Genome-wide profiling of non-smoking-related lung cancer cells reveals common RB1 rearrangements associated with histopathologic transformation in EGFR-mutant tumors.

BACKGROUND: The etiology and the molecular basis of lung adenocarcinomas (LuADs) in nonsmokers are currently unknown. Furthermore, the scarcity of available primary cultures continues to hamper our biological understanding of non-smoking-related lung adenocarcinomas (NSK-LuADs). PATIENTS AND METHODS: We established patient-derived cancer cell (PDC) cultures from metastatic NSK-LuADs, including two pairs of matched EGFR-mutant PDCs before and after resistance to tyrosine kinase inhibitors (TKIs), and then performed whole-exome and RNA sequencing to delineate their genomic architecture. For validation, we analyzed independent cohorts of primary LuADs. RESULTS: In addition to known non-smoker-associated alterations (e.g. RET, ALK, EGFR, and ERBB2), we discovered novel fusions and recurrently mutated genes, including ATF7IP, a regulator of gene expression, that was inactivated in 5% of primary LuAD cases. We also found germline mutations at dominant familiar-cancer genes, highlighting the importance of genetic predisposition in the origin of a subset of NSK-LuADs. Furthermore, there was an over-representation of inactivating alterations at RB1, mostly through complex intragenic rearrangements, in treatment-naive EGFR-mutant LuADs. Three EGFR-mutant and one EGFR-wild-type tumors acquired resistance to EGFR-TKIs and chemotherapy, respectively, and histology on re-biopsies revealed the development of small-cell lung cancer/squamous cell carcinoma (SCLC/LuSCC) transformation. These features were consistent with RB1 inactivation and acquired EGFR-T790M mutation or FGFR3-TACC3 fusion in EGFR-mutant tumors. CONCLUSIONS: We found recurrent alterations in LuADs that deserve further exploration. Our work also demonstrates that a subset of NSK-LuADs arises within cancer-predisposition syndromes. The preferential occurrence of RB1 inactivation, via complex rearrangements, found in EGFR-mutant tumors appears to favor SCLC/LuSCC transformation under growth-inhibition pressures. Thus RB1 inactivation may predict the risk of LuAD transformation to a more aggressive type of lung cancer, and may need to be considered as a part of the clinical management of NSK-LuADs patients.

Blood monocyte profiles in COPD patients with PiMM and PiZZ α1-antitrypsin.

Human blood monocytes are divided into populations based on the differential expression of CD14 and CD16 receptors: CD14 + CD16(classical), CD14 + CD16 + (intermediate), and CD14-CD16+ (non-classical). Given their functional differences and their role in pathogenesis of chronic obstructive pulmonary disease (COPD), monocyte profiling is of clinical interest. Here we investigated blood monocyte subsets in clinically stable COPD patients with alpha1-antitrypsin (AAT) deficiency (PiZZ, n = 7) and with normal AAT variant (PiMM, n = 7). Peripheral whole blood was collected in sodium heparin tubes and incubated with LPS (from E. coli; 1 µg/ml) or placebo for 6 h at 37 °C, 5% CO2. To profile monocyte subsets we performed flow cytometry analysis based on HLA-DR and CD14/CD16 staining. HLA-DR + subsets of cells did not differ between PiZZ and PiMM COPD, and healthy controls (n = 7), used as a reference. Monocyte profiling, which express the CD14 and CD16, but not the HLA-DR (HLA-DR-) showed that intermediate monocytes subset was lowest in PiZZ group, and almost totally disappeared from blood treated with LPS. The non-classical subset was almost absent in PiZZ patients independently of LPS treatment. Recent studies demonstrate that non-classical monocytes exhibit a unique ability to protect the vascular endothelium under both homeostatic and inflammatory conditions whereas intermediate monocytes are recruited at a later stage of inflammation, and are associated with secretion of cytokines/chemokines and wound healing. Evident alterations in blood monocyte subsets together with a partial reduction of AAT levels, an important anti-inflammatory protein, can be key factors for the early manifestation of emphysema in some PiZZ AATD carriers.

MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours.

BACKGROUND: Hereditary breast cancer comprises 5-10% of all breast cancers. Mutations in two high-risk susceptibility genes, BRCA1 and BRCA2, along with rare intermediate-risk genes and common low-penetrance alleles identified, altogether explain no more than 45% of the high-risk breast cancer families, although the majority of cases are unaccounted for and are designated as BRCAX tumours. Micro RNAs have called great attention for classification of different cancer types and have been implicated in a range of important biological processes and are deregulated in cancer pathogenesis. METHODS: Here we have performed an exploratory hypothesis-generating study of miRNA expression profiles in a large series of 66 primary hereditary breast tumours by microarray analysis. RESULTS: Unsupervised clustering analysis of miRNA molecular profiles revealed distinct subgroups of BRCAX tumours, 'normal-like' BRCAX-A, 'proliferative' BRCAX-B, 'BRCA1/2-like' BRCAX-C and 'undefined' BRCAX-D subgroup. These findings introduce a new insight in the biology of hereditary breast cancer, defining specific BRCAX subgroups, which could help in the search for novel susceptibility pathways in hereditary breast cancer. CONCLUSION: Our data demonstrate that BRCAX hereditary breast tumours can be sub-classified into four previously unknown homogenous groups characterised by specific miRNA expression signatures and histopathological features.

Current and future aggressive peripheral T-cell lymphoma treatment paradigms, biological features and therapeutic molecular targets.

Prognosis of PTCL is generally poor when treated with conventional chemotherapy regimens used in B-cell aggressive lymphomas. Recent advances in genomic and molecular profiling of PTCL have allowed to further insight this heterogeneous group of neoplasias and their main prognostic factors. This review will try to summarize the main clinical problems related to standard frontline and salvage therapy, including the use of conventional chemotherapy and high-dose, dose-dense and immunotherapeutic strategies, as well as new approaches based on biological knowledge and the use of new drugs or immunotherapy.

Peripheral T-cell lymphoma gene expression profiles.

Expression profiling using DNA microarrays has been very helpful to improve our knowledge of the pathobiology of many tumour types, including lymphomas. Peripheral T-cell lymphomas (PTCL) constitute an heterogeneous group of tumours with different morphologic, immunophenotypic, and clinical characteristics. Their complexity and their low frequency in the western countries have made difficult the identification of molecular events responsible of the development of these tumours. The first studies on expression profiling of PTCL have also revealed heterogeneity at this level, mainly regarding the PTCL NOS subgroup. Different molecular subgroups within PTCL unspecified have been identified associated to different expression profiles. However, the clinical significance of this molecular sub-classification remains to be probed in studies involving larger number of samples. In addition, the expression level of NF-kB pathway genes allowed to differentiate two PTCL subgroups, and this difference could have clinical interest. In general, PTCL expression profiles are difficult to interpret due to the significant proportion of other infiltrating cells accompanying the tumour. However, microarrays are being a helpful tool in the initial task of dissecting the PTCL expression profile.

A haplotype containing the p53 polymorphisms Ins16bp and Arg72Pro modifies cancer risk in BRCA2 mutation carriers.

Germline mutations in the BRCA1 and BRCA2 genes confer a high lifetime risk of developing breast and other cancers; however, remarkable differences exist regarding disease manifestation in mutation carriers. It has been suggested that other genetic and/or environmental factors modify not only the appearance but also the age of onset and type of tumor in BRCA1/2-associated cases. The aim of the present study was to investigate the role of two p53 polymorphisms (c.97-147ins16bp and c.215c>g, p.Arg72Pro) as potential modifiers. For this purpose we investigated the possible association between the two polymorphisms and disease status in 447 BRCA1/2 mutation carriers belonging to 170 Spanish breast and/or ovarian cancer families. Genotype and haplotype analyses revealed that the presence of a specific haplotype carrying the allele without the 16-bp insertion and the variant allele for the Arg72Pro (No Ins-72Pro haplotype) was associated with an earlier age of onset in BRCA2 mutation carriers. We found an increased risk of developing a first primary tumor (breast or ovarian) before 35 years of age for individuals who carried at least one No Ins-72Pro haplotype (OR: 2.69; 95% CI: 1.15-6.29; P=0.022). We confirmed these data by a functional study in which we compared different p53 genotypes in relation to their apoptotic response after cell treatment with a cytotoxic drug (AraC). Our results revealed a decrease in p53 apoptotic rate associated with the No Ins-72Pro haplotype.

Differential expression of NF-kappaB pathway genes among peripheral T-cell lymphomas.

Nuclear factor kappa B (NF-kappaB) is one important pathway in T-cell proliferation and survival. In a previously reported microarray study, we found NF-kappaB pathway genes differentially expressed between peripheral (PTCL) and lymphoblastic lymphomas. Here, we investigated the expression of NF-kappaB pathway genes using cDNA microarrays in a group of 62 PTCL and in reactive lymph nodes. We found two different subgroups of PTCL based on the expression of NF-kappaB pathway genes. One-third of PTCL showed clearly reduced expression of NF-kappaB genes, while the other group was characterized by high expression of these genes. This distinction was found among all T-cell lymphoma categories analyzed (PTCL unspecified, angioimmunoblastic, cutaneous and natural killer/T lymphomas) with the exception of anaplastic lymphomas (ALCL), which were characterized by reduced NF-kappaB expression in anaplastic cells. Quantitative RT-PCR and immunohistochemical analysis of NF-kappaB-p65 protein confirmed these differences among PTCL subgroups. Importantly, we found that differentiation between NF-kappaB-positive and -negative PTCL could be of clinical interest. The expression profile associated to reduced expression of NF-kappaB genes was significantly associated with shorter survival of patients and seems to be an independent prognostic factor in a multivariate analysis.

Characterization of the A673 cell line (Ewing tumor) by molecular cytogenetic techniques.

The A673 cell line was established from a patient with a primary rhabdomyosarcoma (RMS), which is referred to in the literature either as a Ewing tumor (ET) or as RMS. Although the two tumoral types are associated with specific and well-characterized translocations, no cytogenetic report on this cell line has been published. We characterized the A673 cell line using a combination of spectral karyotyping (SKY), fluorescence in situ hybridization (FISH), and reverse transcriptase polymerase chain reaction (RT-PCR), which revealed the presence of a complex karyotype and a translocation involving chromosomes 11 and 22 and the fusion of EWS and FLI1 genes, both events being specific to ET. Neither cytogenetics nor molecular alterations specific to RMS were found.

Complex cytogenetic abnormalities including telomeric associations and MEN1 mutation in a pediatric ependymoma.

Ependymomas are neuroectodermal tumors of the brain and spinal cord. Some recurrent cytogenetic aberrations have been reported in these tumors, including alterations involving chromosomes 22, 6, and 11. However, consistent molecular alterations have not been identified in ependymal tumors. We studied a recurrent ependymoma in a 3-year-old patient by standard cytogenetic and molecular analysis of TP53 and MEN1 genes. In the present case, we found many of the cytogenetic features previously described as being recurrent in ependymomas, including unstable telomeric alterations. Furthermore, we detected a novel acquired heterozygous mutation in the MEN1 gene. The chromosomal instability produced by the telomeric alterations and the mutation in the MEN1 gene could be important events in the tumorigenesis of ependymomas.

Multiplex-polymerase chain reaction assay for the detection of prognostically significant translocations in acute lymphoblastic leukemia.

BACKGROUND AND OBJECTIVES: The presence of specific chromosomal translocations in acute lymphoblastic leukemias (ALL) plays an important role in determining the prognosis of the patients. Our aim is to develop a highly sensitive and specific method to screen simultaneously for the four most frequent translocations in ALL: t(9;22), t(1;19), t(4;11), t(12;21). DESIGN AND METHODS: Our approach uses a multiplex-polymerase chain reaction (PCR) method, which involves two rounds of PCR using fluorescence-labeled nested primers. The chimeric transcripts resulting from these translocations can be identified by agarose gel electrophoresis or by fluorescence analysis. To validate this method we carried out the analysis in 42 pediatric ALL samples previously studied by cytogenetic and fluorescent in situ hybridization (FISH) techniques. RESULTS: In all samples with a known translocation detected by cytogenetic or FISH techniques, the same translocation was identified by the multiplex-PCR assay. Moreover, with this method we detected rearrangements in five patients in clinical remission and in two patients at diagnosis for whom karyotypes were normal and rearrangements had not been detected. The application of this multiplex-PCR assay was also useful in cases without cytogenetic results. INTERPRETATION AND CONCLUSIONS: These results show that the multiplex-PCR method allows reliable, sensitive and rapid detection of the prognostically significant translocations in ALL. We believe that this assay combined with cytogenetic analysis should be the strategy of choice for the initial diagnostic phase of acute lymphoblastic leukemia, and that it could be used not only at diagnosis but also to follow-up these alterations in remission samples without previous controls.

Chromosomal changes pattern and gene amplification in T cell non-Hodgkin's lymphomas.

T cell non-Hodgkin's lymphomas are a heterogeneous group of lymphomas with poor prognosis, and whose genetic alterations are not well understood. Comparative genomic hybridization (CGH) is a technique that allows the identification of DNA imbalances without cytogenetic studies. We have studied 37 samples from 29 T cell non-Hodgkin's lymphomas (25 peripheral and four lymphoblastic lymphomas) by CGH in order to detect DNA sequence copy number changes of putative importance in the biology and prognosis of these neoplasms. We detected abnormal CGH profiles in 16/27 (59%) of samples at diagnosis, a ratio that increased to 66% (23/37) when we included the relapsed samples. The most common recurrent changes were gains related to the X chromosome, either the whole chromosome or partially the Xq26-27 bands (19%). Other recurrent changes included gains of bands 9q34, gains of chromosomes 17, 19, and 20, and complete or partial deletions of chromosome 13 (10%). Cancer-related genes located at Xq26-28 region were analyzed by Southern blot and fluorescence in situ hybridization (FISH). Low level amplification of some of these genes was detected by this technique confirming the results obtained by CGH in this region. The detection of abnormal CGH profiles in these T cell lymphomas could have clinical implications. Patients with abnormal CGH profiles showed significant associations with advanced stage of disease, overexpression of P53, and higher proliferative index.

IgH, TCR-gamma, and TCR-beta gene rearrangement in 80 B- and T-cell non-Hodgkin's lymphomas: study of the association between proliferation and the so-called "aberrant" patterns.

The current study analyzes the rearrangement pattern of immunoglobulin H (IgH), T-cell receptor (TCR)-gamma, and TCR-beta genes in a group of 80 non-Hodgkin's lymphomas (NHL) of different histologic subtypes (43 B-cell and 37 T-cell types). The sensitivity and specificity provided by polymerase chain reaction amplification of these loci are evaluated. The association between the proliferation index and the presence of the so-called "aberrant" or "dual" rearrangements is also considered. Ninety-one percent of B-cell NHL showed IgH gene monoclonality, and 21% also exhibited a monoclonal pattern in one of the TCR genes. Among T-cell NHL, the sensitivity of the study was 65% for the TCR-gamma gene and 46% for the TCR-beta gene. The total sensitivity was 76%, amplifying both loci. IgH gene aberrant rearrangements were observed in 16% of T-cell neoplasms. A substantial percentage of dual rearrangements were detected in precursor and mature B- and T-cell NHL. B-cell NHL showed a tendency toward higher values of proliferation when aberrant rearrangements were present; however, this trend was not significant. Furthermore, in the case of T-cell NHL there was a significant negative association between these two variables.

[Distribution of dominant hereditary ataxias and Friedreich's ataxia in the Spanish population]. / Distribución de ataxias hereditarias dominantes y ataxia de Friedreich en la población española.

BACKGROUND: To establish the distribution of the different forms of dominant ataxias and Friedreich ataxia in Spanish population. PATIENTS AND METHODS: We have performed a molecular study in 121 patients presenting ataxia as the first sign of neurodegenerative disease. In these patients, we have performed a molecular study of SCA 1, SCA 2, SCA 3, SCA 6, SCA 7, SCA 8, DRPLA, alpha-TTP (tocopherol transfer protein) and Friedreich's ataxia genes. RESULTS: The study showed that the Friedreich ataxia is the most frequent form representing 34.4% of the total of the hereditary ataxias. One patient presented mutation in alpha-TTP gene. Among the dominant forms SCA 3 was the most frequent (27.3%) followed by SCA 7 (16%), SCA 6 (9%) and SCA 2 (4.5%). We have not found mutations in SCA 1 and DRPLA genes. Two of 60 apparently sporadic cases presented mutations in the SCA 6 and SCA 8. CONCLUSIONS: The genetic analysis is the principal method to distinguish the different clinic forms of ataxia. We have not found mutations in 41.2% of dominant forms and in 43.3% of recessive forms. These results suggest the existence of new candidates genes.

Hypermethylation of P16ink4a and P15ink4b genes as a marker of disease in the follow-up of non-Hodgkin's lymphomas.

The hypermethylation of p16ink4a and p15ink4b genes have been described as an inactivating mechanism alternative to deletions and mutations that accounts for a relatively high proportion of cancers, including non-Hodgkin's lymphomas (NHLs). To investigate whether detection of abnormal methylation could have clinical applications in the management and follow-up of lymphomas, we have analysed the behaviour and evolution of p16ink4a and p15ink4b methylation in 13 NHL cases undergoing chemotherapy. All cases were also analysed for the presence of monoclonal rearrangements of immunoglobulin or T-cell receptor genes. Six patients showed methylation in at least one of these genes at diagnosis, whereas in two other cases methylation appeared during the treatment. The other five cases were always unmethylated. Methylation was detected when any histological or molecular evidence of disease was present, suggesting a good correlation between methylation and disease. In some cases, we were able to detect methylation in patients at complete remission and without evidence of monoclonal cell population, indicating a high sensitivity of the PCR to detect methylation. These results suggest that p16ink4a and p15ink4b methylation could be good markers of disease and could be helpful in identifying lymphoma patients at risk of relapse.

Identification by comparative genomic hybridization of genetic changes involved in tumoral progression of a T-cell non-Hodgkin lymphoma.

Comparative genomic hybridization (CGH) was used to detect chromosomal imbalances in tumor DNA from two relapsed samples obtained in stages II and IV of a T-cell non-Hodgkin lymphoma in order to identify genetic mechanisms involved in tumor progression of this neoplasm. With conventional cytogenetic techniques (CCT), a complex hyperdiploid karyotype was obtained in stage IV. Using CGH analysis, a normal profile was observed in stage II, whereas gains of 6p11.2, 7q11.2, 7q21-->q32, 7q34, 10p13, Xp11.4, and loss of 4q33-->qter chromosomal regions were detected in stage IV.

[Identification of a de novo mutation in a patient without von Hippel-Lindau syndrome: clinical and diagnostic implications]. / Identificación de una mutación de novo en una paciente con síndrome de Von Hippel-Lindau: implicaciones clínicas y diagnósticas.

Von Hippel-Lindau (VHL) disease is characterized by a high predisposition to develop retinal angiomas, hemangioblastomas of the central nervous systems, renal cysts and renal carcinomas, pheochromocytomas, pancreatic cysts, and cystadenomas of the epididymis. The VHL gene was isolated in 1993; this fact allows to carry out presymptomatic diagnostic of this disease. We report on the case of patient with the suspicious++ and of hereditary VHL, although she had not familial history. By means of sequence the VHL gene was studied a mutation in exon 2 (GTT130CTT) that results in an amino acid change was found. This mutation could not be detected in her parents, pointing out that this is a de novo case. Patient has two sons, of 18 and 13 years old. The genetic analysis of the youngest showed that he was not a mutation carrier; while the eldest denied to be explored. The genetic study allows, in cases without familial history, to determine if they have the hereditary form of the disease and to study the siblings periodically until the beginning of the disease.

Genetic and clinical analysis in 10 Spanish patients with multiple endocrine neoplasia type 1.

Multiple endocrine neoplasia type 1 (MEN 1) is characterised by the combination of tumours of the parathyroid, endocrine pancreas and anterior pituitary glands. In 1988 the MEN 1 gene was mapped to chromosome 11q13 and it was cloned in 1997. This gene contains 10 exons and extends across 9 Kb of genomic DNA; it encodes for a product of 610 amino acid named menin whose function is unknown. We have studied 10 unrelated MEN 1 kindreds by a complete sequencing analysis of the entire gene; mutations were identified in nine of them: five deletions, one insertion, two nonsense mutation and a complex alteration consisting of a deletion and an insertion that can be explained by a hairpin loop model. Two of the mutations have been previously described; the other seven were novel, and they were scattered throughout the coding sequence of the gene. As in previous series, no correlation was found between phenotype and genotype.

[MLL rearrangements in acute leukemias]. / Reordenamientos del gen MLL en las leucemias agudas.

PURPOSE: In present study we have studied MLL rearrangements in a serie of acute myeloid, lymphoblastic and biphenotypic leukaemias. PATIENTS AND METHODS: We analyzed a total of 11 cases: 9 acute myeloid leukaemias (M4 and M5 subtypes in FAB classification), 1 lymphoid leukaemia, and 1 acute biphenotypic leukaemia. We studied bone marrow samples from all patients by using conventional cytogenetic techniques and fluorescence in situ hybridization (FISH) with an MLL probe. We also analyzed the correlation between clinical features and genetic results. RESULTS: Cells from 6 patients showed to contain MLL rearrangements and these arose in all types of leukaemias included in this study. Some MLL rearrangements were detected by FISH in kariotypically normal cases or without cytogenetic evidence of 11q23 aberration. MLL gene duplication has been observed in two cases with M4 and biphenotypic leukaemia, respectively. The presence of MLL gene rearrangements does not shape a group of patients with a common clinical pattern. CONCLUSIONS: MLL rearrangements occurs in a wide variety of leukemias. These rearrangements should be screened by FISH techniques, taking into account that gene duplications could arise in cases with normal karyotype. MLL rearrangements appear to have a considerable clinicopathologic heterogeneity.

[Application of modified comparative genomic hybridization in the genetic analysis of 5 lymphoid neoplasms]. / Aplicación de la hibridación genómica comparativa modificada en 5 neoplasias linfoides.

To analyze the utility of performing modified comparative genomic hybridization (mCGH) as a complementary technique to conventional cytogenetic techniques in the genetic analysis of lymphoid neoplasms. Modified comparative genomic hybridization and subsequent FISH techniques were performed in 5 lymphoid neoplasms cases diagnosed in Fundación Jiménez Díaz. The latter was done in order to confirm the results obtained with mCGH. Gains of chromosomal regions not detected with conventional cytogenetic techniques were detected by mCGH. A good correlation in the results obtained between conventional cytogenetic and mCGH techniques was observed. Nevertheless, mCGH enables the detection and subsequent identification of gains of genetic sequences undetectable with cytogenetic techniques with possible diagnostic and prognostic value.