Specific Chromosomal Changes Research Articles

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification.

In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.

CRISPR/Cas9 based manipulating oncogenic chromosomal changes in vivo

Chromosomal changes are important factors in the development of human cancers, leading to the creation of gene fusions that can be targeted by therapeutic treatments. One such gene fusion is EML4-ALK, which results from an inversion on chromosome 1 and is found in a subset of non-small cell lung cancers. This gene fusion is clinically significant because it makes the cancer cells sensitive to ALK inhibitors. However, modeling these genetic events in mice has been difficult and requires complex manipulation of the germ line. This study presents an efficient method of inducing specific chromosomal changes in vivo using viral-mediated delivery of the CRISPR/Cas9 system to somatic cells of adult animals. The method was used to create a mouse model of EML4-ALK-driven lung cancer. The resulting tumors consistently exhibited EML4-ALK inversion, expressed the EML4-ALK fusion gene and had molecular features of human NSCLCs and react to handling with ALK inhibitors. The capacity to simulate human malignancies in mice is substantially improved by this method.

Mucosal melanomas of different anatomic sites share a common global DNA methylation profile with cutaneous melanoma but show location-dependent patterns of genetic and epigenetic alterations.

Cutaneous, ocular, and mucosal melanomas are histologically indistinguishable tumors that are driven by a different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging. DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Here we explore the DNA methylation landscape of melanomas from different sites and analyze if different melanoma origins can be distinguished by their epigenetic profile. We performed DNA methylation analysis, next generation DNA panel sequencing, and copy number analysis of 82 non-cutaneous and 25 cutaneous melanoma samples. We further analyzed eight normal melanocyte cell culture preparations. DNA methylation analysis separated uveal melanomas from melanomas of other primary sites. Mucosal, conjunctival, and cutaneous melanomas shared a common global DNA methylation profile. Still, we observed location-dependent DNA methylation differences in cancer-related genes, such as low frequencies of RARB (7/63) and CDKN2A promoter methylation (6/63) in mucosal melanomas, or a high frequency of APC promoter methylation in conjunctival melanomas (6/9). Furthermore, all investigated melanomas of the paranasal sinus showed loss of PTEN expression (9/9), mainly caused by promoter methylation. This was less frequently seen in melanomas of other sites (24/98). Copy number analysis revealed recurrent amplifications in mucosal melanomas, including chromosomes 4q, 5p, 11q and 12q. Most melanomas of the oral cavity showed gains of chromosome 5p with TERT amplification (8/10), while 11q amplifications were enriched in melanomas of the nasal cavity (7/16). In summary, mucosal, conjunctival, and cutaneous melanomas show a surprisingly similar global DNA methylation profile and identification of the site of origin by DNA methylation testing is likely not feasible. Still, our study demonstrates tumor location-dependent differences of promoter methylation frequencies in specific cancer-related genes together with tumor site-specific enrichment for specific chromosomal changes and genetic mutations. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Massively Parallel Sequencing of Esophageal Brushings Enables an Aneuploidy-Based Classification of Patients With Barrett’s Esophagus

Aneuploidy has been proposed as a tool to assess progression in patients with Barrett's esophagus (BE), but has heretofore required multiple biopsies. We assessed whether a single esophageal brushing that widely sampled the esophagus could be combined with massively parallel sequencing to characterize aneuploidy and identify patients with disease progression to dysplasia or cancer. Esophageal brushings were obtained from patients without BE, with non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), or adenocarcinoma (EAC). To assess aneuploidy, we used RealSeqS, a technique that uses a single primer pair to interrogate ∼350,000 genome-spanning regions and identify specific chromosome arm alterations. A classifier to distinguish NDBE from EAC was trained on results from 79 patients. An independent validation cohort of 268 subjects was used to test the classifier at distinguishing patients at successive phases of BE progression. Aneuploidy progression was associated with gains of 1q, 12p, and 20q and losses on 9p and 17p. The entire chromosome 8q was often gained in NDBE, whereas focal gain of 8q24 was identified only when there was dysplasia. Among validation subjects, a classifier incorporating these features with a global measure of aneuploidy scored positive in 96% of EAC, 68% of HGD, but only 7% of NDBE. RealSeqS analysis of esophageal brushings provides a practical and sensitive method to determine aneuploidy in BE patients. It identifies specific chromosome changes that occur early in NDBE and others that occur late and mark progression to dysplasia. The clinical implications of this approach can now be tested in prospective trials.

Rapid chromosomal evolution in enigmatic mammal with XX in both sexes, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 (Mammalia, Rodentia).

Evolutionary history and taxonomic position for cryptic species may be clarified by using molecular and cytogenetic methods. The subterranean rodent, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 is one of three sibling species constituting the subgenus Ellobius Fischer, 1814, all of which lost the Y chromosome and obtained isomorphic XX sex chromosomes in both males and females. E.alaicus is evaluated by IUCN as a data deficient species because their distribution, biology, and genetics are almost unknown. We revealed specific karyotypic variability (2n = 52–48) in E.alaicus due to different Robertsonian translocations (Rbs). Two variants of hybrids (2n = 53, different Rbs) with E.tancrei Blasius, 1884 were found at the Northern slopes of the Alay Ridge and in the Naryn district, Kyrgyzstan. We described the sudden change in chromosome numbers from 2n = 50 to 48 and specific karyotype structure for mole voles, which inhabit the entrance to the Alay Valley (Tajikistan), and revealed their affiliation as E.alaicus by cytochrome b and fragments of nuclear XIST and Rspo1 genes sequencing. To date, it is possible to expand the range of E.alaicus from the Alay Valley (South Kyrgyzstan) up to the Ferghana Ridge and the Naryn Basin, Tien Shan at the north-east and to the Pamir-Alay Mountains (Tajikistan) at the west. The closeness of E.tancrei and E.alaicus is supported, whereas specific chromosome and molecular changes, as well as geographic distribution, verified the species status for E.alaicus. The case of Ellobius species accented an unevenness in rates of chromosome and nucleotide changes along with morphological similarity, which is emblematic for cryptic species.

Abstract 5174: Toward understanding the genomic alterations in human gastric cancer

Abstract Gastric cancer is one of the most prevalent and aggressive cancers worldwide, and its molecular mechanism remains largely elusive. Although recent genome sequencing studies have uncovered rich information on cancer evolutions of many types, little is known about the genetic basis of gastric cancer due to its complexity. Here we report genomic mutations in primary gastric adenocarcinoma of human, based on the whole genome sequences of five pairs of cancer and matching normal samples. In total, 407 non-synonymous somatic point mutations have been identified in these genomes and the most recurrent mutations were harbored by genes such as Mucins (MUC3A and MUC12) and transcription factors (ZNF717, ZNF595 and TP53). 679 genomic rearrangements were detected which affect 355 protein-coding genes; and 76 genes show copy number changes. The focus of the functional analysis is to validate the biological relevance of each variant to cancer formation and progression, particularly to explore the to-be-determined causal relationships between the observed mutations in cancer genomes and cancer development. Additionally, we have attempted to investigate the mechanism of how these variants form in each tumor and discuss about multiple possible factors that may affect the susceptibility to each specific chromosomal changes. For examples, structural correlation between two boundaries of most rearrangements was observed based on the Hi-C data analysis, which indicate these rearrangements may happen among DNA fragments in close spatial proximity, especially when two endpoints stay in a similar replication phase. Sequence analysis on the flacking region of those rearrangements also showed clear evidences that about half of these genomic changes may be involved in the mechanism of microhomology-mediated break induced replication (MMBIR). Furthermore, DNA integrations from Helicobacter pylori have been detected for the first time, for instance, in the gene region of PREX2, which may reflect a new mechanism about how H. pylori induce cancer development. Overall, the in-depth analyses on these sequenced genomes lead to the detection of a myriad of novel genomic variations in gastric cancer, which in turn bring new insights in our understanding of the genetic basis and indicate new molecular mechanism of the gastric tumorigenesis. Citation Format: Juan Cui, Ying Xu. Toward understanding the genomic alterations in human gastric cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5174. doi:10.1158/1538-7445.AM2014-5174

Genome Wide Profiling Of Chromosomal Abnormalities In 37 Patients With Monoclonal Gammopathy Of Undetermined Significance (MGUS)

IntroductionThe incidence of clonal DNA copy number alterations (CNAs) in plasma cells (PCs) is considered as one of the most important and independent prognostic factors in patients with multiple myeloma (MM). Also in the premalignancy MGUS, there are specific chromosomal changes in PCs such as del(13)(q14), IGHtranslocation, gain(1)(q21) and hyperdiploidy. However, not much is known about their significance in relation to malignant transformation. Also, MGUS research is further complicated by small number of malignant cells that could be obtained from patients. AimArray-CGH technique optimization and DNA CNAs analysis in relation to prognosis at genome-wide level in MGUS patients. Material and methodsWe have analysed 37 MGUS patients (22M/15F; median age 62) using array-CGH, Agilent platforms “Human Genome CGH, 4×44K” (n=10) and “SurePrint G3 CGH+SNP, 4×180K” (n=27). DNA was isolated from separated PCs (using CD138, CD19 and CD56 markers) and amplified by multiple displacement amplification (MDA). ResultsCNAs were observed in 57% (21/37) MGUS patients. Numerical and structural CNAs were found in 46% (17/37) and 41% (15/37) MGUS patients, respectively. We distinguished two genetic subgroups similar to MM patients: hyperdiploid and non-hyperdiploid. Hyperdiploidy was present in 32% (12/37) MGUS patients. The most frequent whole-chromosome gains were: 9 (83%, 10/12), 19 (83%, 10/12), 3 (75%, 9/12), 11 (67%, 8/12) and 15 (58%, 7/12). Non-hyperdiploidy was detected in 68% (25/37) MGUS patients. In both, hyperdiploid and non-hyperdiploid subgroups we have found loss of chromosomes 13 (25% vs. 20%) and Y (17% vs. 4%). Loss of chromosome 8 was detected only in hyperdiploid subgroup (8%) and losses of chromosomes 21, 22 and X only in non-hyperdiploid subgroup (8%, 4% and 8%, respectively). Structural changes were significantly more often present in hyperdiploid than in non-hyperdiploid patients (67% vs. 28%, p<0.05). We have identified whole-arm chromosome changes 1q gain and 16q loss in both hyperdiploid and non-hyperdiploid patients (17% vs. 12%, 8% vs. 8%, respectively), but 16p gain was seen only in hyperdiploid patients (8%). Segmental chromosome changes were also present in both hyperdiploid and non-hyperdiploid patients (58% vs. 24%). Interestingly, we have detected more segmental losses (15 vs. 8) and gains (6 vs. 2) in hyperdiploid than in non-hyperdiploid patients, but size median of these losses (3.33 Mb vs. 19.6 Mb) and gains (36.1 Mb vs. 63.5 Mb) was smaller in hyperdiploid than in non-hyperdiploid patients.Moreover, we found one MGUS patient who has progressed to MM and required therapy after 6 months from MGUS diagnosis. Genome-wide profile of MGUS patient was especially unique by high number of structural changes (n=11) compared to other 15 MGUS patients with structural CNAs (median 1; 1 – 6). MGUS patient's profile showed hyperdiploidy (gains of chromosomes 3, 5, 9, 11, 15 and 19), losses of chromosomes 8, 13 and Y, 7 segmental losses in areas 1p34.2-p13.1, 6p23, 6q12-q27, 7q36.3, 12p12.1-p11.23, 12q12, 12q21.2-q23.3 and 4 segmental gains in areas 6p25.3-p23, 6p23-p11.1, 6q11.1-q12, Xq21.33-q28. In addition, gains and losses, which included whole or large parts of chromosomes, showed unusual profile associated with other alterations. These findings have suggested a complex karyotype. SummaryIn our study we have optimized protocol of array-CGH analysis from amplified DNA and we have used it in first 37 MGUS patients. We found there are various chromosomal changes (numerical, whole-arm and segmental) in more than half of MGUS patients. Similar to MM, hyperdiploid and non-hyperdiploid genetic subgroups were identified. We also described one MGUS case with unique genome-wide profile indicating unfavourable prognosis. SupportNT13492, NT13190, NT11154, OPVK CZ.1.07/2.3.00/20.0183, MSM0021622434, GAP304/10/1395 Disclosures:No relevant conflicts of interest to declare.

An international study of intrachromosomal amplification of chromosome 21 (iAMP21): cytogenetic characterization and outcome

Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). To date, fluorescence in situ hybridisation (FISH), with probes specific for the RUNX1 gene, provides the only reliable detection method (five or more RUNX1 signals per cell). Patients with iAMP21 are older (median age 9 years) with a low white cell count. Previously, we demonstrated a high relapse risk when these patients were treated as standard risk. Recent studies have shown improved outcome on intensive therapy. In view of these treatment implications, accurate identification is essential. Here we have studied the cytogenetics and outcome of 530 iAMP21 patients that highlighted the association of specific secondary chromosomal and genetic changes with iAMP21 to assist in diagnosis, including the gain of chromosome X, loss or deletion of chromosome 7, ETV6 and RB1 deletions. These iAMP21 patients when treated as high risk showed the same improved outcome as those in trial-based studies regardless of the backbone chemotherapy regimen given. This study reinforces the importance of intensified treatment to reduce the risk of relapse in iAMP21 patients. This now well-defined patient subgroup should be recognised by World Health Organisation (WHO) as a distinct entity of BCP-ALL.

Molecular tumor profiling (MTP) of poorly differentiated neoplasms (PDN) of unknown primary site.

11080 Background: The inability to definitively determine the lineage of neoplasms is less common with modern immunohistochemistry (IHC) and genetic profiling. Nonetheless some PDN defy lineage classification by extensive standard pathologic evaluation. The advent of MTP may provide a new method of improving the diagnosis of these challenging cancers. Methods: A total of 30 of 751 (4%) patients (pts) seen from 2000 – 2012 with cancer of unknown primary (CUP) had PDN without a definitive lineage determined by IHC (median 18 IHC stains, range 9 – 51). From 2008 – 2012 the 30 biopsies had MTP (RT-PCR mRNA CancerTYPE ID, bioTheranostics, Inc.). Additional IHC, genetic sequencing, fluorescent in situ hybridization for specific chromosomal changes and repeat biopsies were performed when feasible to support the MTP diagnosis, and clinical features correlated. Results: MTP lineage diagnoses were made in 25 of 30 (83%), including 10 carcinomas (3 germ cell, 2 neuroendocrine, 5 others), 5 melanomas, 8 sarcomas (3 peritoneal mesothelioma, 1 PNET) and 2 hematopoietic neoplasms (1 lymphoma, 1 chloroma). Additional IHC, genetic testing [BRAF, i(12)p] or repeat biopsies confirmed the MTP diagnoses in 11 of 15 tumors, and the clinical features were consistent with the MTP diagnoses in the majority of patients. Conclusions: This MTP assay can frequently provide a diagnosis for CUP pts and PDN without a definitive lineage defined by extensive IHC. The earlier application of MTP will likely provide an expedited diagnosis, and for some neoplasms is the only test capable of defining lineage and a more specific diagnosis. Appropriate therapy, particularly for pts with germ cell tumors, melanoma, and lymphoma depends on a specific tissue of origin diagnosis.

Polycythemia Vera: Redefinition in the Genomic Era

AbstractAbstract 1754For more than 100 years since the initial descriptions, polycythemia vera (PV) was defined by an aggregation of clinical and laboratory features, reported to be more common in males than females, and diagnosed on average at age 60 (Modan Blood 1965, Berlin Sem Hematol 1975). The 2005 discovery of somatic mutations in the JAK2 gene introduced the molecular era of PV and required redefinition of this disease entity. We established a prospective, observational cohort of 556 patients evaluated in our center between 2005 and 2011, of which 273 had a PV phase at some point during their myeloproliferative neoplasm (MPN). Serial samples were obtained from each patient for genomic analyses, including neutrophil JAK2V617F allele burdens, clinical karyotypes, SNP-array karyotypes, JAK2 and ASXL1 sequencing and copy number variation, allele burden analysis in sorted hematopoietic stem cell (HSC) fractions, and whole exome sequencing. These data were used to define the relationship of genotype to clinical phenotype with regard to PV epidemiology, natural history and disease transformation. Thirty three percent of the cohort was evaluated within 1 year from PV diagnosis and the median MPN disease duration at the last update of the cohort was 9 years (range 1–52 years). As of 7/2012, of the 273 PV patient cohort, 47 had antecedent essential thrombocytosis (ET/PV), 176 had PV, 43 had developed post-PV myelofibrosis (PPVMF) and 7 had developed acute leukemia (AML) (PPVAML). 270 of the 273 PV patients had JAK2 mutations, either V617F (264, 97%) or exon 12 (6, 2%); the remaining 3 (1%) are molecularly undefined. Women outnumbered men (169/104; ratio 1.6), even when stratified by ET/PV (2.1), PV (1.6), PPVMF (1.4) and PPVAML (1.3). Age at PV diagnosis was significantly younger in women, 54 (range 8–88), compared to men, 56.5 (range 15–77) (p=0.022), and the proportion diagnosed before age 40 was 26% in women compared to 10.5% in men. PPVMF occurred on average after 9 years (range 2–53 years) of PV at a median age of 62.5 years. PPVAML occurred on average after 10 years (range 3–28 years) of PV, at a median age of 71 years, significantly higher than the age at PPVMF (p=0.038). Aside from JAK2V617F, acquired 9pUPD was the most common genomic lesion in PV, occurring in 57% within the first year after PV diagnosis, in 84% of PPVMF and 100% of PPVAML patients. Studied prospectively, the prevalence of 9pUPD increased from 0 to 40% in 11 patients transitioning from ET to PV, and increased from 59% to 75% in 30 PV patients from year 1 to year 6 after diagnosis, but stayed at 90% in 11 patients pre and post transformation to PPVMF. Chromosomal loss/gain was not highly prevalent during PV (2%) in contrast to PPVMF (64%) and PPVAML (100%). The most frequent chromosomal abnormalities in PPVMF were trisomy 9 (27%), 13q deletion (12%), 1q gain(12%), 20qdeletion (8%) and 11qdel (8%), whereas the most common chromosomal abnormalities in PPVAML were 5qdel or −5 (75%), and 7qdeletion (50%), both of which were often found in the setting of complex changes (75%). Genomic lesions identified in PV and PPVMF, including JAK2V617F, 9pUPD, 11qdel, and ASXL1 mutations, were detected at high allele burdens by quantitative allele assays in flow-sorted, pluripotent HSCs. We conclude that acquisition of a JAK2 mutation is implicated in the vast majority (99%) of PV patients, that PV occurs more often in women, and that younger women (<40) particularly are at higher risk than younger men. Genomic lesions in PV and PPVMF arise and accumulate in a primitive HSC population. 9pUPD is a common occurrence during transition from JAK2V617F+ ET to PV, and while highly prevalent, age and time dependent in PV, 9pUPD is not sufficient to generate PPVMF or PPVAML. In PPVMF, JAK2 mutations associate with specific recurrent chromosomal changes that are also found in normal individuals with advancing age (9pUPD, 13qdel, 20qdel, 11qdel; Nature Genetics 44, 2012). JAK2 mutations with 9pUPD enhance the acquisition of age-associated and therapy- associated genomic instability lesions, promoting the development of PPVMF and PPVAML. Given the molecular epidemiology of PV, it will be crucial recognize and reduce the risk factors that lead to the excess acquisition of PV in young women, to identify the risk factors that lead to 9pUPD, to study whether targeted therapy can prevent the development of 9pUPD, and to avoid genotoxic therapy that accelerates genomic instability in PV. Disclosures:Streiff:sanofi-aventis: Consultancy, Honoraria; BristolMyersSquibb: Research Funding; Eisai: Consultancy; Janssen Healthcare: Consultancy; Daiichi-Sankyo: Consultancy.

SKY analysis revealed recurrent numerical and structural chromosome changes in BDII rat endometrial carcinomas

BackgroundGenomic alterations are common features of cancer cells, and some of these changes are proven to be neoplastic-specific. Such alterations may serve as valuable tools for diagnosis and classification of tumors, prediction of clinical outcome, disease monitoring, and choice of therapy as well as for providing clues to the location of crucial cancer-related genes.Endometrial carcinoma (EC) is the most frequently diagnosed malignancy of the female genital tract, ranking fourth among all invasive tumors affecting women. Cytogenetic studies of human ECs have not produced very conclusive data, since many of these studies are based on karyotyping of limited number of cases and no really specific karyotypic changes have yet been identified. As the majority of the genes are conserved among mammals, the use of inbred animal model systems may serve as a tool for identification of underlying genes and pathways involved in tumorigenesis in humans. In the present work we used spectral karyotyping (SKY) to identify cancer-related aberrations in a well-characterized experimental model for spontaneous endometrial carcinoma in the BDII rat tumor model.ResultsAnalysis of 21 experimental ECs revealed specific nonrandom numerical and structural chromosomal changes. The most recurrent numerical alterations were gains in rat chromosome 4 (RNO4) and losses in RNO15. The most commonly structural changes were mainly in form of chromosomal translocations and were detected in RNO3, RNO6, RNO10, RNO11, RNO12, and RNO20. Unbalanced chromosomal translocations involving RNO3p was the most commonly observed structural changes in this material followed by RNO11p and RNO10 translocations.ConclusionThe non-random nature of these events, as documented by their high frequencies of incidence, is suggesting for dynamic selection of these changes during experimental EC tumorigenesis and therefore for their potential contribution into development of this malignancy. Comparative molecular analysis of the identified genetic changes in this tumor model with those reported in the human ECs may provide new insights into underlying genetic changes involved in EC development and tumorigenesis.

Scoliosis and Rett syndrome

Our understanding of the rare progressive neuromuscular disorder associated with the name of Andreas Rett has advanced significantly in the last 20 years. This includes the consequences for the musculoskeletal system. What have we learned? Scoliosis is exceedingly common in Rett syndrome, developing in 50 to 90% of individuals with the condition. It often appears during juvenile growth, worsens rapidly during adolescence, and continues to progress in severity after skeletal maturation. In its more severe forms it can impair sitting and positioning, reduce pulmonary function, and cause pain. Like scoliosis associated with cerebral palsy, it occurs with greater frequency in individuals with more extensive developmental impairment, particularly when regression of skills is noted before 6 months of age and when walking is never achieved or is lost before maturation. Unlike cerebral palsy, the risk of scoliosis in Rett syndrome appears to be linked to specific chromosomal changes. Of the numerous mutations of the methyl-CpG-binding protein 2 gene (MECP2) at chromosome Xq28, two mutations (R294X and R306C) are known to be associated with milder developmental impairment and reduced risk for developing scoliosis.1, 2 Other mutations of MECP2 may be found to be associated with increased risk of severe developmental impairment and the formation of scoliosis. The study of Riise et al.3 affirms the link between more severe developmental impairment and increased risk of scoliosis. The authors also suggest that a link may exist between patterns of scoliosis in Rett syndrome and the severity of the developmental impairment. They found a tendency for individuals with more severe manifestations of Rett syndrome to have long single curves in which the pelvis acts as an end-vertebra, resulting in pelvic obliquity. Milder manifestations of Rett syndrome were associated with balancing double curves, usually of smaller magnitude. In Rett syndrome, physiotherapy is valued for encouraging flexibility, strength, and movement but therapy appears to have no effect on curve behavior. Spinal bracing slows the pace of curve progression but seems incapable of preventing the formation of large curves. Slowing the rate at which curves progress (and improving trunk shape and balance) has merit but braces can be difficult to wear. Successful spinal fusion surgery yields a smaller deformity and a more balanced trunk, and may improve pulmonary function and reduce pain. The result is appreciated by parents and other care providers but it is a complex technical procedure and a major physiological challenge that is prone to complications.4, 5 If future studies demonstrate a relationship between specific MEPC2 mutations and the risk for developing certain patterns of scoliosis or large, severe, curves then we, as clinicians, may be able to properly focus our worry and our interventions. For the group of patients prone to severe curves or curves associated with pelvic obliquity and poor sitting posture, spine fusion could be completed before the deformity necessitates both anterior and posterior surgical approaches, and before the general deterioration of health increases the risk of serious complications.6 For other patients, physiotherapy, bracing, and specialized seating arrangements could be employed as needed to assist in individual care.

Molecular Heterogeneity of Multiple Myeloma: Pathogenesis, Prognosis, and Therapeutic Implications

Multiple myeloma (MM) is characterized by a significant heterogeneity at the molecular level. The first level is the chromosomal one. Although cytogenetics is difficult to assess in MM, patients can be divided into two categories: hyperdiploidy and non-hyperdiploidy (about half in each group). Using molecular cytogenetic techniques, several subgroups of patients are identified, particularly on the basis of 14q32 translocations. This chromosomal heterogeneity is confirmed by genomic techniques (gene expression profiling or single nucleotide polymorphism/comparative genomic hybridization arrays). Unsupervised analyses of gene expression profiles identified several subgroups of patients, essentially on the basis of chromosomal abnormalities such as hyperdiploidy or 14q32 translocations. However, these analyses failed to separate MM into subentities, which could lead to specific therapeutic approaches, as is the case for non-Hodgkin's lymphomas. Nevertheless, these chromosomal/genomic data can be used for prognostication of patients. Specific chromosomal changes, such as loss of the short arm of chromosome 17, or specific gene expression profiles clearly identify patients with short survival. No molecular change so far has been associated with long survival or even cure, probably because of the short follow-up observed in all studies. So far, it is unclear how to use this massive amount of data to treat patients. Because of the complex and heterogeneous picture of the molecular profiles, it is unexpected that targeted therapies might play a role in MM. The only recognized indication is to propose bortezomib-based approaches for the treatment of patients displaying the translocation t(4;14).

Chromosomal aberrations in iris melanomas

BackgroundUveal melanomas can develop in the choroid, ciliary body and iris. In choroidal and ciliary body melanomas, specific chromosomal changes correlate with metastatic disease. Iris melanomas have a better prognosis...

Widespread Occurrence of Dosage Compensation in Candida albicans

The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, insuring survival. In the absence of the adverse environment, the altered portion of the genome can be restored to its normal condition. One major question is how C. albicans copes with gene imbalance arising by transitory aneuploid states. Here, we compared transcriptomes from cells with either two copies or one copy of chromosome 5 (Ch5) in, respectively, a diploid strain 3153A and its representative derivative Sor55. Statistical analyses revealed that at least 40% of transcripts from the monosomic Ch5 are fully compensated to a disomic level, thus, indicating the existence of a genome-wide mechanism maintaining cellular homeostasis. Only approximately 15% of transcripts were diminished twofold in accordance with what would be expected for Ch5 monosomy. Another minor portion of approximately 6% of transcripts, unexpectedly, increased up to twofold and higher than the disomic level, demonstrating indirect control by monosomy. Array comparative genome hybridization revealed that only few out of approximately 500 genes on the monosomic Ch5b were duplicated, thus, not causing a global up regulation. Dosage compensation was confirmed with several representative genes from another monosomic Ch5a in the mutant Sor60. We suggest that C. albicans's unusual regulation of gene expression by the loss and gain of entire chromosomes is coupled with widespread compensation of gene dosage at the transcriptional level.

Trisomy 8 as a sole aberration in embryonal rhabdomyosarcoma (sarcoma botryoides) of the vagina

Sarcoma botryoides (SB) is a subtype of embryonal rhabdomyosarcoma (ERMS), which belongs to the most common soft-tissue sarcoma in infancy and childhood, the rhabdomyosarcoma (RMS). Most of the vaginal RMS belong to SB, which is five times more common than the cervical ERMS. To date, there is no doubt regarding the significance and importance of chromosomal aberrations in cancer. So far, to our knowledge, no specific chromosomal changes have been reported for ERMS in general and for SB in particular. We describe cytogenetic results of a case of vaginal SB affecting a 1-year-old girl. A clone of trisomy 8 was found in all the analyzed cells as the only chromosomal aberration. The significance of this finding is discussed.

Epidemiology of Chronic Lymphocytic Leukemia in Taiwan: The Incidence Trend and Its Comparison with That in Caucasian Americans.

Abstract 4378Chronic lymphocytic leukemia (CLL) is a prevalent leukemia in western countries. However, the incidence of CLL in Taiwan, is markedly lower but shows an increasing trends. We explored the incidence of CLL in Taiwan during the past two decades and compared it with Caucasian Americans. The epidemiologic data of CLL (1979-2003) in Taiwan was obtained from Taiwan Cancer Registry, and the corresponding data of Caucasian Americans was from the Surveillance, Epidemiology, and End Results Program (SEER). From 1979-2003, the age-adjusted annual incidence (with WHO 2000 standard population) of CLL in Taiwan increased from 0.08 to 0.36 per 100,000 people with about 4.5 folds increment, while that in Caucasian Americans was much higher but remained in steady state in this period (2.6 to 3.1 per 100,000 people). Age-specific incidence rate of CLL plotted by calendar year at diagnosis revealed a stronger period effect in Taiwanese (Figure 1A). The estimation of age-specific annual percentage changes (AAPC) of incidences revealed that, in every age group, the annual increase of the overall incidence throughout the past 2 decades was much higher for Taiwanese compared with that for Caucasian Americans (Figure 1B). Age-specific incidence rates plotted by birth cohort showed that the CLL incidence was higher for later birth cohorts for every age group in Taiwanese but not in Caucasian Americans (Figure 1C). The individual effects of time period and birth cohort on the trends of incidence of CLL in both populations were analyzed using the age-period-cohort analysis for comparison. These analyses showed a much stronger birth-cohort effect on the incidence trend of CLL in Taiwanese than in Caucasian Americans. This strong birth-cohort effect corresponded to the Westernization of lifestyle in Taiwan since 1960. This finding suggests that, in addition to the racial differences of genetic backgrounds that may be responsible for the differences in the CLL incidence, the environmental effects also play some roles. We also analyzed the cytogenetic abnormalities (CA) by conventional cytogenetics (CG) and fluorescence in situ hybridization (FISH) and assessed their clinical significance in Taiwanese patients who were diagnosed and treated at National Taiwan University Hospital. Thirty-nine patients (45.9%) out of 85 patients possessed CG-CA and 58 (69.9%) out of 83 patients had FISH-CA. FISH was more sensitive to detect CA than CG. Those who had neither CG-CA nor FISH-GA had excellent overall survival (OS). Patients with hypodiploidy or complex CG-CA had poorer prognosis than others (p=0.043 and 0.037, respectively). Among those specific chromosome changes detected by CG, trisomy 12 was the most common CA (14.1% among 85 patients). Detection of 17p- by CG was independently associated with poor prognosis. By FISH, 13q- was the most common CA (45.8% among 83 patients), followed by trisomy 12 (20.5%); the frequencies of these two abnormalities were similar to those reported in western countries. Both FISH-CA of 17p- and 11q- were significantly independent factors for poor prognosis. Trisomy 3 was found in five patients; all were of Binet A stage but had a poor prognosis, suggesting that CLL with trisomy 3 may be a distinct disease entity. From these data we conclude that the incidence of CLL in Taiwan was dramatically increased in recent years and was associated with a birth-cohort effect. The CA of CLL in Taiwanese patients are similar to those in Western countries, indicating that although the incidence of CLL is lower in Taiwan than in the West, the pathogenesis of this disease in these two areas is similar. The finding from combined CG and FISH analysis can help predict prognosis. The clinical significance of trisomy 3 in CLL needs to be further investigated. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Modeling interactions between leukemia‐specific chromosomal changes, somatic mutations, and gene expression patterns during progression of core‐binding factor leukemias

In cancer genomes, changes observed during tumor progression can be difficult to separate from nonspecific accumulation of cytogenetic changes due to cancer-associated genetic instability. We studied genetic changes occurring over time in cancers presenting with a relatively simple karyotype, namely two related core-binding factor (CBF) acute myeloid leukemias (AMLs), to assess how specific chromosomal changes are selected based on tumor subtype and acquired somatic mutations. Expression profiles for DNA replication/repair genes and the mutation status of KRAS, NRAS, FLT3, and KIT were compared with the karyotypic changes at diagnosis and relapse(s) in 94 cases of inv(16)(p13.1q22)-AML and 82 cases of t(8;21)(q22;q22)-AML. The majority of both AML types demonstrated a simple aneuploid pattern of cytogenetic progression, with highly distinctive patterns of chromosome copy number changes, such as +22 and +13 exclusively in inv(16)-AML and -Y and -X in t(8;21)-AML. Selection of certain cytogenetic changes correlated with particular somatic mutations, such as +8 with RAS mutation, and absence of kinase pathway mutations in t(8;21)-AML with localized deletions at chromosome band 9q22. Alterations in transcript levels of mitotic spindle kinases such as CHEK1, AURKA, and AURKB were associated with the aneuploid progression pattern, particularly in t(8;21) cases. Despite the similarity in the initiating genetics of the two CBF AML types, highly tumor-specific patterns of limited aneuploidy are noted that persist and continue to accumulate at relapse. Thus, activation of genetic instability, possibly through mitotic spindle dysregulation, leads rapidly to the selection of advantageous single chromosome aneuploidy.

Other Targetable Sarcomas

Despite complex genetics, aneuploid tumors like dedifferentiated liposarcoma have specific and reproducible chromosomal changes such as amplification of HDM2 and CDK4 that represent potential targets for systemic therapy. In addition, there are cancer cell survival pathways that may not be the target of chromosomal translocations or mutations that are still estimable targets for new systemic therapeutics, be it pathways involved in angiogenesis or apoptosis. In this review, we examine target selection for specific sarcoma subtypes, and demonstrate with a few examples new techniques being used to delineate novel therapeutic inroads for patients with sarcoma.

Specific chromosome changes in malignancy: studies in rat sarcomas induced by two polycyclic hydrocarbons.

Karyotypes were analyzed and deviations from normality recorded in conventional preparations of 10 rat sarcomas induced by 20-methylcholanthrene (MC) and 13 induced by 3, 4-benzpyrene (BP). Whenever possible these observations were supplemented with banding analyses in direct preparations and early cultures. The variation both of the normal chromosomes and of the markers was nonrandom. Of the normal rat chromosomes only a few specific ones participated regularly in the formation of markers, and structurally identical or similar markers were demonstrated repeatedly in different sarcomas, often the same marker in both MC and BP inductions. This is compatible with recent observations in human malignancies. The variability of several parameters—chromosome numbers, karyotypic multiformity, incidence of markers and double minutes—was generally more pronounced in the BP- than in the MC-induced sarcomas, and both groups showed more variable conditions than the sarcomas induced by 7, 12-dimethylbenz (α) anthracene (DMBA). Tentatively, this fact was associated with the differences in oncogenic capacity among the 3 compounds: DMBA > MC > BP. It is suggested — along the lines of the mutation theory—that a less potent oncogen launches a less precise attack on the significant genie sites, and consequently more extreme chromosome changes will accompany the malignant transformation.