1
|
Tolomeo D, Agostini A, Solimando AG, Cunsolo CL, Cimarosto L, Palumbo O, Palumbo P, Carella M, Hernández-Sánchez M, Hernández-Rivas JM, Storlazzi CT. A t(4;13)(q21;q14) translocation in B-cell chronic lymphocytic leukemia causing concomitant homozygous DLEU2/miR15a/miR16-1 and heterozygous ARHGAP24 deletions. Cancer Genet 2023; 272-273:16-22. [PMID: 36641997 DOI: 10.1016/j.cancergen.2023.01.003] [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: 04/20/2022] [Revised: 12/06/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
13q14 deletion is the most recurrent chromosomal aberration reported in B-CLL, having a favorable prognostic significance when occurring as the sole cytogenetic alteration. However, its clinical outcome is also related to the deletion size and number of cells with the del(13)(q14) deletion. In 10% of cases, 13q14 deletion arises following a translocation event with multiple partner chromosomes, whose oncogenic impact has not been investigated so far due to the assumption of a possible role as a passenger mutation. Here, we describe a t(4;13)(q21;q14) translocation occurring in a B-CLL case from the diagnosis to spontaneous regression. FISH and SNP-array analyses revealed a heterozygous deletion at 4q21, leading to the loss of the Rho GTPase Activating Protein 24 (ARHGAP24) tumor suppressor gene, down-regulated in the patient RNA, in addition to the homozygous deletion at 13q14 involving DLEU2/miR15a/miR16-1 genes. Interestingly, targeted Next Generation Sequencing analysis of 54 genes related to B-CLL indicated no additional somatic mutation in the patient, underlining the relevance of this t(4;13)(q21;q14) aberration in the leukemogenic process. In all tested RNA samples, RT-qPCR experiments assessed the downregulation of the PCNA, MKI67, and TOP2A proliferation factor genes, and the BCL2 anti-apoptotic gene as well as the up-regulation of TP53 and CDKN1A tumor suppressors, indicating a low proliferation potential of the cells harboring the aberration. In addition, RNA-seq analyses identified four chimeric transcripts (ATG4B::PTMA, OAZ1::PTMA, ZFP36::PTMA, and PIM3::BRD1), two of which (ATG4B::PTMA and ZFP36::PTMA) failed to be detected at the remission, suggesting a possible transcriptional remodeling during the disease course. Overall, our results indicate a favorable prognostic impact of the described chromosomal aberration, as it arises a permissive molecular landscape to the spontaneous B-CLL regression in the patient, highlighting ARHGAP24 as a potentially relevant concurrent alteration to the 13q14 deletion in delineating B-CLL disease evolution.
Collapse
Affiliation(s)
- Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Agostini
- Department of Precision and Regenerative Medicine and Jonic area, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Precision and Regenerative Medicine and Jonic area, University of Bari Aldo Moro, Bari, Italy
| | | | | | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Maria Hernández-Sánchez
- Universidad de Salamanca, IBSAL, Centro de Investigación del Cáncer, IBMCC-CSIC, Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy.
| |
Collapse
|
2
|
Livermore C, Simon M, Reeves R, Stévant I, Nef S, Pope M, Mallon AM, Wells S, Warr N, Greenfield A. Protection Against XY Gonadal Sex Reversal by a Variant Region on Mouse Chromosome 13. Genetics 2020; 214:467-477. [PMID: 31836612 PMCID: PMC7017026 DOI: 10.1534/genetics.119.302786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/12/2019] [Indexed: 12/30/2022] Open
Abstract
XY C57BL/6J (B6) mice harboring a Mus musculus domesticus-type Y chromosome (Y POS ), known as B6.Y POS mice, commonly undergo gonadal sex reversal and develop as phenotypic females. In a minority of cases, B6.Y POS males are identified and a proportion of these are fertile. This phenotypic variability on a congenic B6 background has puzzled geneticists for decades. Recently, a B6.Y POS colony was shown to carry a non-B6-derived region of chromosome 11 that protected against B6.Y POS sex reversal. Here. we show that a B6.Y POS colony bred and archived at the MRC Harwell Institute lacks the chromosome 11 modifier but instead harbors an ∼37 Mb region containing non-B6-derived segments on chromosome 13. This region, which we call Mod13, protects against B6.Y POS sex reversal in a proportion of heterozygous animals through its positive and negative effects on gene expression during primary sex determination. We discuss Mod13's influence on the testis determination process and its possible origin in light of sequence similarities to that region in other mouse genomes. Our data reveal that the B6.Y POS sex reversal phenomenon is genetically complex and the explanation of observed phenotypic variability is likely dependent on the breeding history of any local colony.
Collapse
MESH Headings
- Animals
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 13/metabolism
- DNA-Binding Proteins/genetics
- Disorders of Sex Development/genetics
- Disorders of Sex Development/metabolism
- Female
- Gene Expression Regulation, Developmental/genetics
- Genome
- Gonadal Dysgenesis, 46,XY/genetics
- Gonadal Dysgenesis, 46,XY/metabolism
- Gonads/metabolism
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/genetics
- Ovary/metabolism
- Sex Determination Processes/genetics
- Testis/metabolism
- Transcription Factors/genetics
- Y Chromosome/genetics
Collapse
Affiliation(s)
| | - Michelle Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Richard Reeves
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva Medical School, CH 1211 Geneva 4, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, CH 1211 Geneva 4, Switzerland
| | - Madeleine Pope
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Nick Warr
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Andy Greenfield
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| |
Collapse
|
3
|
Fernández-Martínez JL, de Andrés-Galiana EJ, Fernández-Ovies FJ, Cernea A, Kloczkowski A. Robust Sampling of Defective Pathways in Multiple Myeloma. Int J Mol Sci 2019; 20:ijms20194681. [PMID: 31546608 PMCID: PMC6801400 DOI: 10.3390/ijms20194681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/12/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
We present the analysis of defective pathways in multiple myeloma (MM) using two recently developed sampling algorithms of the biological pathways: The Fisher's ratio sampler, and the holdout sampler. We performed the retrospective analyses of different gene expression datasets concerning different aspects of the disease, such as the existing difference between bone marrow stromal cells in MM and healthy controls (HC), the gene expression profiling of CD34+ cells in MM and HC, the difference between hyperdiploid and non-hyperdiploid myelomas, and the prediction of the chromosome 13 deletion, to provide a deeper insight into the molecular mechanisms involved in the disease. Our analysis has shown the importance of different altered pathways related to glycosylation, infectious disease, immune system response, different aspects of metabolism, DNA repair, protein recycling and regulation of the transcription of genes involved in the differentiation of myeloid cells. The main difference in genetic pathways between hyperdiploid and non-hyperdiploid myelomas are related to infectious disease, immune system response and protein recycling. Our work provides new insights on the genetic pathways involved in this complex disease and proposes novel targets for future therapies.
Collapse
Affiliation(s)
- Juan Luis Fernández-Martínez
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo 33007, Asturias, Spain.
| | - Enrique J de Andrés-Galiana
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo 33007, Asturias, Spain.
- Department of Computer Science, University of Oviedo, Oviedo 33007, Asturias, Spain.
| | - Francisco Javier Fernández-Ovies
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo 33007, Asturias, Spain.
| | - Ana Cernea
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo, Oviedo 33007, Asturias, Spain.
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan.
| |
Collapse
|
4
|
Quezada MS, Gil MM, Francisco C, Oròsz G, Nicolaides KH. Screening for trisomies 21, 18 and 13 by cell-free DNA analysis of maternal blood at 10-11 weeks' gestation and the combined test at 11-13 weeks. Ultrasound Obstet Gynecol 2015; 45:36-41. [PMID: 25251385 DOI: 10.1002/uog.14664] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [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: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To examine in a general population the performance of cell-free DNA (cfDNA) testing for trisomies 21, 18 and 13 at 10-11 weeks' gestation and compare it to that of the combined test at 11-13 weeks. METHODS In 2905 singleton pregnancies, prospective screening for trisomies was performed by chromosome-selective sequencing of cfDNA in maternal blood at 10-11 weeks' gestation and by the combined test at 11-13 weeks' gestation. RESULTS Median maternal age of the study population was 36.9 (range, 20.4-51.9) years. Results from cfDNA analysis were provided for 2851 (98.1%) cases and these were available within 14 days from sampling in 2848 (98.0%) cases. The trisomic status of the pregnancies was determined by prenatal or postnatal karyotyping or clinical examination of the neonates. Of the 2785 pregnancies with a cfDNA result and known trisomic status, cfDNA testing correctly identified all 32 cases with trisomy 21, nine of 10 with trisomy 18 and two of five with trisomy 13, with false-positive rates of 0.04%, 0.19% and 0.07%, respectively. In cases with discordant results between cfDNA testing and fetal karyotype, the median fetal fraction was lower than in those with concordant results (6% vs 11%). Using the combined test, the estimated risk for trisomy 21 was ≥ 1/100 in all trisomic cases and in 4.4% of the non-trisomic pregnancies. CONCLUSION The performance of first-trimester cfDNA testing for trisomies 21 and 18 in the general population is similar to that in high-risk pregnancies. Most false-positive and false-negative results from cfDNA testing could be avoided if the a priori risk from the combined test is taken into account in the interpretation of individual risk.
Collapse
Affiliation(s)
- M S Quezada
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, UK
| | | | | | | | | |
Collapse
|
5
|
Gastinne T, Leleu X, Duhamel A, Moreau AS, Franck G, Andrieux J, Lai JL, Coiteux V, Yakoub-Agha I, Bauters F, Harousseau JL, Zandecki M, Facon T. Plasma cell growth fraction using Ki-67 antigen expression identifies a subgroup of multiple myeloma patients displaying short survival within the ISS stage I. Eur J Haematol 2007; 79:297-304. [PMID: 17692103 DOI: 10.1111/j.1600-0609.2007.00915.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The current most powerful prognostic model in Multiple Myeloma (MM) combines beta-2 microglobulin (b2m) with albumin, corresponding to the International Staging System (ISS). However, the prognosis of patients within the ISS stage I (high albumin and low b2m) may vary. Ki-67 is a nuclear protein associated with cell proliferation. We retrospectively evaluated the percentage of bone marrow plasma cells expressing Ki-67 antigen (Ki-67 index) in a series of 174 untreated MM patients at diagnosis. Median survival was 51, 41 and 20 months respectively, and median Ki-67 index was 3.0%, 6.1% and 6.5% in ISS stages I, II, and III respectively. Independently of ISS, Ki-67 index > or =4% was highly predictive of adverse prognosis. Ki-67 index correlated with markers of intrinsic malignancy and with markers of tumour burden. Within ISS stage I, median survival was of 31 months (RR of death 2.65) in patients with Ki-67 index > or =4%. Eventually, the combination of Ki-67 with b2m produced an efficient prognostic model, which appeared most effective in our series when compared with b2m and KI-67 with chromosome 13 deletion models. In this series, we demonstrated that a proliferation marker provides clear-cut additional survival prognostic information to b2m into the ISS model.
Collapse
|
6
|
Archangelo LF, Gläsner J, Krause A, Bohlander SK. The novel CALM interactor CATS influences the subcellular localization of the leukemogenic fusion protein CALM/AF10. Oncogene 2006; 25:4099-109. [PMID: 16491119 DOI: 10.1038/sj.onc.1209438] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Clathrin Assembly Lymphoid Myeloid leukemia gene (CALM or PICALM) was first identified as the fusion partner of AF10 in the t(10;11)(p13;q14) translocation, which is observed in acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL) and malignant lymphoma. The CALM/AF10 fusion protein plays a crucial role in t(10;11)(p13;q14) associated leukemogenesis. Using the N-terminal half of CALM as a bait in a yeast two-hybrid screen, a novel protein named CATS (CALM interacting protein expressed in thymus and spleen) was identified. Multiple tissue Northern blot analysis showed predominant expression of CATS in thymus, spleen and colon. CATS codes for two protein isoforms of 238 and 248 amino acids (aa). The interaction between CALM and CATS could be confirmed using pull down assays, co-immunoprecipitation and colocalization experiments. The CATS interaction domain of CALM was mapped to aa 221-335 of CALM. This domain is contained in the CALM/AF10 fusion protein. CATS localizes to the nucleus and shows a preference for nucleoli. Expression of CATS was able to markedly increase the nuclear localization of CALM and of the leukemogenic fusion protein CALM/AF10. The possible implications of these findings for CALM/AF10-mediated leukemogenesis are discussed.
Collapse
MESH Headings
- 3T3 Cells
- Active Transport, Cell Nucleus/genetics
- Animals
- Base Sequence
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Nucleolus/genetics
- Cell Nucleolus/metabolism
- Cell Transformation, Neoplastic/genetics
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 10/metabolism
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 13/metabolism
- Gene Expression Regulation/genetics
- Humans
- Intracellular Signaling Peptides and Proteins
- Mice
- Molecular Sequence Data
- Monomeric Clathrin Assembly Proteins/genetics
- Monomeric Clathrin Assembly Proteins/metabolism
- Nuclear Proteins
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Organ Specificity
- Protein Binding/genetics
- Translocation, Genetic/genetics
Collapse
Affiliation(s)
- L Fröhlich Archangelo
- Department of Medicine III, University of Munich Hospital Grosshadern, Marchioninistr, Munich, Germany
| | | | | | | |
Collapse
|
7
|
Kimura M, Cao X, Patel S, Aviv A. Survival advantage of cultured human vascular endothelial cells that lost chromosome 13. Chromosoma 2004; 112:317-22. [PMID: 15045511 DOI: 10.1007/s00412-004-0276-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Revised: 02/26/2004] [Accepted: 03/02/2004] [Indexed: 10/26/2022]
Abstract
We explored the nature of chromosome 13 loss in cultured human vascular endothelial cells (HUVECs). Chromosome 13 loss detected by metaphase and interphase analysis was noted in earlier passages of HUVEC strains with no relation to telomere length or replicative senescence. Ectopic expression of telomerase did not influence the loss of chromosome 13. HUVECs losing chromosome 13 demonstrated increased migratory potential and loss of heterozygosity. Collectively, these observations suggest that the loss of chromosome 13 gives cultured HUVECs a replicative advantage.
Collapse
Affiliation(s)
- Masayuki Kimura
- Hypertension Research Center, Cardiovascular Research Institute, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ 07103, USA
| | | | | | | |
Collapse
|
8
|
Abstract
The Cox proportional hazards model is often used for estimating the association between covariates and a potentially censored failure time, and the corresponding partial likelihood estimators are used for the estimation and prediction of relative risk of failure. However, partial likelihood estimators are unstable and have large variance when collinearity exists among the explanatory variables or when the number of failures is not much greater than the number of covariates of interest. A penalized (log) partial likelihood is proposed to give more accurate relative risk estimators. We show that asymptotically there always exists a penalty parameter for the penalized partial likelihood that reduces mean squared estimation error for log relative risk, and we propose a resampling method to choose the penalty parameter. Simulations and an example show that the bootstrap-selected penalized partial likelihood estimators can, in some instances, have smaller bias than the partial likelihood estimators and have smaller mean squared estimation and prediction errors of log relative risk. These methods are illustrated with a data set in multiple myeloma from the Eastern Cooperative Oncology Group.
Collapse
Affiliation(s)
- Jie Huang
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA.
| | | |
Collapse
|
9
|
Abstract
It has been suggested that DNA organized into replication foci during S-phase remains stably aggregated in non-S-phase cells and that these stable aggregates provide fundamental units of nuclear or chromosome architecture [C. Meng and R. Berezney (1991) J. Cell Biol. 115, 95a; E. Sparvoli et al. (1994) J. Cell Sci. 107, 3097-3103; D. A. Jackson and A. Pombo (1998) J. Cell Biol. 140, 1285-1295; D. Zink et al. (1998) Hum. Genet. 112, 241-251]. To test this hypothesis, early and late replicating DNA of human diploid fibroblasts was labeled specifically by incorporating two different thymidine analogs [J. Aten (1992) Histochem. J. 24, 251-259; A. E. Visser (1998) Exp. Cell Res. 243, 398-407], during distinct time segments of S-phase. On mitotic chromosomes the amount and spatial distribution of early and late replicating DNA corresponded to R/G-banding patterns. After labeling cells were grown for several cell cycles. During this growth period individual replication labeled chromosomes were distributed into an environment of unlabeled chromosomes. The nuclear territories of chromosomes 13 and 15 were identified by additional chromosome painting. The distribution of early and late replicating DNA was analyzed for both chromosomes in quiescent (G0) cells or at G1. Early and late replicating DNA occupied distinct foci within chromosome territories, displaying a median overlap of only 5-10%. There was no difference in this regard between G1 and G0 cells. Chromosome 13 and 15 territories displayed a similar structural rearrangement in G1 cells compared to G0 cells resulting in the compaction of the territories. The findings demonstrate that early and late replicating foci are maintained during subsequent cell cycles as distinctly separated units of chromosome organization. These findings are compatible with the hypothesis that DNA organized into replicon clusters remains stably aggregated in non-S-phase cells.
Collapse
Affiliation(s)
- D Zink
- Institut für Anthropologie und Humangenetik, LMU München, Goethestrasse 31, München, D-80336, Germany.
| | | | | | | | | |
Collapse
|