Integrated genomic analysis of breast cancers.

Breast cancer is the most frequent and the most deadly cancer in women in Western countries. Different classifications of disease (anatomoclinical, pathological, prognostic, genetic) are used for guiding the management of patients. Unfortunately, they fail to reflect the whole clinical heterogeneity of the disease. Consequently, molecularly distinct diseases are grouped in similar clinical classes, likely explaining the different clinical outcome between patients in a given class, and the fact that selection of the most appropriate diagnostic or therapeutic strategy for each patient is not done accurately. Today, treatment is efficient in only 70.0-75.0% of cases overall. Our repertoire of efficient drugs is limited but is being expanded with the discovery of new molecular targets for new drugs, based on the identification of candidate oncogenes and tumor suppressor genes (TSG) functionally relevant in disease. Development of new drugs makes therapeutical decisions even more demanding of reliable classifiers and prognostic/predictive tests. Breast cancer is a complex, heterogeneous disease at the molecular level. The combinatorial molecular origin and the heterogeneity of malignant cells, and the variability of the host background, create distinct subgroups of tumors endowed with different phenotypic features such as response to therapy and clinical outcome. Cellular and molecular analyses can identify new classes biologically and clinically relevant, as well as provide new clinically relevant markers and targets. The various stages of mammary tumorigenesis are not clearly defined and the genetic and epigenetic events critical to the development and aggressiveness of breast cancer are not precisely known. Because the phenotype of tumors is dependent on many genes, a large-scale and integrated molecular characterization of the genetic and epigenetic alterations and gene expression deregulation should allow the identification of new molecular classes clinically relevant, as well as among the altered genes and/or pathways, the identification of more accurate molecular diagnostic, prognostic/predictive factors, and for some of them, after functional validation, the identification of new therapeutic targets.

Treatment of myelodysplastic syndromes with 5q deletion before the lenalidomide era; the GFM experience with EPO and thalidomide.

Anemia in MDS with 5q deletion was generally considered, until the advent of lenalidomide, unresponsive to available treatments. We analyzed erythroid response to erythropoetin (EPO) or darbepoetin (DAR) and thalidomide in MDS with 5q deletion treated by French centers (GFM) and in whom karyotype was successfully performed. Of 345 patients treated with EPO or DAR+/-G-CSF, 48 had 5q deletion. The response rate was 46% (31% major, 15% minor) according to International Working Group (IWG) 2000 criteria versus 64% in patients without 5q deletion (p=0.03). According to IWG 2006 criteria, the response rate in patients with 5q deletion was 39% versus 52% in patients without 5q deletion (p=0.10). Mean duration of response was 14 months versus 25 months (IWG 2000) and 13 months versus 27 months (IWG 2006) in 5q deletion and non-5q deletion patients (p=0.019 and 0.003, respectively). Of 120 MDS treated with thalidomide, all of whom had successful cytogenetic analysis, 37% of the 24 patients with 5q deletion responded (IWG 2000 criteria, 20% major, 17% minor) with a mean duration of 9.5 months, versus 32% (18% major, 14% minor) in MDS without 5q deletion and a mean response duration of 9 months (p=NS). Our results confirm that response rates to EPO or DAR and thalidomide are clearly inferior to those obtained with lenalidomide.

Common deleted genes in the 5q- syndrome: thrombocytopenia and reduced erythroid colony formation in SPARC null mice.

The commonly deleted region (CDR) for the 5q- syndrome has been identified as a 1.5-megabase interval on human chromosome 5q32. We studied, by real-time reverse-transcription (RT)-PCR, the expression of 33 genes within the CDR that are known to be expressed in CD34+ hematopoietic stem cells. Genes in the 5q- samples that showed the most pronounced decrease in expression compared to non-5q- samples were: solute carrier family 36, member 1 (SLC36A1; 89% downregulated), Ras-GTPase-activating protein SH3 domain-binding (G3BP; 79%), antioxidant protein 1 (ATOX1; 76%), colony-stimulating factor-1 receptor precursor (CSF1R; 76%), ribosomal protein S14 (RPS14; 74%), platelet-derived growth factor receptor-beta (PDGFRB; 73%), Nef-associated factor 1 (TNIP1; 72%), secreted protein, acidic and rich in cysteine (SPARC; 71%), annexin VI (ANAX6; 69%), NSDT (66%) and TIGD (60%). We further studied the hematopoietic system in SPARC-null mice. These mice showed significantly lower platelet counts compared to wild-type animals (P=0.008). Although hemoglobin, hematocrit and mean corpuscular volume (MCV) were lower in mice lacking SPARC, differences were not statistically significant. SPARC-null mice showed a significantly impaired ability to form erythroid burst-forming units (BFU-E). However, no significant differences were found in the formation of erythroid colony-forming units (CFU-E), granulocyte/monocyte colony-forming units (CFU-GM) or megakaryocyte colony-forming units (CFU-Mk) in these animals. We conclude that many of the genes within the CDR associated with the 5q- syndrome exhibit significantly decreased expression and that SPARC, as a potential tumor suppressor gene, may play a role in the pathogenesis of this disease.

Discovery of epigenetically silenced genes in acute myeloid leukemias.

The demethylating 5-aza-2'deoxycytidine (DAC) and the histone deacetylase inhibitor (HDACi) suberoyl anilide bishydroxamide (SAHA) possess potent antitumorigenic properties in myeloid disorders. However, the transcriptome alterations mediated by these drugs are poorly understood. We analyzed the transcriptional effects of DAC and SAHA in the AML cell line KG-1. Microarray analyses revealed 76 genes expressed in normal CD34+ cells, absent in KG-1 cells but whose expression was induced after drug treatment. A total of 39 of these genes harbored CpG islands in their promoters. We examined the expression level of these genes in 120 AML patient samples representing diverse karyotpyes. Gas2l1, tfIIs, ehd3, enolase 2, mx1, dral, astml and pxdn were diminished across all AML karyotypes examined. Ehd3 was methylated in 63% of AML patients examined. This methylation was lost upon complete remission, and not observed in normal CD34+ cells. CD34+ cells expressed ehd3 at approximately 10-fold higher levels than AML samples. Another highlighted gene, alpha-catenin, is located at q31 of chromosome 5. Analyses of 29 5q- AML/myelodysplastic syndrome (MDS) samples revealed marked decreases in expression of alpha-catenin, compared to non-5q- MDS samples (6.6+/-9-fold). However, no methylation was detected, suggesting indirect effects of these drugs on the expression of alpha-catenin.

Allogeneic stem cell transplantation improves the outcome of adults with t(1;19)/E2A-PBX1 and t(4;11)/MLL-AF4 positive B-cell acute lymphoblastic leukemia: results of the prospective multicenter LALA-94 study.

Adult patients with acute lymphoblastic leukemia (ALL) and t(1;19)/E2A-PBX1 or t(4;11)/MLL-AF4 have a poor outcome. We have evaluated the impact of an intensified post-remission therapy using a high-dose chemotherapy course followed by allogeneic or autologous SCT on the outcome of 58 patients with t(1;19)/E2A-PBX1 (E2A group, n=24) or t(4;11)/MLL-AF4 (MLL group, n=34) treated in the LALA-94 multicenter prospective study. Patients in the MLL group had higher WBC counts and more frequent DIC. CR rates achieved by MLL and E2A groups were similar to other B-cell ALL (87, 82 and 86% respectively). While in CR, patients with a donor were assigned to alloSCT (n=22), the remaining patients with were randomized between autoSCT (n=15) or chemotherapy (n=8). Five-year overall survival was 31 and 45% for E2A and MLL groups, respectively. In both groups, DFS was higher in the alloSCT arm as compared to autoSCT and chemotherapy arms. The results of this study show that chemotherapy intensification did not overcome the poor prognosis of adults with t(1;19)/E2A-PBX1. Allogeneic SCT should thus be offered in first CR to patients with t(1;19)/E2A-PBX1 or t(4;11)/MLL-AF4. New therapeutic approaches are needed for patients without donor.

Dissemination and persistence of Shiga toxin-producing Escherichia coli (STEC) strains on French dairy farms.

Some Shiga toxin-producing Escherichia coli strains (STEC), and in particular E. coli O157:H7, are known to cause severe illness in humans. STEC have been responsible for large foodborne outbreaks and some of these have been linked to dairy products. The aim of the present study was to determine the dissemination and persistence of STEC on 13 dairy farms in France, which were selected out of 151 randomized dairy farms. A total of 1309 samples were collected, including 415 faecal samples from cattle and 894 samples from the farm environment. Bacteria from samples were cultured and screened for Shiga toxin (stx) genes by polymerase chain reaction (PCR). STEC isolates were recovered from stx-positive samples after colony blotting, and characterized for their virulence genes, serotypes and XbaI digestion patterns of total DNA separated by pulsed-field gel electrophoresis (PFGE). Stx genes were detected in 145 faecal samples (35%) and 179 (20%) environmental samples, and a total of 118 STEC isolates were recovered. Forty-six percent of the STEC isolates were positive for stx1, 86% for stx2, 29% for intimin (eae-gene) and 92% for enterohemolysin (ehx), of which 16% of the STEC strains carried these four virulence factors in combination. Furthermore, we found that some faecal STEC strains belonged to serotypes involved in human disease (O26:H11 and O157:H7). PFGE profiles indicated genetic diversity of the STEC strains and some of these persisted in the farm environment for up to 12 months. A large range of contaminated samples were collected, in particular from udders and teats. These organs are potential sources for contamination and re-contamination of dairy cattle and constitute an important risk for milk contamination.

Amplification of FGF-related genes in human tumors: possible involvement of HST in breast carcinomas.

In order to document a possible involvement of structural alterations of FGF (Fibroblast Growth Factor)-like genes in human oncogenesis, we have screened a large series of human tumors for amplification of five FGF-related genes (Basic-FGF, INT2, HST, FGF5 and FGF6). None of 37 hematopoietic neoplasms, one out of 13 melanomas (8%), three out of 43 bladder tumors (7%) and 41 out of 238 breast carcinomas (17%) contained amplified FGF-related sequences, namely HST and INT2. Only these two genes, both located on band q13 of chromosome 11 have been found amplified. In all cases they were co-amplified and in only one instance did amplification extend to the ETS1 locus at position 11q23. INT2 and HST RNA could be evidenced by RNA/RNA in situ hybridization in breast carcinomas. Our results indicate a correlation between RNA expression and gene amplification in the case of HST but not of INT2. Although evaluation of the clinical significance of HST amplification and expression must await long-term follow-up of the patients, we suggest that HST gene product could play a role in development and/or progression of human breast cancer.

Rearrangement of proximal 11q13 band in a CMML in acute transformation.

Fluorescence in situ hybridization (FISH) was performed on bone marrow cells thought to contain a t(7;11)(p22;q13) from a patient with chronic myelomonocytic leukemia in transformation. FISH analysis using a panel of 10 probes previously mapped to 11q13 revealed a cytogenetically undetected complex rearrangement that involved chromosomes 7 and 11 as well as a chromosome 3 at band p24. Two distinct translocation breakpoints, both proximal to the BCL1 locus, were found in chromosome 11 that perforce separate it into three subregions. The two breakpoints appear distinct from the two previously described ones which involved the FAU and GSTP1 genes. Our observations add to the involvement of proximal 11q13 in myeloid malignancies.

Cytogenetic abnormalities associated with the t(12;21): a collaborative study of 169 children with t(12;21)-positive acute lymphoblastic leukemia.

The t(12;21)(p13;q22) is a cryptic abnormality observed in 25% of children with B-lineage acute lymphoblastic leukemia (ALL), associated with a favorable prognosis. To determine whether specific cytogenetic abnormalities accompany the t(12;21), we analyzed the cytogenetic profiles of blast cells from 169 ALL cases positive for the t(12;21), previously identified by molecular methods. Only 13.6% of samples had normal karyotypes. Structural changes were detected in 89.7% of abnormal karyotypes, and numerical abnormalities in 47%. Rearrangements of 12p were the most frequent structural aberration (57 out of 146 patients with chromosomal abnormalities). Nonspecific deletions of chromosomes 6 and 9 were also found. The most frequent numerical abnormalities was trisomy for chromosomes 21. Blast cells were pseudodiploid (45.6%), hyperdiploid with 47 to 51 chromosomes (24.3%), hypodiploid with 44 to 45 chromosomes (10%), near-triploid (0.6%), or near-tetraploid (5.9%). Our results show that the t(12;21) is not associated with hyperdiploidy of 52 to 68 chromosomes or with the prognostic t(1;19), t(4;11) or t(9;22). Only children with B-lineage ALL who lack these abnormalities detected by conventional cytogenetics will probably benefit from additional testing by molecular methods to detect the t(12;21).

Recurrent cytogenetic abnormalities observed in complete remission of acute myeloid leukemia do not necessarily mark preleukemic cells.

We have undertaken the cytogenetic monitoring of 39 adult patients treated for de novo acute myeloid leukemia (AML) by intensive chemotherapy. We describe this monitoring in seven patients in continuous complete clinical and morphologic remission (CR) of AML. Although in CR, these patients exhibit the emergence of cytogenetically abnormal clones. Abnormalities observed include monosomy 7, del(20)(q11), partial trisomy 1q, and 6p12-22 rearrangements. They correspond to well-known chromosomal rearrangements commonly found in myelodysplasia (MDS), and myeloproliferative syndromes (MPS), as well as AML. Present as the sole detected chromosomal change, they preceded by months the onset of overt leukemia or MDS. In some cases, the abnormal clone showed a proliferative advantage (some patients exhibited up to 100% of abnormal bone marrow metaphases in subsequent analyses). AML relapse, when it occurred, was associated with a different chromosomal modification. Altogether the question arises, whether the abnormalities pointed out in our study (monosomy 7, del(20)(q11), partial trisomy for the long arm of chromosome 1 (q21qter), 6p12-22 rearrangements), and seen after chemotherapy, mark preleukemic cells or not, and whether they participate indirectly, or not at all in the leukemic process.

ETV6 is the target of chromosome 12p deletions in t(12;21) childhood acute lymphocytic leukemia.

The presence of ETV6 deletions was investigated in 215 children with acute lymphoblastic leukemia (ALL) using the loss of heterozygosity (LOH) approach. We used four intragenic or juxtagenic microsatellite markers to detect allelic deletions. In this series of unselected patients, LOH of ETV6 markers was found in 23% of cases (6% of T-ALL and 26% of B lineage ALL) confirming that chromosome 12p12-13 deletions represent a major genetic alteration in childhood ALL, frequently missed by cytogenetic analysis. The presence of a t(12;21)(p13;q22) was studied by RT-PCR and/or FISH in a total of 134 patients (125 B lineage ALL, nine T-ALL) including 42 cases with LOH. Thirty-four out of 44 patients (77%) for whom a t(12;21) was observed displayed LOH of the ETV6 markers. When associated with a t(12;21), ETV6 is very likely to be the target of deletions as indicated by the detection of intragenic deletions in three patients. Although deletion of ETV6 and t(12;21) were associated in most patients, in eight cases (six B lineage and two T-ALL) LOH was detected at the ETV6 locus without ETV6-AML1 hybrid RNA. FISH studies conducted in five of these eight patients confirmed the absence of translocation involving ETV6. In such patients, the other allele of ETV6 could be disrupted by either a small deletion, a point mutation, or an epigenetic modification and it will be of interest to study the structure and expression of the remaining allele of ETV6 in these cases. Alternatively, a tumor suppressor gene located close to ETV6 and CDKN1B could be the target of deletions.

Calcium phosphate apatites with variable Ca/P atomic ratio II. Calcination and sintering.

The calcination and natural sintering of calcium deficient hydroxyapatite powders Ca(10-x)(PO4)(6-x)(HPO4)x(OH)(2-x) (with 0 < or = x < or = 1) were studied. For temperature below 700 degrees C, particle coalescence occurs without densification. The particle coalescence is associated with a reduction of the specific surface area. This surface decreases all the more as the Ca/P molar ratio of the powder is small. The mechanism agrees with a transfer of matter occurring by superficial diffusion, which is enhanced by the augmentation of vacancies in the apatitic structure (i.e. by a decrease of the Ca/P ratio). The sintering of compacted powders begins at 700 degrees C. At the same temperature, the calcium deficient hydroxyapatites dissociate into biphasic mixtures of hydroxyapatite and tricalcium phosphate. The sintering is slowed down when the content of TCP in the biphasic mixture increases. In parallel, the grain size increases. This result relates to the augmentation of the coalescence of particles at low temperature.

Calcium phosphate apatites with variable Ca/P atomic ratio I. Synthesis, characterisation and thermal stability of powders.

Single phased apatitic calcium phosphate powders Ca(10-x)(PO4)(6-x)(HPO4)x(OH)(2-x) with Ca/P molar ratio ranging from 1.5 to 1.667 (0 < or = x < or = 1) were synthesised using wet method. Outside this compositional range the powders were biphasic mixtures composed of a calcium phosphate apatite and CaHPO4 (Ca/P < 1.5) or Ca(OH)2 (Ca/P > 1.667). Temperature and pH of synthesis were the preponderant parameters for the control of the precipitate composition. The precise determination of the chemical composition requires the use of several complementary techniques and thermal treatments of powders. These techniques include high resolution and high temperature X-ray diffractometry and FTIR spectroscopy and show that very small variations of the Ca/P molar ratio of the powder lead to great changes in powder composition and characteristics after thermal treatment.

Calcium phosphate apatites with variable Ca/P atomic ratio III. Mechanical properties and degradation in solution of hot pressed ceramics.

Calcium deficient hydroxyapatite powders Ca(10-x)(PO4)(6-x)(HPO4)x(OH)(2-x) (0 < or = x < or = 1) were hot pressed to produce dense hydroxyapatite-tricalcium phosphate (HAP/TCP) biphasic materials. Ceramics hot pressed at 1000 degrees C were composed of an homogeneous distribution of the HAP and beta-TCP grains with an average size of 0.2 microm. Grain growth was observed for TCP loading > 70 wt%. The strength exhibited a maximum of sigma(f) = 150 MPa for 90/10 (w/w) HAP/TCP and it dropped for smaller and greater amounts of TCP. This value was twice that of pure HAP. When placed in Ringer's solution, only the surface of biphasic compounds was degraded after 60 days of immersion with a preferential etching of the TCP phase. After hot pressing at 1200 degrees C, grain growth was observed and the mechanical properties were decreased. This was explained by the allotropic transformation alpha/beta of TCP.

Variant translocation t(8;21;15) in an acute myeloblastic leukemia with phenotypic differential evolution.

A new case of a variant form of the translocation (8;21) in an AML-M2, including in addition involvement of chromosome #15 is reported. The selection of two abnormal lines, probably resulting from two successive rearrangements of the (8;15) translocated segment, is observed. It is suggested that these rearrangements change the cellular morphology and seem to play a part similar to additional autosomal abnormalities in the course of the disease, such as those found in CML.

Cytogenetic study of 88 cases of refractory anemia.

Data obtained on 88 patients with refractory anemia or preleukemia, without previous cytotoxic treatment, showed medullar chromosomal abnormalities in 32%. In 45% of the cases, the disease had progressed to acute nonlymphocytic leukemia. A high frequency of acute transformation (78%) was observed in patients with abnormal clones. These results are different from those of the Second International Workshop on chromosomes in Leukemia. The discrepancies may be related to the difference between the cases selected for submission to the workshop and those of this study. Serial studies on 28 patients with abnormal karyotypes showed that two different populations of patients were investigated: one with a terminal smoldering phase of leukemia and the other with true preleukemic disease. In the latter group, no predictive karyotype evolution was seen.

Antitumoral effects of squamocin on parental and multidrug resistant MCF7 (human breast adenocarcinoma) cell lines.

The antiproliferative effects of squamocin, one of the easiest annonaceous acetogenins to obtain, were studied in the parental (MCF7-S) and the multidrug resistant (MCF7-R) human breast adenocarcinoma cell lines. Squamocin inhibited proliferation of both cell lines identically, by blocking the cell cycle in the G1-phase. This inhibition was reversible in the long term. Squamocin decreased the ATP pool in both MCF7 cell lines, but did not seem to induce apoptosis. Cytotoxic activity of adriamycin was not restored in MCF7-R Pgp expressing cells by squamocin addition.

Antiplasmodial activity of acetogenins and inhibitory effect on Plasmodium falciparum adenylate translocase.

Three Annonaceous acetogenins exhibited in vitro antimalarial activities on a chloroquine-resistant Plasmodium falciparum strain, with IC50s ranging from 5 to 10 microM. Structure-activity relationships showed that maximal antimalarial activity occurred in the presence of at least one tetrahydrofuran moiety and a synergistic action with chloroquine was observed. These acetogenins partially inhibited the P. falciparum adenylate translocase.