10.3897/compcytogen.18.115784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024]
Abstract
This study provides data on chromosome number (2n♂♀=26), sex determination mechanism (XY♂/XX♀), C-banding pattern, distribution of clusters of telomeric TTAGG repeats and 18S ribosomal DNA in the karyotype of the stonefly Skwalacompacta (McLachlan, 1872). For the first time in the history of stoneflies cytogenetics, we provide photos of the chromosomes of the Plecoptera insects. The karyotype of males and females of S.compacta consists of 12 pairs of autosomes. Three pairs of large autosomes and four pairs of medium-sized autosomes are subacrocentric. The remaining pairs of autosomes are small, with unclear morphology. Pericentromeric C-bands were revealed in all autosomes. The sex chromosomes are also subacrocentric. The short arms of X and Y chromosomes are entirely heterochromatic and are rich in ribosomal DNA sequences. In the X chromosome this arm is larger than in the Y chromosome. It is likely that this arm associated with the nucleolar organizer (NOR). Telomeric DNA (TTAGG)n repeats were detected in the terminal regions of all chromosomes.
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Affiliation(s)
- Alexander Bugrov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia Novosibirsk State University Novosibirsk Russia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia Institute of Systematics and Ecology of Animals, Russian Academy of Sciences Novosibirsk Russia
| | - Tatyana Karamysheva
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia Novosibirsk State University Novosibirsk Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia Institute of Cytology and Genetics, Russian Academy of Sciences Novosibirsk Russia
| | - Olesya Buleu
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia Novosibirsk State University Novosibirsk Russia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia Institute of Systematics and Ecology of Animals, Russian Academy of Sciences Novosibirsk Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia Institute of Cytology and Genetics, Russian Academy of Sciences Novosibirsk Russia
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28
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Lavernia J, Claramunt R, Romero I, López-Guerrero JA, Llombart-Bosch A, Machado I. Soft Tissue Sarcomas with Chromosomal Alterations in the 12q13-15 Region: Differential Diagnosis and Therapeutic Implications. Cancers (Basel) 2024; 16:432. [PMID: 38275873 PMCID: PMC10814159 DOI: 10.3390/cancers16020432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The chromosomal region 12q13-15 is rich in oncogenes and contains several genes involved in the pathogenesis of various mesenchymal neoplasms. Notable genes in this region include MDM2, CDK4, STAT6, DDIT3, and GLI1. Amplification of MDM2 and CDK4 genes can be detected in various mesenchymal and nonmesenchymal neoplasms. Therefore, gene amplification alone is not entirely specific for making a definitive diagnosis and requires the integration of clinical, radiological, morphological, and immunohistochemical findings. Neoplasms with GLI1 alterations may exhibit either GLI1 rearrangements or amplifications of this gene. Despite the diagnostic implications that the overlap of genetic alterations in neoplasms with changes in genes within the 12q13-15 region could create, the discovery of coamplifications of MDM2 with CDK4 and GLI1 offers new therapeutic targets in neoplasms with MDM2/CDK4 amplification. Lastly, it is worth noting that MDM2 or CDK4 amplification is not exclusive to mesenchymal neoplasms; this genetic alteration has also been observed in other epithelial neoplasms or melanomas. This suggests the potential use of MDM2 or CDK4 inhibitors in neoplasms where alterations in these genes do not aid the pathological diagnosis but may help identify potential therapeutic targets. In this review, we delve into the diagnosis and therapeutic implications of tumors with genetic alterations involving the chromosomal region 12q13-15, mainly MDM2, CDK4, and GLI1.
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Affiliation(s)
- Javier Lavernia
- Oncology Unit, Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - Reyes Claramunt
- Laboratory of Molecular Biology, Instituto Valenciano de Oncología, 46009 Valencia, Spain; (R.C.); (J.A.L.-G.)
| | - Ignacio Romero
- Oncology Unit, Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - José Antonio López-Guerrero
- Laboratory of Molecular Biology, Instituto Valenciano de Oncología, 46009 Valencia, Spain; (R.C.); (J.A.L.-G.)
| | | | - Isidro Machado
- Pathology Department, University of Valencia, 46010 Valencia, Spain;
- Pathology Department, Instituto Valenciano de Oncología, 46010 Valencia, Spain
- CIBERONC Cancer, 28029 Madrid, Spain
- Patologika Laboratory, Hospital Quiron-Salud, 46010 Valencia, Spain
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Joksic I, Toljic M, Milacic I, Stankovic A, Karadzov Orlic N, Mikovic Z. Small supernumerary marker chromosomes in prenatal diagnosis-molecular characterization and clinical outcomes. Front Genet 2024; 14:1326985. [PMID: 38259626 PMCID: PMC10800731 DOI: 10.3389/fgene.2023.1326985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Small supernumerary marker chromosomes (sSMCs) are infrequent findings in prenatal diagnostics, however they pose a great challenge for prenatal genetic counseling. Methods: We report prenatal 12 sSMC cases detected in a single center during 10 years period, their molecular characterization by fluorescence in situ hybridization (FISH) or chromosomal microarray (CMA). Those cases were found among 9620 prenatal diagnostic analyzes by GTG-banding technique. In selected cases, additional UPD testing was also done. Results: Incidence of sSMCs in our study was 0.12%. sSMC characterization was done by FISH in 9 cases, in the remainder of three CMA was employed. The most common sSMC shape was centric minute, followed by inverted duplication and one case with ring conformation. sSMCs originating from acrocentric chromosomes (chromosomes 14, 21 and 22), sex chromosomes (X, Y) and non-acrocentric autosomal chromosomes (chromosome 4 and 18) were confirmed in 3 cases each; no result could be obtained in 3 further cases. Discussion: No anomalies were detected by prenatal ultrasound in any of the cases. In 58% of the cases, outcome was reported as normal at birth, while anomalies at birth were described in one case. Only two patients opted for pregnancy termination. Preterm labor occurred in case of twin pregnancy resulting in stillbirth and early neonatal death of twins. Overall, our study highlights the importance of a sSMC characterization by molecular cytogenomic methods in order to make appropriate genotype-phenotype correlations and ensure adequate genetic counseling.
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Affiliation(s)
- Ivana Joksic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Mina Toljic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Iva Milacic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Andjela Stankovic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Natasa Karadzov Orlic
- High-Risk Pregnancy Department, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zeljko Mikovic
- High-Risk Pregnancy Department, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
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Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M, Kwasniewska J. Phaseolus vulgaris mutants reveal variation in the nuclear genome. Front Plant Sci 2024; 14:1308830. [PMID: 38239224 PMCID: PMC10794375 DOI: 10.3389/fpls.2023.1308830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.
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Affiliation(s)
- Nasya Tomlekova
- Laboratory of Molecular Biology, Department of Breeding, Marisa Vegetable Crops Research Institute, Plovdiv, Agricultural Academy, Sofia, Bulgaria
| | - Dominika Idziak-Helmcke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paula Franke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Tse JLK, Ng JHY. GLI1-Altered Soft Tissue Tumor in the Tongue-A Case Report and Literature Review. Int J Surg Pathol 2024:10668969231216986. [PMID: 38166443 DOI: 10.1177/10668969231216986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Background: Soft tissue tumors with fusions or amplifications of the GLI1 gene have distinctive molecular characteristics and have recently been considered a unique pathological entity, thus named "GLI1-altered soft tissue tumors." It is a rare mesenchymal neoplasm that involves soft tissues at any site. Case presentation: We report an example of this condition in a 13-year-old Chinese male patient who presented with a mass in the tongue. The tumor was multilobulated; the tumor cells were arranged in nests and sheets, had a rich, delicate fibrovascular network, and were separated by a hyalinized fibrous stroma. The tumor cells were epithelioid to ovoid, with variable eosinophilic to pale vacuolated cytoplasm and round to oval nuclei. Immunostaining revealed that the tumor cells were positive for CDK4 and CD56. Fluorescence in situ hybridization (FISH) for GLI1 translocation was positive, with a high level of amplification of the translocated segment. Literature review: We present a comprehensive literature review of this condition, focusing on its clinical presentation, histological features, immunohistochemical profile, molecular characteristics, and prognosis.
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Affiliation(s)
- Jenny Lik-Ka Tse
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Joshua Hoi-Yan Ng
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong
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32
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Huang K, Meyers BC, Caplan JL. Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA- FISH. Methods Mol Biol 2024; 2784:101-111. [PMID: 38502481 DOI: 10.1007/978-1-0716-3766-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
- Molecular Imaging Core, Dana-Farber Cancer Institute, Boston, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Plant Science and Technology, University of Missouri - Columbia, Columbia, MO, USA.
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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Suydam C, Chibane F, Brown N, Schlafly M, Arnold AH, Ghleilib I, Easley M, White J. Are There More HER2 FISH in the Sea? An Institution's Experience in Identifying HER2 Positivity Using Fluorescent In Situ Hybridization in Patients with HER2 Negative Immunohistochemistry. Ann Surg Oncol 2024; 31:376-381. [PMID: 37936021 PMCID: PMC10695864 DOI: 10.1245/s10434-023-14439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Approximately 20% of breast cancers express HER2-positive receptors in the USA. HER2 receptor immunohistochemistry (IHC) staining with equivocal (2+) results commonly undergoes fluorescence in-situ hybridization (FISH) for further classification. Current guidelines do not recommend routine FISH testing in IHC-negative (0 or 1+) cases. This study investigates an institution that performs both IHC and FISH testing on all cases to identify the true HER2-positive rate. PATIENTS AND METHODS A retrospective chart review from 2015 to 2021 was conducted at an institution where both HER2 IHC and FISH testing were performed at the time of diagnosis for all invasive breast cancers. The rate of true HER2-positive patients was determined, and patient and tumor characteristics were further explored. RESULTS A total of 1835 invasive breast cancer cases were primarily treated at this institution. A total of 289 cases were HER2 positive on IHC and FISH testing (15.7%). An additional 38 cases were identified as HER2 negative on IHC, but reclassified as HER2 positive on reflex FISH testing. Total HER2 positive cases increased from 289 (15.7%) to 327 cases (17.8%) with reflex FISH testing. CONCLUSIONS The additional HER2-positive cases after completing FISH testing on IHC-negative tumors suggests there may be a role for routine FISH testing in addition to standard IHC staining to determine HER2 status for breast cancer. The ethical, prognostic and even benefits of a correct diagnosis outweigh the added expense of FISH testing.
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Affiliation(s)
- Camille Suydam
- Department of Surgery, Eisenhower Army Medical Center, Fort Gordon, GA, USA.
| | - Fairouz Chibane
- Department of Surgery, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Nicole Brown
- Department of Surgery, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Madeleine Schlafly
- Department of Surgery, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Alicia H Arnold
- Department of Surgery, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Intisar Ghleilib
- Department of Pathology, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Melissa Easley
- Department of Surgery, Medical College of Georgia at Augusta Health, Augusta, GA, USA
| | - Joseph White
- Department of Pathology, Medical College of Georgia at Augusta Health, Augusta, GA, USA
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Laforga JB, Othman BK. A diagnostic algorithm for sinonasal papillary non-keratinizing squamous cell carcinoma with DEK::AFF2 fusion and mimickers. Rev Esp Patol 2024; 57:67-70. [PMID: 38246714 DOI: 10.1016/j.patol.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 01/23/2024]
Abstract
Sinonasal carcinomas represent a rare and diverse group of tumors, presenting diagnostic complexities due to their varied histological and molecular features. To ensure accurate differentiation among these malignancies, a systematic and stepwise approach is paramount. Even with the morphological similarities between poorly differentiated (non) keratinizing sinonasal squamous cell carcinoma (SNSCC) and DEK::AFF2 SNSCC, the two lesions are distinguishable using the surrogate immunohistochemical marker AFF2 or molecular testing for DEK::AFF2 mutation. We report a rare case of SMARCB1-retained DEK::AFF2 papillary non-keratinizing SNSCC in a 53-year-old female, who presented with a polypoid mass corresponding to the left middle turbinate. Following the surgical resection of the tumor and locoregional lymph nodes, adjuvant radiotherapy was administered to eradicate any residual cancer cells that may have remained after surgery.
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Affiliation(s)
- Juan B Laforga
- Department of Pathology, Hospital de Dénia, Alicante, Spain
| | - Bacem K Othman
- Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Czech Republic.
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35
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Abdullah B, Al Qeshty OAM, El-Nagdy SY, Ismail LE. Heterogeneity in PD-L1 expression in MAML2-rearranged mucoepidermoid carcinoma. Pathol Res Pract 2024; 253:155005. [PMID: 38091884 DOI: 10.1016/j.prp.2023.155005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
OBJECTIVE Mucoepidermoid carcinoma (MEC) is a malignant tumor with diverse morphologies, some of which have poor prognostic indicators and others that challenge the grading system. This study investigated the expression of PD-L1 in different grades and phenotypes of MEC. METHODS The present study was carried out on twenty-four archival formalin-fixed, paraffin-embedded blocks of salivary MEC. Fluorescence in situ hybridization was used to detect MAML2 rearrangement in MEC cases to be included. The studied cases were then subcategorized based on their grading and phenotype and immunohistochemically stained for PD-L1. RESULTS PD-L1 expression in MEC varied, with some variants showing moderate to strong immunoexpression, while others did not express it at all. In the Warthin-like MEC, some tumors show high expression of PD-L1, while in the same pattern, a few cases showed low or no expression. Intraosseous MEC exhibited moderate PD-L1 expression. Sclerosing MEC featured lower PD-L1 expression, from weak to moderate. Oncocytic MEC displayed relatively low PD-L1 expression levels (weak to moderate). CONCLUSION The histomorphologic features of MEC may predict clinicopathologic behavior, and subtyping MEC may pose a significant therapeutic value, particularly for intraosseous MECs and clear-cell MECs. PD-L1 expression is a good predictor of survival outcomes in MECs.
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Affiliation(s)
- Bacem Abdullah
- Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Egypt.
| | - Osama A M Al Qeshty
- Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Egypt
| | - Sherif Y El-Nagdy
- Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Egypt; Department of Oral Pathology, Faculty of Dentistry, Horus University in Egypt, Egypt
| | - Lawahez El Ismail
- Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Egypt
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36
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Li L, Yue P, Du Q, Zhang H, Song Y. MDM2 FISH testing criteria in adipose tissue tumors with mature adipocytic morphology - A resection case-based study. Pathol Res Pract 2024; 253:155039. [PMID: 38134838 DOI: 10.1016/j.prp.2023.155039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
The current criteria for utilizing MDM2 Fluorescence In Situ Hybridization (FISH) in adipose-derived tumors were first introduced in 2015 and have been widely adopted. However, these criteria may fail to identify some atypical lipomatous tumors / well-differentiated liposarcoma (ALT/WDL) with mature adipocytic morphology in clinical practice, possibly due to the fact that the existing criteria are primarily based on biopsy cases. Hence, a criterion based on resection cases is needed. In this study, we included 87 adipose tissue tumors with mature adipocytic morphology which were first resected, as well as 9 consultation cases and 25 recurrent resection cases. The final diagnosis was based on MDM2 amplification status. Among the 87 first-time resection cohort, MDM2 FISH amplification was observed in only 2 (5%) of the 39 superficial cases. Marginal infiltration was significantly different in both the MDM2 FISH negative and positive groups (p < 0.05). Of the 37 intramuscular tumors, 17 (46%) showed MDM2 FISH amplification. The MDM2 amplification positive group had a larger tumor size than MDM2 amplification negative group (p = 0.042). Tumors of larger size (≥11 cm) were highly correlated with MDM2 amplification (p = 0.003), but still, 35.3% of the MDM2 amplification-positive cases had tumor sizes less than 11 cm. Eight (66.7%) out of twelve retroperitoneal/ pelvic cases were MDM2 FISH positive. Among the 25 recurrent cases, twenty (80%) of them had MDM2 FISH amplification. In conclusion, we recommend MDM2 FISH for: 1. superficial cases with marginal infiltration based on adequate margin sampling; 2. all intramuscular tumors, retroperitoneal/pelvic tumors and recurrent tumors, both in resection cases and biopsy cases.
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Affiliation(s)
- Lihong Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Pinli Yue
- State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qiang Du
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hongtu Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Yan Song
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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37
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Al Shboul S, Boyle S, Singh A, Saleh T, Alrjoub M, Abu Al Karsaneh O, Mryyian A, Dawoud R, Gul S, Abu Baker S, Ball K, Hupp T, Brennan PM. FISH analysis reveals CDKN2A and IFNA14 co-deletion is heterogeneous and is a prominent feature of glioblastoma. Brain Tumor Pathol 2024; 41:4-17. [PMID: 38097874 DOI: 10.1007/s10014-023-00473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024]
Abstract
Deletion of CDKN2A occurs in 50% of glioblastomas (GBM), and IFNA locus deletion in 25%. These genes reside closely on chromosome 9. We investigated whether CDKN2A and IFNA were co-deleted within the same heterogeneous tumour and their prognostic implications. We assessed CDKN2A and IFNA14 deletions in 45 glioma samples using an in-house three-colour FISH probe. We examined the correlation between p16INK4a protein expression (via IHC) and CDKN2A deletion along with the impact of these genomic events on patient survival. FISH analyses demonstrated that grades II and III had either wildtype (wt) or amplified CDKN2A/IFNA14, whilst 44% of GBMs harboured homozygous deletions of both genes. Cores with CDKN2A homozygous deletion (n = 11) were negative for p16INK4a. Twenty p16INK4a positive samples lacked CDKN2A deletion with some of cells showing negative p16INK4a. There was heterogeneity in IFNA14/CDKN2A ploidy within each GBM. Survival analyses of primary GBMs suggested a positive association between increased p16INK4a and longer survival; this persisted when considering CDKN2A/IFNA14 status. Furthermore, wt (intact) CDKN2A/IFNA14 were found to be associated with longer survival in recurrent GBMs. Our data suggest that co-deletion of CDKN2A/IFNA14 in GBM negatively correlates with survival and CDKN2A-wt status correlated with longer survival, and with second surgery, itself a marker for improved patient outcomes.
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Affiliation(s)
- Sofian Al Shboul
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan.
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ashita Singh
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, Scotland, UK
| | - Tareq Saleh
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Moath Alrjoub
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Ola Abu Al Karsaneh
- Department of Microbiology, Pathology, and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Amel Mryyian
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Rand Dawoud
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Sinem Gul
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, Scotland, UK
| | - Shaden Abu Baker
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Kathryn Ball
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, Scotland, UK
| | - Ted Hupp
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, Scotland, UK.
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Translational Neurosurgery, Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SB, Scotland, UK.
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38
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Serbus LR. A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging. Methods Mol Biol 2024; 2739:349-373. [PMID: 38006562 DOI: 10.1007/978-1-0716-3553-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.
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Affiliation(s)
- Laura Renee Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
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39
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Perez MW, Camplisson CK, Beliveau BJ. Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP. Methods Mol Biol 2024; 2784:177-189. [PMID: 38502486 DOI: 10.1007/978-1-0716-3766-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Fluorescent in situ hybridization (FISH) enables the visualization of the position and abundance of nucleic acid molecules in fixed cell and tissue samples. Many FISH-based methods employ sets of synthetic, computationally designed DNA oligonucleotide (oligo) FISH probes, including massively multiplexed imaging spatial transcriptomics and spatial genomics technologies. Oligo probes can either be designed de novo or accessed from an existing database of pre-discovered probe sequences. This chapter describes the use of PaintSHOP, a user-friendly, web-based platform for the design of sets of oligo-based FISH probes. PaintSHOP hosts large collections of pre-discovered probes from many model organisms and also provides collections of functional sequences such as primers and readout domains and interactive tools to add these functional sequences to selected probes. Detailed examples are provided for three common experimental scenarios.
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Affiliation(s)
- Monika W Perez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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40
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Ichikawa J, Kawasaki T. Primary synovial sarcomas of the bone: clinical perspectives and correlation between the application of SS18-SSX and decalcification status. Front Oncol 2023; 13:1265824. [PMID: 38169964 PMCID: PMC10759219 DOI: 10.3389/fonc.2023.1265824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- Jiro Ichikawa
- Department of Orthopaedic Surgery, Interdisciplinary Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Tomonori Kawasaki
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka, Japan
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41
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Golub NV, Anokhin BA, Kuznetsova VG. Karyotype diversity in the genus Nysius Dallas, 1852 (Hemiptera, Heteroptera, Lygaeidae) is much greater than you might think. Comp Cytogenet 2023; 17:287-293. [PMID: 38152388 PMCID: PMC10752037 DOI: 10.3897/compcytogen.17.116628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
We studied the karyotype and chromosomal distribution of 18S rDNA clustered in nucleolar organizer regions (NORs) in Nysiusgraminicola (Kolenati, 1845), belonging to the subfamily Orsillinae (Lygaeidae). It is shown that this species has a karyotype with 2n = 22(18+mm+XY), previously known in only one of 24 studied species of the genus Nysius Dallas, 1852, characterized by a similar karyotype, 2n = 14(12+mm+XY). In N.graminicola, 18S loci are located on sex chromosomes, which is a previously unknown trait for this genus. Our results in a compilation with previous data revealed dynamic evolution of rDNA distribution in Nysius. It is concluded that molecular chromosomal markers detected by FISH contribute to a better understanding of the structure and evolution of the taxonomically complex genus Nysius.
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Affiliation(s)
- Natalia V. Golub
- Department of Karyosystematics, Zoological Institute,
Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St. Petersburg,
RussiaDepartment of Karyosystematics, Zoological Institute, Russian Academy of
SciencesSt. PetersburgRussia
| | - Boris A. Anokhin
- Department of Karyosystematics, Zoological Institute,
Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St. Petersburg,
RussiaDepartment of Karyosystematics, Zoological Institute, Russian Academy of
SciencesSt. PetersburgRussia
| | - Valentina G. Kuznetsova
- Department of Karyosystematics, Zoological Institute,
Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St. Petersburg,
RussiaDepartment of Karyosystematics, Zoological Institute, Russian Academy of
SciencesSt. PetersburgRussia
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42
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Xia D, Kuo F, Hughes M, Lindeman N, Manning D, Files J, Strauss S, Kirkner G, Mohammed-Abreu A, Winer E, Tolaney SM, Lin NU, Dillon DA. HER2/ERBB2 copy number analysis by targeted next-generation sequencing in breast cancer. Am J Clin Pathol 2023:aqad167. [PMID: 38104247 DOI: 10.1093/ajcp/aqad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
OBJECTIVES A combination of immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) is the current standard of care for HER2 evaluation in breast cancer. Here, we investigate the potential clinical utility of next-generation sequencing (NGS)-derived HER2/ERBB2 copy number (CN) data for predicting HER2 status as defined by American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines. METHODS In total, 294 locally recurrent and metastatic breast cancers previously tested by targeted hybrid capture-based NGS and by HER2 IHC/FISH were included. Analyses focused on the ERBB2 median log2 ratios and start-end genomic coordinates from NGS, average HER2 CN and HER2/CEP17 ratios from FISH, and the HER2 IHC scores. We also determined a more stringent log2 ratio cutoff to predict HER2-positive status with 100% specificity. RESULTS Sixty-four (22%) cases were HER2 positive and 230 (78%) were HER2 negative by ASCO/CAP guidelines. The ERBB2 median log2 ratios from NGS strongly correlated with HER2 status by IHC/FISH (area under receiver operator characteristic curve = 0.951). ERBB2 log2 ratio more than 1.7 was 100% specific for HER2-positive results by IHC/FISH. Start and end genomic coordinates for regions of gain near ERBB2 by NGS also predicted HER2 status. CONCLUSIONS Copy number data from our NGS panel strongly correlate with HER2 status. Using a stringent cutoff, ERBB2 log2 ratio accurately predicts HER2 positivity with high specificity. The NGS CN assessment may have utility in determining HER2 status in certain clinical settings.
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Affiliation(s)
- Daniel Xia
- Department of Pathology, University Health Network, Toronto, Canada
| | - Frank Kuo
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
| | - Melissa Hughes
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | - Neal Lindeman
- Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, NY, US
| | - Danielle Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
| | - Janet Files
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | - Sarah Strauss
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | - Greg Kirkner
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | | | | | - Sara M Tolaney
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | - Nancy U Lin
- Breast Oncology, Dana Farber Cancer Institute, Boston, MA, US
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
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43
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Nguyen TH, Kang BY, Kim HH. Chromosomal dynamics in Senna: comparative PLOP- FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations. Front Plant Sci 2023; 14:1288220. [PMID: 38173930 PMCID: PMC10762312 DOI: 10.3389/fpls.2023.1288220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024]
Abstract
Introduction Tandem repeats (TRs) occur abundantly in plant genomes. They play essential roles that affect genome organization and evolution by inducing or generating chromosomal rearrangements such as duplications, deletions, inversions, and translocations. These impact gene expression and chromosome structure and even contribute to the emergence of new species. Method We investigated the effects of TRs on speciation in Senna genus by performing a comparative analysis using fluorescence in situ hybridization (FISH) with S. tora-specific TR probes. We examined the chromosomal distribution of these TRs and compared the genome sizes of seven Senna species (estimated using flow cytometry) to better understand their evolutionary relationships. Results Two (StoTR03_159 and StoTR04_55) of the nine studied TRs were not detected in any of the seven Senna species, whereas the remaining seven were found in all or some species with patterns that were similar to or contrasted with those of S. tora. Of these studies species, only S. angulata showed significant genome rearrangements and dysploid karyotypes resembling those of S. tora. The genome sizes varied among these species and did not positively correlate with chromosome number. Notably, S. angulata had the fewest chromosomes (2n = 22) but a relatively large genome size. Discussion These findings reveal the dynamics of TRs and provide a cytogenetic depiction of chromosomal rearrangements during speciation in Senna. To further elucidate the dynamics of repeat sequences in Senna, future studies must include related species and extensive repeatomic studies, including those on transposable elements.
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Affiliation(s)
| | | | - Hyun Hee Kim
- Chromosome Research Institute, Department of Chemistry & Life Science, Sahmyook University, Seoul, Republic of Korea
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Zhao K, Bai Y, Zhang Q, Zhao Z, Cao Y, Yang L, Wang N, Xu J, Wang B, Wu L, Gong X, Lin T, Wang Y, Wang W, Cai X, Yin Y, Xiong Z. Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing. BMC Plant Biol 2023; 23:630. [PMID: 38062348 PMCID: PMC10704825 DOI: 10.1186/s12870-023-04650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. RESULTS In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. CONCLUSIONS This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qingyu Zhang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zhen Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lu Yang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ni Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Bo Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiufeng Gong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Wei Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Xingkui Cai
- Key Laboratory of Horticultural Plant Biology, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Cuello M, García-Rivello H, Huamán-Garaicoa F, Irigoyen-Piñeiros P, Lara-Torres CO, Rizzo MM, Ticona-Castro M, Trejo R, Zoroquiain P. Detection of NTRK gene fusions in solid tumors: recommendations from a Latin American group of oncologists and pathologists. Future Oncol 2023; 19:2669-2682. [PMID: 38088163 DOI: 10.2217/fon-2023-0552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
NTRK gene fusions have been detected in more than 25 types of tumors and their prevalence is approximately 0.3% in solid tumors. This low prevalence makes identifying patients who could benefit from TRK inhibitors a considerable challenge. Furthermore, while numerous papers on the evaluation of NTRK fusion genes are available, not all countries have guidelines that are suitable for their setting, as is the case with Latin America. Therefore, a group of oncologists and pathologists from several countries in Latin America (Argentina, Chile, Ecuador, Mexico, Peru and Uruguay) met to discuss and reach consensus on how to identify patients with NTRK gene fusions in solid tumors. To do so, they developed a practical algorithm, considering their specific situation and limitations.
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Affiliation(s)
- Mauricio Cuello
- Academic Unit of Oncology, Hospital de Clínicas Dr. Manuel Quintela, Montevideo, Uruguay
| | - Hernán García-Rivello
- Departmento of Clinical Pathology, Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), Hospital Italiano, Buenos Aires, Argentina
| | - Fuad Huamán-Garaicoa
- Instituto de Salud Integral (ISAIN), Universidad Católica, Santiago de Guayaquil (Ecuador), Department of Pathology, Sociedad de Lucha Contra el Cáncer del Ecuador (SOLCA), Guayaquil, Ecuador
| | | | - César O Lara-Torres
- Laboratory of Molecular Pathology, Instituto Nacional de Cancerología, Ciudad de México, México
| | - Manglio M Rizzo
- Cancer Immunobiology Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), Facultad de Ciencias Biomédicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Austral, Derqui-Pilar, Argentina
- Department of Medical Oncology, Hospital Universitario Austral, Derqui-Pilar, Argentina
| | - Miguel Ticona-Castro
- Service of Medical Oncology, Hospital Nacional Edgardo Rebagliati Martins, EsSalud - Jesús María, Lima (Perú), Clínica Montefiori, La Molina, Lima, Perú
| | - Rogelio Trejo
- Department of Medical Oncology, Centro Médico Nacional Siglo XXI, Ciudad de México, México
| | - Pablo Zoroquiain
- Pathology Department, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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Bouzid FZ, Hammou HA, Akallakh H, Dafir K, Tajir M, Aboussair N. [Williams-Beuren syndrome: a retrospective study of a series of 11 cases at the Mohammed VI University Hospital in Marrakech]. Pan Afr Med J 2023; 46:94. [PMID: 38405095 PMCID: PMC10891372 DOI: 10.11604/pamj.2023.46.94.29604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/02/2023] [Indexed: 02/27/2024] Open
Abstract
Williams-Beuren syndrome is a rare genetic disease (1/20 000) characterized by a microdeletion at 7q11.23 encompassing about 28 genes, including the elastin gene, ELN. It is a sporadic disease in the majority of cases. Easily identifiable in childhood, this developmental disorder associates suggestive face dysmorphism, cardiac defect, psychomotor retardation and specific behavioural and cognitive profile. We conducted a retrospective study of 11 patients with Williams-Beuren syndrome whose data were collected in the Genetics Department of the Mohammed VI University Hospital of Marrakech. The average age of patients was 6.05 years (SD=6.56; interquartile range=5), with a female predominance (64%; 7/11 patients). Almost all patients were mentally retarded and the diagnosis was confirmed in 100% (11) of patients using fluorescence in situ hybridisation (FISH).
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Affiliation(s)
- Fatima Zahrae Bouzid
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
- Faculté de Médecine et de Pharmacie de Marrakech, Université Cadi Ayyad, Marrakech, Maroc
| | - Hanane Ait Hammou
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
| | - Hassan Akallakh
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
| | - Kenza Dafir
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
- Faculté de Médecine et de Pharmacie de Marrakech, Université Cadi Ayyad, Marrakech, Maroc
| | - Mariam Tajir
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
- Service de Génétique Médicale, Centre Hospitalier Universitaire Mohammed VI, Oujda, Maroc
| | - Nisrine Aboussair
- Service de Génétique, Centre de Recherche Clinique, Centre Hospitalier Universitaire Mohammed VI, Marrakech, Maroc
- Faculté de Médecine et de Pharmacie de Marrakech, Université Cadi Ayyad, Marrakech, Maroc
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47
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Tu Y, Zhu P, Lao IW, Yu L, Wang J. Epithelioid dedifferentiated liposarcoma: A clinicopathological and molecular study of 6 cases. Ann Diagn Pathol 2023; 67:152203. [PMID: 37634346 DOI: 10.1016/j.anndiagpath.2023.152203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
In this study, we present six cases of epithelioid dedifferentiated liposarcoma to further characterize its clinical and pathological features. The patients are all adult men with age at presentation ranging from 46 to 64 years (median 58.5 years). The patients presented with nonspecific symptoms of retroperitoneal mass, intermittent dull pain or discomfort. None of the patients had any prior history of a primary tumor. Radiological examinations revealed the presence of ill-demarcated heterogenous mass located in the deep soft tissue, including retroperitoneum (4 cases), pelvis and trunk (1 case each). Grossly, they appeared as solid tumors with focal areas of necrosis being presented in 2 cases. Histologically, all tumors were characterized by sheets of epithelioid cells that displayed marked cellular atypia and brisk mitotic activity. Variable portion of atypical lipomatous tumor/well-differentiated liposarcoma was present in 3 cases. By immunohistochemistry, the high-grade epithelioid component in all 6 cases showed strong and diffuse nuclear staining of MDM2, CDK4 and P16, with partial expression of AE1/AE3 in 3 cases. Fluorescence in situ hybridization analysis revealed high-level amplification of MDM2 in all 6 cases, with co-amplification of CDK4 in 3 cases. Follow up information showed that two patients died of the disease within one year despite multidisciplinary treatment. Due to the striking epithelioid appearance, this rare variant of dedifferentiated liposarcoma may be confused with undifferentiated epithelioid sarcoma, poorly differentiated carcinoma, mesothelioma or other malignancies with epithelioid phenotype. The study presented herein further highlights the aggressive clinical behavior of this unique tumor type. For patients with advanced disease, CDK4 inhibitor may provide an optional targeted treatment.
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Affiliation(s)
- Yuan Tu
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, No.2 Hospital of Chengdu 610017, China
| | - Peipei Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lin Yu
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jian Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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48
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Cuadrado Á, Montiel EE, Mora P, Figueroa RI, Lorite P, de Bustos A. Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum. Harmful Algae 2023; 130:102543. [PMID: 38061820 DOI: 10.1016/j.hal.2023.102543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/30/2023] [Accepted: 11/11/2023] [Indexed: 12/18/2023]
Abstract
Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.
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Affiliation(s)
- Ángeles Cuadrado
- Department of Biomedicine and Biotecnology, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid 28805, Spain.
| | - Eugenia E Montiel
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain; Departamento de Biología (Genética), Universidad Autonoma de Madrid, Madrid 28049, Spain
| | - Pablo Mora
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain
| | - Rosa I Figueroa
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo 36390, Spain
| | - Pedro Lorite
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotecnology, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid 28805, Spain
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49
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Laforga JB, Abdullah B. Sinonasal DEK-rearranged Papillary Non-keratinizing Squamous Cell Carcinoma: Expanding the Emerging Entity. Indian J Otolaryngol Head Neck Surg 2023; 75:3866-3870. [PMID: 37974682 PMCID: PMC10645953 DOI: 10.1007/s12070-023-03877-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/07/2023] [Indexed: 11/19/2023] Open
Abstract
The newly emerging sinonasal carcinomas have demonstrated diverse morphologies and specific molecular mutations along with deviant clinical behavior from conventional counterparts. Also, many sinonasal malignancies turned to be SMARCB1/SMARCA4-deficient. Even with the morphological similarities between poorly differentiated (non) keratinizing sinonasal squamous cell carcinoma (SNSCC) from DEK::AFF2 SNSCC, the two lesions are not distinguishable using the surrogate immunohistochemical marker AFF2 or molecular testing for DEK::AFF2 mutation. We report a rare case of SMARCB1-retained DEK-rearranged papillary non-keratinizing SNSCC in a 53-year-old female, who presented with a polypoid mass corresponding to the left middle turbinate. The tumor and locoregional lymph nodes were surgically resected, followed by adjuvant radiotherapy.
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Affiliation(s)
- Juan B. Laforga
- Department of Pathology, Hospital de Dénia, Ptda. Beniadlá, s/n, 0700 Denia, Alicante, Spain
| | - Bacem Abdullah
- Department of Pathology, Mansoura University, Mansoura, Egypt
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Lukšíková K, Pavlica T, Altmanová M, Štundlová J, Pelikánová Š, Simanovsky SA, Krysanov EY, Jankásek M, Hiřman M, Reichard M, Ráb P, Sember A. Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killi fish karyotypes. J Fish Biol 2023; 103:1501-1514. [PMID: 37661806 DOI: 10.1111/jfb.15550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Using African annual killifishes of the genus Nothobranchius from temporary savannah pools with rapid karyotype and sex chromosome evolution, we analysed the chromosomal distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (satDNA; isolated from Nothobranchius furzeri) in 15 species across the Nothobranchius killifish phylogeny, and with Fundulosoma thierryi as an out-group. Our fluorescence in situ hybridization experiments revealed that all analysed taxa share the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes. Nfu-SatC landscape was similar in conspecific populations of Nothobranchius guentheri and Nothobranchius melanospilus but slightly-to-moderately differed between populations of Nothobranchius pienaari, and between closely related Nothobranchius kuhntae and Nothobranchius orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and Nothobranchius krysanovi. We revealed mostly no sex-linked patterns of studied repetitive DNA distribution. Only in Nothobranchius brieni, possessing multiple sex chromosomes, Nfu-SatC repeat occupied a substantial portion of the neo-Y chromosome, similarly as formerly found in the XY sex chromosome system of turquoise killifish N. furzeri and its sister species Nothobranchius kadleci-representatives not closely related to N. brieni. All studied species further shared patterns of expected telomeric repeats at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed (i) the presence of conserved satDNA class in Nothobranchius clades (a rare pattern among ray-finned fishes); (ii) independent trajectories of Nothobranchius sex chromosome differentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species; and (iii) genus-wide shared tendency to loss of telomeric repeats during interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling, and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.
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Affiliation(s)
- Karolína Lukšíková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Pavlica
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Štundlová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Šárka Pelikánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Sergey A Simanovsky
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Yu Krysanov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Marek Jankásek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matyáš Hiřman
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Czech Republic
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Ráb
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Alexandr Sember
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
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