Multiparametric flow cytometry directing the evaluation of CRLF2 rearrangements and JAK2 status in pediatric B cell precursor acute lymphoblastic leukemia

Asbtract Introduction This study aimed to determine whether cytokine receptor-like factor 2 (CRLF2) antigen expression evaluated using multiparametric flow cytometry (MFC) could predict the genotype of CRLF2 and Janus kinase 2 (JAK2) status for application in the diagnosis of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Methods A total of 321 BCP-ALL bone marrow samples were collected, 291 at diagnosis and 13 at first relapse, while 17 samples were excluded due to low cellular viability. The CRLF2 antigen expression was evaluated using flow cytometry (percentage of positivity and median fluorescence intensity [MFI]). The CRLF2 transcript levels were assessed via quantitative reverse transcription polymerase chain reaction using SYBR Green. The CRLF2 rearrangements (CRLF2-r) were identified using the CRLF2 break-apart probe via fluorescence in situ hybridization. Sanger sequencing was performed to identify the JAK2 exon 16 mutations. Results We observed that 60 of the 291 cases (20.6%) presented CRLF2 antigen positivity, whereas the CRLF2 transcript overexpression was found in 19 of 113 cases (16.8%). The JAK2 mutation was found in four out of 116 cases (3.4%), all of which had CRLF2 ≥10% of positive cells and intermediate or high MFI (p < 0.0001). In addition, in the 13 cases with the CRLF2-r, a positive correlation was found with the CRLF2 antigen intermediate (61.5%) MFI (p= 0.017). Finally, the CRLF2-positive antigen was identified in the BCP-ALL subclones. Conclusion The identification of the CRLF2 antigen using the MFC, based on the percentage of positivity and MFI values, is a useful tool for predicting JAK2 mutations and CRLF2-r.

ALK, ROS1 and EGFR status of lung cancers in the Aegean Region of Turkey

Background/Aims: As targeted therapies are promising in the treatment of lung cancer (LC), it is important to identify the genetic variations in tumors. The present research aimed to determine the regional prevalence of alterations in ALK, ROS1, and EGFR genes. Materials and Methods: ALK rearrangement in 1152, ROS1 rearrangement in 390, and EGFR mutations in 1054 cases with LC were evaluated. Results: Alteration rates of ALK, ROS1, and epidermal growth factor receptor (EGFR) genes were 3.5%, 0.4%, and 11.2% in the samples, respectively. ALK rearrangements were mainly detected in young patients (P < 0.01) and in females (P < 0.01). Females were also more often inflicted by EGFR variations, especially from the exon 19 deletion. Exon 21 L858R mutations were more frequently found in men. However, any statistical significance between EGFR alterations and gender or age was not discovered. Conclusion: In this study, molecular changes were less frequent than expected. We thought that this low rate confirmed the aphorism of “smokes like a Turk, ” which could be because almost all patients were active or passive smokers.

Investigation of the genetic etiology in male infertility with apparently balanced chromosomal structural rearrangements by genome sequencing / 亚洲男科学杂志(英文版)

Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1% of azoospermia or severe oligospermia. However, the underlying mechanisms of pathogenesis and etiologies are still largely unknown. Herein, we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants. In addition, high read-depth genome sequencing (GS) (30-fold) was performed to investigate point mutations causative of male infertility. Mate-pair GS (4-fold) revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements. Overall, the breakpoints caused truncations of 30 RefSeq genes, five of which were associated with spermatogenesis. Furthermore, the breakpoints disrupted 43 topological-associated domains. Direct disruptions or potential dysregulations of genes, which play potential roles in male germ cell development, apoptosis, and spermatogenesis, were found in all cases (n = 6). In addition, high read-depth GS detected dual molecular findings in case MI6, involving a complex rearrangement and two point mutations in the gene DNAH1. Overall, our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility. We demonstrated the complexity of chromosomal structural rearrangements, potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.

Novel rearrangements between different chromosomes with direct impact on the diagnosis of 5p- syndrome

Abstract Objectives Copy Number Variations (CNVs) in the human genome account for common populational variations but can also be responsible for genetic syndromes depending on the affected region. Although a deletion in 5p is responsible for a syndrome with highly recognizable phenotypical features, other chromosomal abnormalities might overlap phenotypes, especially considering that most studies in 5p use traditional cytogenetic techniques and not molecular techniques. Methods The authors have investigated 29 patients with clinical suspicion of 5p- syndrome using Chromosomal Microarray (CMA), and have gathered information on previous tests, clinical signs, symptoms, and development of the patients. Results The results showed 23 pure terminal deletions, one interstitial deletion, one deletion followed by a 3 Mb duplication in 5p, three cases of 5p deletion concomitant to duplications larger than 20 Mb in chromosomes 2, 9, and 18, and one 5p deletion with a chromosome Y deletion. CMA showed relevant CNVs not typically associated with 5p- that may have contributed to the final phenotype in these patients. Conclusions The authors have identified three novel rearrangements between chromosomes 5 and 2 (Patient 27), 5 and 18 (Patient 11), and 5 and Y (Patient 22), with breakpoints and overlapped phenotypes that were not previously described. The authors also highlight the need for further molecular investigation using CMA, in different chromosomes beyond chromosome 5 (since those cases did not show only the typical deletion expected for the 5p- syndrome) to explain discordant chromosomal features and overlapped phenotypes to unravel the cause of the syndrome in atypical cases. HIGHLIGHTS The authors The authors have described three novel rearrangements between chromosomes 5 and 2, 5 and 18, and 5 and Y with chromosomal breakpoints and overlapped phenotypes that were not previously described. One of the main atypical features for 5p- syndrome that the authors report was the presence of seizures that was found in the three patients with rearrangements between different chromosomes and in a patient with a deletion followed by duplication in 5p. The authors suggest physicians conduct further molecular investigation in the presence of atypical clinical features for patients with 5p- syndrome suspicion.

Enfermedad residual medible mediante reordenamientos de inmunoglobulinas y receptores de linfocitos-T / Measurable residual disease by rearrangements of immunoglobulins and T-lymphocyte receptors

Resumen Las leucemias agudas constituyen la neoplasia más frecuente en pacientes pediátricos. Actualmente, el 80% de los niños con leucemia linfoblástica aguda (LLA) logran curarse con quimioterapia con vencional pero el 20% de los mismos presentarán una reaparición de la enfermedad. La enfermedad residual medible (ERM) ha sido descripta como un importante factor pronóstico, que permite evaluar la respuesta de los pacientes al tratamiento. Una de las técnicas más sensibles par a estudiar ERM es la cuantificación de reordena mientos génicos de inmunoglobulinas (Ig) y receptores de linfocitos-T (TCR). Los objetivos del presente trabajo fueron describir los reordenamientos detectados de Ig/TCR, evaluar el efecto de la ERM en la supervivencia de niños con LLA y comparar la ERM por Ig/TCR con la cuantificada mediante citometría de flujo multiparamétrica (CFM). Del total de 455 pacientes estudiados, en el 96% fue posible caracterizar al menos un reordenamiento de Ig/TCR. El total de reordenamientos clonales detectados fue de 1550. La ERM pudo ser estudiada en forma exitosa en el 89% de los casos. El valor de ERM positiva combinada al día 33 y 78 de tratamiento, permitió identificar pacientes de alto riesgo, entre los previamente estratificados por la ERM mediante CFM al día 15. La comparación entre la determinación de ERM mediante reordenamientos Ig/TCR y CFM mostró una excelente correlación. El presente trabajo constituye un estudio de ERM mediante Ig/TCR realizado en un número muy significativo de pacientes diagnosticados en forma consecutiva, tratados en el marco de un protocolo homogéneo y con excelente seguimiento clínico.

Abstract Acute leukemias are the most common neoplasm in pediatric patients. Currently, 80% of children with diagnosis of acute lymphoblastic leukemia (ALL) are cured with conventional chemotherapy, but 20% of them will have a recurrence of the disease. Measurable Residual Disease (MRD) has been described as an important prognostic factor that allows evaluating the response of patients to treatment. One of the most sensitive techniques to study MRD is the quantification of immunoglobulins (Ig) and T-lymphocyte receptors (TCR) genes rearrangements. The aims of this study were to describe the detected Ig/TCR rearrangements, to evaluate the prognostic impact of MRD in our population of children with ALL and to compare the MRD values by Ig/TCR with those obtained by multiparametric flow cytometry (MFC). A total of 455 patients were studied. In 96% of the cases, it was possible to characterize at least one Ig/TCR rearrangement. The total number of Ig/TCR rear rangements detected was 1550. MRD was successfully applied in 89% of the cases. The combined positive MRD values at day 33 and 78 of treatment allow the identification of high-risk patients in cases previously stratified by MRD using flow cytometry at day 15. The comparison between MRD determination by Ig/TCR rearrangements and FC showed excellent correlation. The present work constitutes a study of MRD by Ig/TCR carried out in a very significant number of patients consecutively diagnosed, treated within a homogeneous protocol and with excellent clinical follow-up.

Caracterización del perfil de reordenamientos génicos de inmunoglobulinas y receptores de linfocitos T en leucemia linfoblástica aguda pediátrica / Pattern of immunoglobulins and T lymphocyte receptor gene rearrangements in childhood acute lymphoblastic leukemia / Caracterização do perfil de rearranjos gênicos de imunoglobulinas e receptores de linfócitos T na leucemia linfoide aguda pediátrica

Resumen Durante la ontogenia linfocitaria se produce el reordenamiento de los segmentos génicos V-(D)-J que codifican para la región variable de las cadenas de inmunoglobulinas (Ig) y receptores de linfocitos T (TCR). Durante este proceso, los segmentos se reordenan al azar y ocurren deleciones e inserciones de nucleótidos en la región de unión entre ellos. Los objetivos del presente trabajo fueron describir las incidencias de los reordenamientos Ig/TCR y de los segmentos V-(D)-J involucrados, en niños con leucemia linfoblástica aguda (LLA). Para ello se estudiaron 769 pacientes pediátricos con LLA, diagnosticados entre 1999 y 2018 por los centros de la Sociedad Argentina de Hemato-Oncología Pediátrica. Se caracterizaron reordenamientos de Ig/TCR mediante PCR-multiplex y secuenciación para la búsqueda de recombinaciones génicas IGH, IGK, TCRB, TCRG y TCRD, en muestras de ADN obtenidas de médula ósea o sangre periférica al diagnóstico. El 95% (n=730) de los casos presentaron reordenamientos Ig/TCR. En el 68% de los casos se caracterizaron recombinaciones génicas IGH, en 43% IGK, en 25% TCRB, en 49% TCRG y en el 55% TCRD. Se caracterizó un total de 2506 reordenamientos de Ig/TCR que correspondían 1161 a inmunoglobulinas y 1345 a TCR. En la mayoría de los casos los reordenamientos de IGH fueron completos, IGK involucró a IGKde, TRCB se reordenó frecuentemente con el segmento Jb2, TCRG involucró preferentemente a Vg9 y los TCRD fueron principalmente reordenamientos incompletos. Este trabajo constituye el primer estudio realizado en la Argentina sobre la caracterización de reordenamientos Ig/TCR en un número muy significativo de pacientes con LLA pediátrica.

Abstract During lymphocyte ontogeny, the variable region of immunoglobulin (Ig) and T-cell receptor (TCR) is generated by rearrangements of the V-(D)-J gene segments. In this random process, nucleotide deletions and insertions occur between V-(D)-J segments. The aims of this work were to describe the incidence of Ig/TCR rearrangements, and the V-(D)-J segments involved in acute lymphoblastic leukemia (ALL) patients. With this purpose, 769 pediatric ALL patients belonging to Sociedad Argentina de Hemato-Oncología Pediátrica, diagnosed between 1999 and 2018, were studied. Ig/TCR rearrangements were characterized by multiplex PCR and sequencing to evaluate IGH, IGK, TCRB, TCRG and TCRD rearrangements in DNA samples obtained at diagnosis from bone marrow or peripheral blood. In total, 95% (n=730) of patients disclosed Ig/TCR rearrangements. IGH rearrangements were detected in 68% of cases; in 43% IGK, in 25% TCRB, in 49% TCRG and in 55% of cases, TCRD. A total of 2506 Ig/TCR rearrangements were characterized, being 1161 immunoglobulins and 1345 TCR. In most cases, IGH rearrangements were complete, IGK involved IGKde, TRCB was frequently rearranged with the Jb2 segment, TCRG preferentially involved Vg9, and TCRDs were mostly incomplete rearrangements. This work is the first study of Ig/TCR rearrangements characterization in a very significant number of childhood ALL carried out in Argentina.

Resumo Durante a ontogenia dos linfócitos, ocorre um rearranjo dos segmentos gênicos V-(D)-J que codificam para a região variável das cadeias de imunoglobulinas (Ig) e receptores de linfócitos T (TCR). Durante esse processo, os segmentos reorganizam-se aleatoriamente e exclusões e inserções de nucleotídeos ocorrem na região da união entre eles. Os objetivos do presente trabalho foram descrever as incidências dos rearranjos Ig/TCR e dos segmentos V-(D)-J envolvidos, em crianças com leucemia linfoide aguda (LLA). Para tanto, foram estudados 769 pacientes pediátricos com LLA, diagnosticados entre 1999 e 2018 pelos centros da Sociedade Argentina de Hemato-Oncologia Pediátrica. Rearranjos de Ig/TCR foram caracterizados através de PCR-multiplex e sequenciação para procurar recombinações gênicas IGH, IGK, TCRB, TCRG e TCRD em amostras de DNA obtidas da medula óssea ou sangue periférico no diagnóstico. Do total de pacientes estudados, 95% (n=730) apresentaram rearranjos de Ig/TCR. Os rearranjos gênicos IGH foram caracterizados em 68% dos casos, em 43% de IGK, em 25% de TCRB, em 49% de TCRG e em 55% de TCRD. Foi caracterizado um total de 2506 rearranjos de Ig/TCR, correspondendo 1161 a imunoglobulinas e 1345 a TCR. Na maioria dos casos, os rearranjos de IGH foram concluídos, o IGK envolveu o IGKde, o TRCB foi frequentemente rearranjado com o segmento Jb2, o TCRG preferencialmente envolveu o Vg9 e os TCRDs foram principalmente os rearranjos incompletos. Este trabalho constitui o primeiro estudo realizado na Argentina sobre a caracterização de rearranjos de Ig/TCR em um número muito significativo de pacientes com LLA pediátrica.

Linfocitose extrema associada à leucemia linfoblástica aguda (LLA) de células T em um cão jovem: relato de caso / Extreme lymphocytosis associated with acute T-cell lymphoblastic leukemia (ALL) in a young dog: case report

A leucemia linfoblástica aguda (LLA) é uma enfermidade de origem linfóide e consiste na proliferação de células neoplásicas na medula óssea. O objetivo desse trabalho é relatar o caso de um cão macho, sem raça definida, de apenas um ano de idade, atendido no Hospital Universitário de Medicina Veterinária Prof. Firmino Mársico Filho (HUVET) da Universidade Federal Fluminense (UFF) com queixa principal de inapetência e diarreia há três dias e que foi diagnosticado com essa neoplasia por meio da sintomatologia clínica, resultados do hemograma e do mielograma. O paciente apresentava valores exacerbados de linfócitos (553.094 células/µL), além de anemia, trombocitopenia, hipoalbuminemia e elevação da atividade das enzimas fosfatase alcalina e ALT. Foram observadas manchas de Gümprecht, linfócitos atípicos apresentando anisocitose, anisocariose, intensa basofilia citoplasmática e monócitos ativados. O mielograma apresentou também um aumento de linfócitos e contagem de linfoblastos superior a 30% na medula, confirmando o diagnóstico de leucemia linfoblástica aguda. Ademais, posteriormente, foi realizado exame de Reação em Cadeia de Polimerase (PCR) para rearranjos de receptores de antígenos e foi detectado clonalidade para linfócitos T. O animal foi submetido à quimioterapia (protocolo com ciclofosfamida, vincristina e prednisona) mas não resistiu à gravidade do quadro, vindo a óbito após a primeira sessão, pouco tempo após o diagnóstico.

Acute lymphoblastic leukemia (LLA) is a disease with a lymphoid origin and consists of the proliferation of neoplastic cells in the bone marrow. The aim of this study was to report the case of only one year old mixed breed male dog, attended at the University Hospital of Veterinary Medicine Prof. Firmino Mársico Filho (HUVET) from Universidade Federal Fluminense (UFF), with major complaint of inappetence and diarrhea three days ago and which was diagnosed with this neoplasm through clinical symptoms, complete blood count and myelogram results. The patient had increased values of lymphocytes (553,094 cells/µL), in addition to anemia, thrombocytopenia, hypoalbuminemia and elevated alkaline phosphatase and ALT activities. Gümprecht shadows, atypical lymphocytes presenting anisocytosis, anisocariosis, and severe cytoplasmic basophilia and activated monocytes were observed. Myelogram also showed an increase in lymphocytes and a lymphoblastic count greater than 30% in the marrow, confirming the diagnosis of LLA. In addition, polymerase chain reaction (PCR) for antigen receptor rearrangements was performed and clonality for T lymphocytes was detected. The animal underwent chemotherapy (protocol with cyclophosphamide, vincristine and prednisone), but did not withstand the severity of the disease, coming to death after the first session, shorly after diagnosis.

Linfocitose extrema associada à leucemia linfoblástica aguda (LLA) de células T em um cão jovem: relato de caso / Extreme lymphocytosis associated with acute T-cell lymphoblastic leukemia(ALL) in a young dog: case report

A leucemia linfoblástica aguda (LLA) é uma enfermidade de origem linfóide e consiste na proliferação de células neoplásicas na medula óssea. O objetivo desse trabalho é relatar o caso de um cão macho, sem raça definida, de apenas um ano de idade, atendido no Hospital Universitário de Medicina Veterinária Prof. Firmino Mársico Filho (HUVET) da Universidade Federal Fluminense (UFF) com queixa principal de inapetência e diarreia há três dias e que foi diagnosticado com essa neoplasia por meio da sintomatologia clínica, resultados do hemograma e do mielograma. O paciente apresentava valores exacerbados de linfócitos (553.094 células/µL), além de anemia, trombocitopenia, hipoalbuminemia e elevação da atividade das enzimas fosfatase alcalina e ALT. Foram observadas manchas de Gümprecht, linfócitos atípicos apresentando anisocitose, anisocariose, intensa basofilia citoplasmática e monócitos ativados. O mielograma apresentou também um aumento de linfócitos e contagem de linfoblastos superior a 30% na medula, confirmando o diagnóstico de leucemia linfoblástica aguda. Ademais, posteriormente, foi realizado exame de Reação em Cadeia de Polimerase (PCR) para rearranjos de receptores de antígenos e foi detectado clonalidade para linfócitos T. O animal foi submetido à quimioterapia (protocolo com ciclofosfamida, vincristina e prednisona), mas não resistiu à gravidade do quadro, vindo a óbito após a primeira sessão, pouco tempo após o diagnóstico.

Acute lymphoblastic leukemia (LLA) is a disease with a lymphoid origin and consists of the proliferation of neoplastic cells in the bone marrow. The aim of this study was to report the case of only one year old mixed breed male dog, attended at the University Hospital of Veterinary Medicine Prof. Firmino Mársico Filho (HUVET) from Universidade Federal Fluminense (UFF), with major complaint of inappetence and diarrhea three days ago and which was diagnosed with this neoplasm through clinical symptoms, complete blood count and myelogram results. The patient had increased values of lymphocytes (553,094 cells/μL), in addition to anemia, thrombocytopenia, hypoalbuminemia and elevated alkaline phosphatase and ALT activities. Gümprecht shadows, atypical lymphocytes presenting anisocytosis, anisocariosis, and severe cytoplasmic basophilia and activated monocytes were observed. Myelogram also showed an increase in lymphocytes and a lymphoblastic count greater than 30% in the marrow, confirming the diagnosis of LLA. In addition, polymerase chain reaction (PCR) for antigen receptor rearrangements was performed and clonality for T lymphocytes was detected. The animal underwent chemotherapy (protocol with cyclophosphamide, vincristine and prednisone), but did not withstand the severity of the disease, coming to death after the first session, shortly after diagnosis.

‘Distal 16p12.2 microdeletion’ in a patient with autosomal recessive deafness-22

The 16p12.2 chromosome band contains three large segmental duplications: BP1, BP2 and BP3, providing a substrate for recombination and recurrent chromosomal rearrangements. The ‘16p12.2 microdeletion’ is a recurrent deletion comprised between BP2 and BP3, associated with variable clinical findings. We identified a heterozygous 16p12.2 microdeletion spanning between BP1 and BP2 in a child evaluated for short stature and mild dyslexia. Unexpectedly, the mother carried the same deletion in the homozygous state and suffered from severe hearing loss. Detailed family history revealed consanguinity of the maternal grandparents. The 16p12.2 microdeletion is a rare condition and contains only three genes: METTL9, IGSF6 and OTOA of which the OTOA is considered responsible for DFNB22 hearing loss (MIM: 607039) under its homozygous condition. A number of OTOA mutations have been described, whereas very few cases of a 16p12.2 microdeletion similar to that observed in our family have been reported. In conclusion, we describe a rare ‘distal 16p12.2microdeletion’ widening the phenotypic spectrum associated with the recurrent 16p12.2 microdeletion and support the causative role of OTOA microdeletion in hearing impairment.

Cytogenetic markers as tools in delimiting species of the highly diverse Neotropical fish Bryconamericus (Characiformes: Characidae)

Bryconamericus is a highly diverse group of characid fishes, being cytogenetic a valuable tool for the delimitation of species. Bryconamericus aff. iheringii (Upper Uruguay/Lower Paraná), B. coeruleus (Upper Paraná), B. cf. ecai e B. cf. eigenmanni (Upper Uruguay) were studied cytogenetically, and presented 2n=52 chromosomes, with interpopulational/interspecific variation of karyotype and fundamental number. Heterochromatin was evidenced in pericentromeric, telomeric and interstitial regions, and it was shown to be an important cytogenetic marker. Single nucleolar organizing regions (NORs) were found in B. cf. eigenmanni, B. cf. ecai and B. aff. iheringii (Lower Paraná), and multiple in B. aff. iheringii (Upper Uruguay) and B. coeruleus, with occurrence of two patterns for the first species, and three for the second. The 5S/18S rDNA-FISH confirmed the location of the NORs and showed single 5S rDNA cistrons only in B. aff. iheringii (Lower Paraná), evidencing the dispersion of both genes, often co-located, in the karyotype of the others species. The data of this work contribute for the delimitation of the species of the genus. Co-localization of ribosomal genes may represent a plesiomorphic condition for the group, and their dispersion suggest the occurrence of duplication, pseudogeneization and transposition events mediated by mobile genetic elements.(AU)

Bryconamericus é um grupo altamente diverso de caracídeos, sendo a citogenética uma valiosa ferramenta para a delimitação de espécies. Bryconamericus aff. iheringii (Alto Uruguai/Baixo Paraná), B. coeruleus (Alto Paraná), B. cf. ecai e B. cf. eigenmanni (Alto Uruguai) foram estudados citogeneticamente, e apresentaram 2n=52 cromossomos, com variação interpopulacional/interespecífica de cariótipo e número fundamental (NF). Heterocromatinas foram evidenciadas nas regiões pericentromérica, telomérica e intersticial, e mostrou-se um importante marcador citogenético. Regiões organizadores de nuclcéolos (RONs) simples foram encontradas em B. cf. eigenmanni, B. cf. ecai e B. aff. iheringii (Baixo Paraná), e múltiplas em B. aff. iheringii (Alto Uruguai) e em B. coeruleus, com a ocorrência de dois padrões de localização para a primeira espécie, e três para a segunda. A FISH-DNAr 5S/18S confirmou a localização das RONs e mostrou cístrons simples de DNAr 5S apenas em B. aff. iheringii (Baixo Paraná), evidenciando a dispersão de ambos os genes, muitas vezes co-localizados, no cariótipo das demais espécies. Os dados deste trabalho contribuem para a delimitação das espécies do gênero. A co-localização dos genes ribossomais pode representar uma condição plesiomórfica para o grupo, e sua dispersão sugere a ocorrência de eventos de duplicação, pseudogenização e transposição mediada por elementos genéticos móveis.(AU)

Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes)

Abstract An extensive karyotype variation is found among species belonging to the Columbidae family of birds (Columbiformes), both in diploid number and chromosomal morphology. Although clusters of repetitive DNA sequences play an important role in chromosomal instability, and therefore in chromosomal rearrangements, little is known about their distribution and amount in avian genomes. The aim of this study was to analyze the distribution of 11 distinct microsatellite sequences, as well as clusters of 18S rDNA, in nine different Columbidae species, correlating their distribution with the occurrence of chromosomal rearrangements. We found 2n values ranging from 76 to 86 and nine out of 11 microsatellite sequences showed distinct hybridization signals among the analyzed species. The accumulation of microsatellite repeats was found preferentially in the centromeric region of macro and microchromosomes, and in the W chromosome. Additionally, pair 2 showed the accumulation of several microsatellites in different combinations and locations in the distinct species, suggesting the occurrence of intrachromosomal rearrangements, as well as a possible fission of this pair in Geotrygon species. Therefore, although birds have a smaller amount of repetitive sequences when compared to other Tetrapoda, these seem to play an important role in the karyotype evolution of these species.

Proliferación linfoide indolente cutánea CD8 positiva a propósito de tres casos con compromiso facial / Indolent CD8-positive t-cell lymphoid proliferation: on purpose three cases of facial commitment

Resumen La proliferación linfoide indolente cutánea CD8 positiva es una variante recientemente descrita de linfoma T cutáneo que se caracteriza por un nódulo, pápula o placa eritematosa de crecimiento lento que puede afectar la región facial o extrafacial. En el estudio de patología se caracteriza por un infiltrado monomorfo de linfocitosTalo largo de la dermis con presencia de zona de Grenz y ausencia de epidermotropismo. El infiltrado es característicamente CD8+ así como CD3+, TIA-1+, CD4-, CD56- CD30-, PD-1-, Granzima B- y EBER negativo. El índice de proliferación Ki-67 es inferior al 10% y se observan reordenamientos clonales de los genes del receptor de antígeno de la célula T, TCR. El seguimiento clínico es favorable y no se ha observado compromiso sistémico. Se presentan tres casos con compromiso facial (dos casos en pabellón auricular y un caso con compromiso nasal), con presentación clínica y hallaz gos histopatológicos típicos (curiosamente un caso con cambio de célula clara), y además se realizaron estudios de clonalidad.

Abstract Primary cutaneous indolent CD8-positive lymphoid proliferation is a recent variant of cutaneous T lymphoma that is characterized by nodule, papule or plaque erythematous with slow growth that can affect the facial or extrafacial region. In the histopathology study it is characterized by an infiltration of monomorphic T lymphocytes throughout the dermis with presence of Grenz zone and absence of epidermotropism. The infiltrate is characteristically CD 8+ and CD3+ TIA-1+ CD4-, CD56- CD30, PD-1, Granzyme B- and negative EBER. Ki-67 Proliferación linfoide indolente cutánea CD8 positiva a propósito de tres casos proliferation index is less than 10% and clonal T-cell receptor gene rearrangements. Clinical follow-up is favorable and has not been observed systemic involvement. We present three cases with facial involvement (two cases in ear and one case with nasal commitment) with typical clinical presentation, histopathological findings (curiously a case with clear cell change) and clonality studies.

Characterization of clonal immunoglobulin heavy (IGH) V-D-J gene rearrangements and the complementarity-determining region in South Indian patients with precursor B-cell acute lymphoblastic leukemia

BACKGROUND: This study characterized clonal IG heavy V-D-J (IGH) gene rearrangements in South Indian patients with precursor B-cell acute lymphoblastic leukemia (precursor B-ALL) and identified age-related predominance in VDJ rearrangements. METHODS: IGH rearrangements were studied in 50 precursor B-ALL cases (common ALL=37, pre-B ALL=10, pro-B ALL=3) by polymerase chain reaction (PCR) heteroduplex analysis. Twenty randomly selected clonal IGH rearrangement sequences were analyzed using the IMGT/V-QUEST tool. RESULTS: Clonal IGH rearrangements were detected in 41 (82%) precursor B-ALL cases. Among the IGHV1-IGHV7 subgroups, IGHV3 was used in 25 (50%) cases. Among the IGHD1-IGHD7 genes, IGHD2 and IGHD3 were used in 8 (40%) and 5 (25%) clones, respectively. Among the IGHJ1-IGHJ6 genes, IGHJ6 and IGHJ4 were used in 9 (45%) and 6 (30%) clones, respectively. In 6 out of 20 (30%) IGH rearranged sequences, CDR3 was in frame whereas 14 (70%) had rearranged sequences and CDR3 was out of frame. A somatic mutation in Vmut/Dmut/Jmut was detected in 14 of 20 IGH sequences. On average, Vmut/Dmut/Jmut were detected in 0.1 nt, 1.1 nt, and 0.2 nt, respectively. CONCLUSION: The IGHV3 gene was frequently used whereas lower frequencies of IGHV5 and IGHV6 and a higher frequency of IGHV4 were detected in children compared with young adults. The IGHD2 and IGHD3 genes were over-represented, and the IGHJ6 gene was predominantly used in precursor-B-ALL. However, the IGH gene rearrangements in precursor-B-ALL did not show any significant age-associated genotype pattern attributed to our population.

Mutations in BRCA1, BRCA2 and other breast and ovarian cancer susceptibility genes in Central and South American populations

Breast cancer (BC) is the most common malignancy among women worldwide. A major advance in the understanding of the genetic etiology of BC was the discovery of BRCA1 and BRCA2 (BRCA1/2) genes, which are considered high-penetrance BC genes. In non-carriers of BRCA1/2 mutations, disease susceptibility may be explained of a small number of mutations in BRCA1/2 and a much higher proportion of mutations in ethnicity-specific moderate- and/or low-penetrance genes. In Central and South American populations, studied have focused on analyzing the distribution and prevalence of BRCA1/2 mutations and other susceptibility genes that are scarce in Latin America as compared to North America, Europe, Australia, and Israel. Thus, the aim of this review is to present the current state of knowledge regarding pathogenic BRCA variants and other BC susceptibility genes. We conducted a comprehensive review of 47 studies from 12 countries in Central and South America published between 2002 and 2017 reporting the prevalence and/or spectrum of mutations and pathogenic variants in BRCA1/2 and other BC susceptibility genes. The studies on BRCA1/2 mutations screened a total of 5956 individuals, and studies on susceptibility genes analyzed a combined sample size of 11,578 individuals. To date, a total of 190 different BRCA1/2 pathogenic mutations in Central and South American populations have been reported in the literature. Pathogenic mutations or variants that increase BC risk have been reported in the following genes or genomic regions: ATM, BARD1, CHECK2, FGFR2, GSTM1, MAP3K1, MTHFR, PALB2, RAD51, TOX3, TP53, XRCC1, and 2q35.

Submicroscopic Deletions of Immunoglobulin Heavy Chain Gene (IGH) in Precursor B Lymphoblastic Leukemia with IGH Rearrangements

Translocations leading to fusions between the immunoglobulin heavy chain gene (IGH) and various partner genes have been reported in B-cell precursor acute lymphoblastic leukemia (B-ALL). However, submicroscopic deletions within IGH in B-ALL have not been rigorously assessed. In this study, we investigated characteristics of IGH submicroscopic deletions, by FISH, in B-ALL with IGH rearrangements. FISH was performed by using commercially available IGH dual-color break-apart rearrangement probes (Abbott/Vysis, Downers Grove, IL, USA; Kreatech, Amsterdam, Netherlands). The study group included seven B-ALL patients with IGH rearrangements, observed by FISH. Among them, two exhibited deletion of the 5' variable region of IGH by FISH. The B-ALL in these two patients included two kinds of abnormal cells; one had an IGH rearrangement without any IGH submicroscopic deletion, while the other had an IGH submicroscopic deletion, which showed that one normal fusion signal and one 3' IGH signal were detected. Thus, submicroscopic deletion of the IGH 5' variable region may have occurred in either the native or rearranged chromosome 14. These findings indicate that B-ALL with IGH rearrangements may be accompanied by submicroscopic deletions of the IGH 5' variable region, which can be detected by FISH. The clinical significance of such deletions is unclear, but the loss of part of the IGH gene in B-ALL warrants further study.

B chromosome and NORs polymorphism in Callichthys callichthys (Linnaeus, 1758) (Siluriformes: Callichthyidae) from upper Paraná River, Brazil

B chromosomes are extra chromosomes from the normal chromosomal set, found in different organisms, highlighting their presence on the group of fishes. Callichthys callichthys from the upper Paraná River has a diploid number of 56 chromosomes (26 m-sm + 30 st-a) for both sexes, with the presence of a sporadically acrocentric B chromosome. Moreover, one individual presented a diploid number of 57 chromosomes, with the presence of a morphologically ill-defined acrocentric B chromosome in all analyzed cells. The physical mapping of 5S and 18S rDNA shows multiple 5S rDNA sites and only one pair of chromosomes with 18S sites in C. callichthys, except for two individuals. These two individuals presented a third chromosome bearing NORs (Ag-staining and 18S rDNA) where 5S and 18S rDNA genes are syntenic, differing only in position. The dispersion of the 18S rDNA genes from the main st-a chromosome pair 25 to one of the chromosomes from the m-sm pair 4 would have originated two variant individuals, one of which with the ill-defined acrocentric B chromosome. Mechanisms to justify the suggested hypothesis about this B chromosome origin are discussed in the present study...

Cromossomos B são cromossomos extras ao conjunto cromossômico normal, encontrado em diferentes organismos, com destaque para sua presença no grupo de peixes. Callichthys callichthys do alto rio Paraná tem um número diploide de 56 cromossomos (26 m-sm + 30 st-a) para ambos os sexos, com a presença esporádica de um cromossomo B acrocêntrico. Além do mais, um indivíduo apresentou número diploide de 57 cromossomos, com a presença de um cromossomo B acrocêntrico morfologicamente mal definido em todas as células analisadas. O mapeamento físico do DNAr 5S e 18S mostrou múltiplos sítios de DNAr 5S e apenas um par de cromossomos com sítio para o DNAr 18S em C. callichthys, com exceção para dois indivíduos. Estes dois indivíduos apresentaram um terceiro cromossomo portador das RONs (Ag-RONs e 18S rDNA), onde os genes DNAr 5S e 18S são sintênicos, diferindo apenas na posição. A dispersão dos genes DNAr 18S do par de cromossomos principal st-a 25 para um dos cromossomos do par m-sm 4 teria originado dois indivíduos variantes, um dos quais com cromossomo B acrocêntrico mal definido. Mecanismos para justificar a hipótese sugerida sobre a origem deste cromossomo B são discutidos no presente estudo...

Utilization of combined flow cytometry and clonal TCR gene rearrangements in the diagnosis of T-cell lymphoma / 实用医学杂志

Objective To study the usefulness of combined flow cytometry (FCM) and polymerasechain reaction examination for clonal TCR gene rearrangements in the diagnosis of T-cell lymphoma (T-NHL). Methods Histopathologic features, immunohistochemistry, flow cytometric immunophenotyping, cytomorphologic evaluation and TCR gene rearrangements of 32 T-NHL were reviewed retrospectively. The control cases were 18 reactive lesions and 1 histiocytic necrotizing lymphaderitis. Results Out of 32 T-NHL,23 were diagnosed as T-NHL by FCM / TCR gene rearrangements. Of 19 control group, 17 were diagnosed as reactive lesions by FCM / TCR gene rearrangements. The sensitivity, specificity and accuracy were 71.9%, 89.5% and 78.4%, respectively. Conclusions FCM / TCR gene rearrangement is a very important technique in diagnosing T-NHL. Thus, patients with fine needle aspiration cytology can be saved from having an invasive surgery.

Subtelomeric chromosomal rearrangements in a large cohort of unexplained intellectually disabled individuals in Indonesia: A clinical and molecular study.

CONTEXT: Unbalanced subtelomeric chromosomal rearrangements are often associated with intellectual disability (ID) and malformation syndromes. The prevalence of such rearrangements has been reported to be 5-9% in ID populations. AIMS: To study the prevalence of subtelomeric rearrangements in the Indonesian ID population. MATERIALS AND METHODS: We tested 436 subjects with unexplained ID using multiplex ligation dependent probe amplification (MLPA) using the specific designed sets of probes to detect human subtelomeric chromosomal imbalances (SALSA P070 and P036D). If necessary, abnormal findings were confirmed by other MLPA probe kits, fluorescent in situ hybridization or Single Nucleotide Polymorphism array. RESULTS: A subtelomeric aberration was identified in 3.7% of patients (16/436). Details on subtelomeric aberrations and confirmation analyses are discussed. CONCLUSION: This is the first study describing the presence of subtelomeric rearrangements in individuals with ID in Indonesia. Furthermore, it shows that also in Indonesia such abnormalities are a prime cause of ID and that in developing countries with limited diagnostic services such as Indonesia, it is important and feasible to uncover the genetic etiology in a significant number of cases with ID.

Translocações cromossômicas entre trigo e centeio: uma alternativa ao melhoramento / Chromosomes translocations between wheat and rye: an alternative to plant breeding

Translocações são rearranjos cromossômicos estruturais que envolvem segmentos cromossômicos de extensão variada pertencentes a cromossomos homólogos ou não homólogos. Tanto a ocorrência natural quanto a induzida de translocações tem possibilitado um avanço no melhoramento varietal, uma vez que esses segmentos translocados podem carregar genes de resistência a estresses bióticos e abióticos. O centeio é uma espécie da famíla Triticeae muito utilizada para transferência de genes para o trigo como, por exemplo, genes de resistência às ferrugens da folha e do colmo e também genes que favorecem o rendimento, tanto em quantidade como em qualidade de grãos. Assim, o objetivo deste artigo foi o de revisar as principais translocações envolvendo o trigo e o centeio, no qual se verificou, a partir dos dados analisados, que as translocações envolvendo os cromossomos 1 e 2 mostraram-se mais vantajosas para o rendimento de grãos em trigo e que as demais foram importantes, principalmente, na transferência de genes de resistência a estresses. Portanto, essa estratégia tem demonstrado efetividade na busca de novos genes que favorecem o cultivo de trigo e sua utilização vem crescendo grandemente nos últimos anos.

Translocations are structural chromosomal rearrangements which involve segments with different length belonging to homologous or non homologous chromosomes. Either natural or induced occurrence of translocations have been enabled an improvement in the plant breeding, when these translocated segments carry resistance genes to biotic and abiotic stress. Rye is a grass largely used to transfer genes to wheat such as resistance genes to leaf rust, stem rust and genes that support the wheat yield, either in grain quantity or in quality. Thus, the aim of this paper was to review the main translocations involving wheat and rye, which demonstrated, from the data analyzed, that translocations involving chromosomes 1 and 2 were more advantageous for grain yield in wheat and that the others were important, especially, in the transfer of resistance genes. Therefore, this strategy has demonstrated effectiveness on search for new genes that favor the cultivation of wheat and its use has grown greatly in recent years.