Abstract OT3-04-01: A phase I of olaparib with radiation therapy in patients with inflammatory, loco-regionally advanced or metastatic TNBC (triple negative breast cancer) or patient with operated TNBC with residual disease

Background and discussion: TNBC shares clinical and pathological features with hereditary BRCA1-related breast cancers, and in sporadic TNBC; dysregulation of BRCA1 has been frequently observed together with other defects in homologous recombination pathways. Preclinical studies have shown that breast cancer cell lines with a triple-negative phenotype are more sensitive to PARP1 inhibitors compared with non-TNBC cells. These lines of evidence provide a strong rationale for developing a new therapeutic approach to TNBC based on targeting the DNA-repair defects via PARP inhibition in these cancers that the most aggressive are the inflammatory, loco-regional advanced and metastatic breast cancer, as well as operated patients with residual disease (after primary systemic treatment-PST).

The aim of this study is to determine the Maximal Tolerated Dose of Olaparib administered with concurrent loco regional RT in the previously described population of patients.

Trial design: Olaparib (oral administration) will be administered at a starting dose of 50 mg bid. The other dose levels will be: 100 mg bid, 150 mg bid, 200 mg bid. The 25 mg bid dose will be included in the model to deal with unexpected high toxicity of the starting dose. Seven days prior to their first fraction of radiation therapy, patients will begin taking Olaparib at the assigned dose twice daily each day. All patients will receive radiotherapy on day 8 after the start of Olaparib of 50 Gy to the whole breast (or chest wall) with or withour lymph nodes (LN) in 25 daily fractions and 5 weeks.

Eligibility Criteria: Women aged >18 years with histologically confirmed TNBC with loco-regional RT indication as :

Non-operated:

Inflammatory and/or advanced BC (T≥3 and/or N≥1) BC in progression during PST (containing anthracyclines or taxanes or the combination of both or containing platinium-based chemotherapy) or inoperable after PST.

Non operable metastatic BC (all T, all N, M1; with evaluable disease).

Or patients operated after PST and surgery with residual disease (non-pCR and pN+ disease, evaluable according to RECIST 1.1 criteria).

Specific aims

To assess the safety profile of Olaparib administered with concurrent RT.

This study should be completed by a methylation study of BRCA1 and RAD51 promoters.

Statistics Phase I dose-finding based on toxicity will be conducted in a sequential and adaptive Bayesian scheme, using the method of Time-to-event Continual Reassessment Method to determine the Maximum Tolerated Dose (MTD) of Olaparib associated with RT. The primary endpoint is Dose-Limiting Toxicity (DLT) occurring within 6 weeks after the end of RT (12 -13 weeks from the first drug intake, depending on the period of the radiotherapy treatment). Dose allocation will be centrally defined, based on DLT observed in all patients previously evaluated, by modeling the probability of DLT. An empiric model will be used for the dose-toxicity relationship. No intra-patient dose-escalation is permitted. No dose skipping in escalation is permitted. The MTD is defined as the dose associated with 25% of DLT.

Target accrual: Twenty-four to 30 pts are expected to be enrolled.

Contact: youlia.kirova@curie.fr

Citation Format: Kirova YM, Ezzalfani M, Rodrigues M, Pierga J-Y, Salomon A, Stern M-H, Laki F, Mosseri V, Berger F, Neffrati S, Armanet S, Fourquet A. A phase I of olaparib with radiation therapy in patients with inflammatory, loco-regionally advanced or metastatic TNBC (triple negative breast cancer) or patient with operated TNBC with residual disease [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT3-04-01.

Abstract P2-05-09: Withdrawn

This abstract was withdrawn by the authors.

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive neoplasm of mature T-cells with an urgent need for rationally designed therapies to address its notoriously chemo-refractory behavior. The median survival of T-PLL patients is <2 years and clinical trials are difficult to execute. Here we systematically explored the diversity of drug responses in T-PLL patient samples using an ex vivo drug sensitivity and resistance testing platform and correlated the findings with somatic mutations and gene expression profiles. Intriguingly, all T-PLL samples were sensitive to the cyclin-dependent kinase inhibitor SNS-032, which overcame stromal-cell-mediated protection and elicited robust p53-activation and apoptosis. Across all patients, the most effective classes of compounds were histone deacetylase, phosphoinositide-3 kinase/AKT/mammalian target of rapamycin, heat-shock protein 90 and BH3-family protein inhibitors as well as p53 activators, indicating previously unexplored, novel targeted approaches for treating T-PLL. Although Janus-activated kinase-signal transducer and activator of transcription factor (JAK-STAT) pathway mutations were common in T-PLL (71% of patients), JAK-STAT inhibitor responses were not directly linked to those or other T-PLL-specific lesions. Overall, we found that genetic markers do not readily translate into novel effective therapeutic vulnerabilities. In conclusion, novel classes of compounds with high efficacy in T-PLL were discovered with the comprehensive ex vivo drug screening platform warranting further studies of synergisms and clinical testing.

Abstract P1-03-05: A comprehensive molecular analysis of medullary breast carcinoma: A model of immunomodulatory triple negative breast cancer subtype

Medullary breast carcinoma (MBC) is a rare subtype of triple negative breast cancer (TNBC)with specific genomic features within the spectrum of basal-like carcinoma. The frequent association between BRCA constitutive mutation and MBC phenotype has been reported previously. In this study including 19 MBC and 36 non-MMB basal-like carcinoma (BLC), we refine the genomic and transcriptomic knowledge about this entity. Using pan genomic Affymetrix genome-wide human SNP6.0 array, we show that i/ MBC harbour more copy number alterations and losses of heterozygocity than BLC and that ii/ the high frequency of BRCAness genomic trait among MBC. Unsupervised and supervised analysis of GeneChip Uman Genome U133 Plus 2.0 Array transcriptomic generated data confirmed that MBC clearly differ from BLC in terms of gene expression level, with 92 genes overexpressed and 154 genes underexpressed in MBC over BLC. Immune response and inflammatory response are the most differentially represented pathways in MBC over BLC. Pro apoptotic gene BCLG is by far the more overexpressed gene in MBC. A validation study conducted with RT-QPCR among 526 breast tumors form all molecular subtype confirmed the specificity of BCLG overexpression in MBC, which was confirmed at protein level using immunohistochemisytry. Moreover, we show that a vast majority of MBC belong o the immunomodulatory TNBC subtype according to Lehman et al. Finally, we confirm the better prognosis of MBC toward BLC. Our observations epitomize the importance of developing DNA repair targeting drugs and immunotherapy based trials in order to improve the outcome of such a specific entity.

Citation Format: Romero P, Deniziaut G, Benhamo V, Fuhrmann L, Berger F, Bhalshankar J, Gruel N, MacGrogan G, Popova T, Manié E, Stern M-H, Stoppa-Lyonnet D, Rouzier R, Delattre O, Bieche I, Vincent-Salomon A. A comprehensive molecular analysis of medullary breast carcinoma: A model of immunomodulatory triple negative breast cancer subtype [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-05.

Genetic landscape of uveal melanoma

Uveal melanoma is genetically one of the simplest malignant tumors in adults. Initiation of these tumors is dependent of an oncogenic mutation in the GNAQ or GNA11 genes present in almost all cases. The nature of second mutational events is of major interest as it monosomy 3, gain of 8q and BAP1 inactivation are associated with unfavorable prognosis while SF3BI or EIF1AX are of good prognosis. Despite their common lineage, cutaneous and uveal melanomas are distinct diseases, implicating different oncogenic pathways and contrasting mutational landscapes. Even if uveal melanoma is a simple tumor, it is also one of the deadliest tumors in adults. There is a major clinical need for drugs targeting either the downstream pathways of Gαq and Gα11 or the biological cell functions dysregulated by BAP1 loss of function.

Abstract P4-04-05: Molecular subtyping reveals the heterogeneity of metaplastic breast cancers

Introduction: Metaplastic breast carcinoma (MBC) is a rare (1%) and aggressive histological special type of breast cancer, which often (&gt;90%) displays a triple-negative (TN) phenotype. Microarray-based gene expression classifications of breast cancer have been described, including the ‘intrinsic subtypes’ (i.e. luminal A, luminal B, basal-like, HER2-enriched, normal breast-like and claudin-low) and the six TN molecular subtypes with therapeutic implications in preclinical models (i.e. basal-like I, basal-like II, mesenchymal-like, mesenchymal stem-like, immunomodulatory and luminal androgen receptor). In addition, single nucleotide polymorphism (SNP) array analyses have led to the development of classifiers to define whether TN breast cancers would have genomic aberrations consistent with those found in tumors arising in BRCA1 germline mutation carriers. Here we sought to define i) the heterogeneity of MBCs using distinct microarray-based classifiers and ii) whether MBCs display gene copy number profiles consistent with those of BRCA1 breast cancers.

Material and Methods: Thirty consecutive MBCs were retrieved from the tumor banks of the authors’ institutions, reviewed by two pathologists and classified into three groups: carcinomas with spindle cell metaplasia (n = 12), with squamous metaplasia (n = 10), and with heterologous elements (n = 8). RNA and DNA were extracted from representative frozen sections containing &gt;50% of cancer cells from each tumor and subjected to gene expression profiling using the HumanHT-12 v4 platform (Illumina) and gene copy number analysis using SNP 6.0 arrays (Affymetrix), respectively. ‘Intrinsic subtyping’ was performed according to the UNC guidelines, and subtyping into the six TN types using a dedicated website (https://cbc.mc.vanderbilt.edu/tnbc/). Classification of MBCs into BRCA1-like or non-BRCA1-like was performed using an algorithm to identify and quantify large-scale state transitions.

Results: PAM50/claudin-low subtyping of MBCs revealed that all spindle cell carcinomas (n = 12) were consistently of claudin-low subtype, whereas MBCs with heterologous elements were classified as of basal-like (n = 6) and normal breast-like (n = 2), and squamous cell carcinomas as of basal-like (n = 5), claudin-low (n = 4) and normal-like (n = 1). Using the six TN subtypes, spindle cell MBCs were classified as mesenchymal stem-like (n = 4), immunomodulatory (n = 3), basal-like 2 (n = 3), or mesenchymal (n = 2) subtype. Carcinomas with heterologous elements were classified as basal-like 1 (n = 5) or mesenchymal (n = 3) subtype, whereas carcinomas with squamous metaplasia were of immunomodulatory (n = 5), basal-like 1 (n = 2), basal-like 2 (n = 2) or mesenchymal (n = 1) subtype. Out of the 26 samples where SNP 6.0 arrays were successfully performed, only 9 (35%) were classified as BRCA1-like, including two spindle cell carcinomas, two carcinomas with heterologous elements and five carcinomas with squamous metaplasia.

Conclusion: MBCs constitute a heterogeneous group of tumors and the histological subclassification of these cancers is of importance, given that tumors with distinct metaplastic elements are classified differently according to current molecular subtyping methods. Only 35% of MBCs display BRCA1-like patterns of gene copy number aberrations.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-05.

Abstract P5-02-03: Large-scale genomic instability consistently identifies BRCA1/2 inactivation in breast cancers

The goal of this study was to identify genomic markers predicting actual BRCA1/2 inactivation in breast cancers. By comparing genomic profiles of BRCA1/2 mutated and wildtype basal-like carcinomas (BLC) we developed a signature of BRCAness. The signature accounts for the level of the large scale genomic instability and was demonstrated to predict BRCA1/2 impairment with 100% sensitivity and 90% specificity in the large series of BLCs. We introduced a bioinformatics procedure evaluating the number of large scale rearrangements (denoted as Large Scale Transition or LST) in the genome and showed that the number of LSTs discriminate homologous recombination deficient and proficient tumors (Popova et al, Cancer Research 2012 Aug).

The efficiency of the signature of BRCAness represented by the number of LSTs was then evaluated for the luminal breast tumors and ovarian carcinomas. Luminal breast tumors and ovarian carcinomas could be stratified into two groups according to the number of LSTs. The performance of the LST signature in all types of breast cancers will be presented.

Measurement of LST is a highly reliable, simple and cost effective method to identify patients who should benefit of a BRCA1/2 testing, and to select tumors which may respond to treatment targeting DNA repair deficiencies (platinium salts, PARP inhibitors).

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-02-03.

P3-06-03: Hypodiploidy, 1pter Loss and Inactive X Chromosome Retention Are Associated with BRCA1 Somatic or Germline Inactivation in Basal-Like Breast Carcinomas: Proposal for a New BRCAness Genomic Signature

Basal-Like Carcinomas (BLCs) are high grade ductal carcinomas identified by large scale transcriptomic analyses among carcinomas with triple-negative phenotype (ER- PR- HER2−). A particular relationship between this phenotype and the BRCA1 breast cancer susceptibility gene has been described based on several observations including high genomic similarities of sporadic and BRCA1 BLCs. BRCA1 mutated patients have been shown to strongly benefit from treatments using PARP inhibitors. However, significant benefit of this treatment was not demonstrated in sporadic triple-negative breast cancers in association to standard chemotherapy in phase III clinical trials, which emphasizes the necessity for a better selection of DNA repair deficient tumors. The goal of this study was to determine whether BRCA1 inactivation leads to particular genomic alterations that could be used to identify BRCA1 deficient sporadic BLCs.

Genomic profiling was performed using SNP-arrays (Affymetrix and Illumina) and high quality profiles were obtained for 60 BLCs with more than 35% of tumor cells. The series contained 28 BRCA1 BLCs and 32 sporadic BLCs consisting in 10 sporadic BLCs with BRCA1 somatic inactivation by promoter methylation (BRCA1-like BLCs) and 22 sporadic tumors without BRCA1 methylation (nonBRCA1 BLCs). Genomic data was mined with GAP methodology (Popova et al, Genome Biol 2009), which allows absolute copy-number evaluation with DNA content calculation and clarification of Loss Of Heterozygosity (LOH) status.

Genomic patterns of BLCs were characterized by frequent and highly recurrent allelic losses. Comparison between BRCA1, BRCA1-like and nonBRCA1 BLCs confirmed their overall similarity, and identified few significant differences enhanced when BRCA1 and BRCA1-like BLCs were considered as one group. Firstly, hypodiploidy characterized BLCs with BRCA1 germline and/or somatic inactivation. Secondly, the lpter region was found more often lost in BRCA1 and BRCA1-like BLCs than in nonBRCA1 BLCs. Thirdly, retention of inactive X chromosome was a characteristic of BLCs with BRCA1 germline and/or somatic inactivation. Finally, a BRCA1ness score based on the above described difference is proposed.

In conclusion, despite a strong similarity of genomic patterns in BLCs, BRCA1 inactivation leads to few key genomic aberrations which constitute a new BRCA1 molecular signature namely hypodiploidy, 1pter loss and inactive X chromosome retention. This signature needs to be further evaluated in terms of response to PARP inhibitors in order to evaluate its capacity to identify patients that will benefit from this treatment.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-03.

[Cancer genetic predisposition: current events and perspectives in 2010]

Studies performed during these last 30 years have had a major impact on the understanding of carcinogenesis. They have opened a new field: cancer genetic predisposition. At the present time, most of the cancer predispositions linked to the alteration of one gene, associated with a high risk of cancer and with a specific phenotype have been identified. About 70 genes have been identified and have led to genetic testing. The indication of genetic testing, the management of at risk patients require the establishment of guidelines. The next challenge is the identification of cancer susceptibility genes associated with low risk or modifying the effect of treatment.

A complex pattern of recurrent chromosomal losses and gains in T-cell prolymphocytic leukemia

T-cell prolymphocytic leukemia (T-PLL) is a rare malignant proliferation of lymphoid cells with a postthymic phenotype. Previous cytogenetic and molecular studies reported complex karyotypes with recurrent chromosomal abnormalities, including translocations involving either TCL1 at 14q32.1 or MTCP1 at Xq28, inactivation of the ATM gene by deletion and/or mutation, and isochromosomes 8. For extensive study of chromosomal imbalances in T-PLL, we analyzed 22 tumoral DNAs using comparative genomic hybridization (CGH). Abnormal CGH profiles were detected in all cases, demonstrating highly recurrent gains and losses and largely extending the abnormalities previously established. Only a few nonrecurrent abnormalities were observed, in contrast to the genetic instability anticipated from ATM inactivation. Nine recurrent regions of loss were identified at 8p (frequency 86%), 11q (68%), 22q11 (45%), 13q (41%), 6q (36%), 9p (27%), 12p (23%), 11p11-p14 (23%), and 17p (23%), as well as four regions of gain at 8q (82%), 14q32 (50%), 22q21-qter (41%), and 6p (23%). Several recurrent chromosomal abnormalities were simultaneously present in each case (mean, 5.7; up to 10), none being mutually exclusive of another. Fluorescence in situ hybridization analysis confirmed and extended 22q11 and 13q losses, giving final frequencies of 55% and 45%, respectively. Analysis of one case over a 7-year period confirmed the overall genetic stability of T-PLL and showed that tumor progression was associated with the onset of a few chromosomal abnormalities. This study establishes a complex pattern of highly recurrent chromosomal abnormalities in T-PLL, including some, such as chromosome 13 deletion, commonly found in other lymphoid malignancies.

Backbone dynamics and solution structure refinement of the 15N-labeled human oncogenic protein p13MTCP1: comparison with X-ray data

Two related oncogenes, TCL1 and MTCP1, are overexpressed in certain T-cell prolymphocytic leukemias as a result of chromosomal rearrangements that involve the translocation of one T-cell receptor gene to either chromosome 14q32 or Xq28, respectively. The human oncoprotein p13MTCP1 is coded by the MTCP1 gene and its primary sequence is highly and only homologous to that of p14TCL1, the product of TCL1. These two proteins likely represent the first members of a new family of oncogenic proteins. A previous model of the three-dimensional solution structure of p13MTCP1 was determined recently using exclusively homonuclear proton two-dimensional NMR methods and, almost simultaneously, high-resolution crystal structures of p13MTCP1 and p14TCL1 appeared in the literature. In order to gain more insight into the details of the solution structure, we uniformly labeled p13MTCP1 with nitrogen-15. The refined structure benefits from 520 additional NOEs, extracted from either 15N-edited 3D experiments or homonuclear 2D NOESY recorded at 800 MHz, and from a nearly complete set of phi angular restraints. Measurements of 15N spin relaxation times and heteronuclear 15N[1H]NOEs at two magnetic field strengths provided additional insights into the dynamics of the protein backbone. On the basis of these new results, a putative binding surface for this particular class of oncogenes is discussed.

Recurrent molecular deletion of the 12p13 region, centromeric to ETV6/TEL, in T-cell prolymphocytic leukemia

INTRODUCTION

T-cell prolymphocytic leukemia is a rare form of mature leukemia which occurs in adults and in younger patients suffering ataxia telangiectasia. Among others, complex chromosome aberrations of chromosome 12 have been described in this disease. We searched for deletions of the 12p13 region as the result of these chromosome rearrangements.

MATERIAL AND METHODS

Paired leukemic and non-leukemic cells were obtained from a series of 21 patients suffering T-cell prolymphocytic leukemia. Loss of heterozygosity was searched for by microsatellite typing using a fluorescent automated laser DNA sequencer to analyze the amplification products. Proteins were analyzed by Western blot. Southern blot analysis of one patient was conducted.

RESULTS AND CONCLUSION

Loss of heterozygosity of the 12p13 region, including the ETV6 and CDKN1B genes, was detected in nine of these 21 cases (43%). Western and Southern blot analyses of one case demonstrated a biallelic deletion which did not include ETV6. Taken together, our results defined a minimal region of deletion of less than one Mb flanked by the markers b312C2T7 and D12S320, excluding ETV6 as a candidate gene. Deletion of the 12p13 region is thus a highly recurrent genetic event in T-cell prolymphocytic leukemia.

Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP1 studied by NMR relaxation

MTCP1 (for Mature-T-Cell Proliferation) was the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8MTCP1 protein encoded by the MTCP1 oncogene has been previously determined by homonuclear proton two-dimensional NMR methods at 600 MHz: it consists of an original scaffold comprising three alpha-helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an alpha-hairpin which resembles an antiparallel coiled-coil. The third helix is orientated roughly parallel to the plane defined by the alpha-antiparallel motif and appears less well defined. In order to gain more insight into the details of this new scaffold, we uniformly labeled with nitrogen-15 a mutant of this protein (C12A-p8MTCP1) in which the unbound cysteine at position 12 has been replaced by an alanine residue, thus allowing reproducibly high yields of recombinant protein. The refined structure benefits from 211 additional NOEs, extracted from 15N-edited 3D experiments, and from a nearly complete set of phi angular restraints allowing the estimation of the helical content of the structured part of the protein. Moreover, measurements of 15N spin relaxation times and heteronuclear 15N¿1H¿NOEs provided additional insights into the dynamics of the protein backbone. The analysis of the linear correlation between J(0) and J(omega) was used to interpret relaxation parameters. It appears that the apparent relative disorder seen in helix III is not simply due to a lack of experimental constraints, but associated with substantial contributions of sub-nanosecond motions in this segment.

TCL1 oncogene expression in AIDS-related lymphomas and lymphoid tissues

AIDS-related non-Hodgkin's lymphoma (AIDS NHL) comprises a diverse and heterogeneous group of high-grade B cell tumors. Certain classes of AIDS NHL are associated with alterations in oncogenes or tumor-suppressor genes or infections by oncogenic herpesviruses. However, the clinically significant class of AIDS NHL designated immunoblastic lymphoma plasmacytoid (AIDS IBLP) lacks any consistent genetic alterations. We identified the TCL1 oncogene from a set of AIDS IBLP-associated cDNA fragments generated by subtractive hybridization with non-AIDS IBLP. Aberrant TCL1 expression has been implicated in T cell leukemia/lymphoma development, and its expression also has been seen in many established B cell tumor lines. However, TCL1 expression has not been reported in AIDS NHL. We find that TCL1 is expressed in the majority of AIDS IBLP tumors examined. TCL1 protein expression is restricted to tumor cells in AIDS IBLP tissue samples analyzed with immunohistochemical staining. Hyperplastic lymph node and tonsil also exhibit strong TCL1 protein expression in mantle zone B cells and in rare interfollicular zone cells, whereas follicle-center B cells (centroblasts and centrocytes) show weaker expression. These results establish TCL1 as the most prevalent of all of the surveyed oncogenes associated with AIDS IBLP. They also indicate that abundant TCL1 expression in quiescent mantle zone B cells is down-regulated in activated germinal center follicular B cells in parallel to the known expression pattern of BCL-2. High-level expression in nonproliferating B cells suggests that TCL1 may function in protecting naïve preactivated B cells from apoptosis.

Transgenic mice for MTCP1 develop T-cell prolymphocytic leukemia

T-cell prolymphocytic leukemia (T-PLL) is a rare form of mature T-cell leukemia associated with chromosomal rearrangements implicating MTCP1 or TCL1 genes. These genes encode two homologous proteins, p13(MTCP1) and p14(TCL1), which share no similarity with other known protein. To determine the oncogenic role of MTCP1, mice transgenic for MTCP1 under the control of CD2 regulatory regions (CD2-p13 mice) were generated. No abnormality was detected during the first year after birth. A late effect of the transgene was searched for in a cohort of 48 CD2-p13 mice aged 15 to 20 months, issued from 3 independent founders. Lymphoid hemopathies, occurring in the three transgenic lines, were characterized by lymphoid cells with an irregular nucleus, a unique and prominent nucleolus, condensed chromatin, a basophilic cytoplasm devoid of granules, and an immunophenotype of mature T cells. The molecular characterization of Tcrb rearrangements demonstrated the monoclonal origin of these populations. Histopathological analysis of the cohort demonstrated early splenic and hepatic infiltrations, whereas lymphocytosis and medullar infiltrations were found infrequently. The engraftment of these proliferations in H2-matched animals demonstrated their malignant nature. Cumulative incidence of the disease at 20 months was 100%, 50%, and 21% in F3, F4, and F7 lines, respectively, and null in the control group. The level of expression of the transgene, as estimated by Western blotting in the transgenic lines correlated with the tumoral incidence, with the highest expression of p13(MTCP1) being found in F3 mice. CD2-p13 transgenic mice developed an hemopathy similar to human T-PLL. These data demonstrate that p13(MTCP1) is an oncoprotein and that CD2-p13 transgenic mice represent the first animal model for mature T-PLL.

Inactivation of the ATM gene in T-cell prolymphocytic leukemias

T-cell prolymphocytic leukemia (T-PLL) is a rare form of mature leukemia that occurs both in adults as a sporadic disease and in younger patients suffering an hereditary condition, ataxia telangiectasia (AT). The ATM gene, located in the 11q22-23 chromosomal region, is consistently mutated in AT patients. The strong predisposition of AT patients to develop T-PLL and the high frequency of T-cell leukemias/lymphomas observed in atm-deficient mice, together with the known functions of the ATM protein, led us to evaluate the ATM gene as a potential tumor suppressor gene involved in T-PLL. Paired leukemic and nonleukemic cells were obtained from a series of 15 patients suffering sporadic T-PLLs, allowing loss of heterozygosity (LOH) analysis. LOH of the 11q22-23 region was detected in 10 of these 15 cases (67%). The minimal deleted region was defined as an approximately 2.5 Mb interval that contained the ATM gene. No ATM rearrangement or biallelic deletion was detected by Southern blotting in the T-PLL series. However, in five T-PLLs with LOH of the 11q22-23 region, Western blot analysis showed either undetectable (3 cases) or decreased levels (1 case) of ATM protein, whereas ATM was present at high levels in cases without LOH. The protein truncation test (PTT) was then used to search for mutations in the ATM gene. Four mutations (1 nonsense, 2 aberrant splicings, and 1 missense) were detected in patients with LOH and none in patients without LOH of the region. The acquired character of these ATM mutations was demonstrated in three patients. Altogether, allelic ATM inactivations by large deletions or mutations were found in approximately two thirds of T-PLL. ATM is thus a tumor suppressor gene whose inactivation is a key event in the development of T-cell prolymphocytic leukemias.

Solution structure of the recombinant human oncoprotein p13MTCP1

The human oncoprotein p13MTCP1 is coded by the MTCP1 gene, a gene involved in chromosomal translocations associated with T-cell prolymphocytic leukemia, a rare form of human leukemia with a mature T-cell phenotype. The primary sequence of p13MTCP1 is highly and only homologous to that of p14TCL1, a product coded by the gene TCL1 which is also involved in T-cell prolymphocytic leukemia. These two proteins probably represent the first members of a new family of oncogenic proteins. We present the three-dimensional solution structure of the recombinant p13MTCP1 determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After proton resonance assignments, a total of 1253 distance restraints and 64 dihedral restraints were collected. The solution structure of p13MTCP1 is presented as a set of 20 DYANA structures. The rmsd values with respect to the mean structure for the backbone and all heavy atoms for the conformer family are 1.07 +/- 0.19 and 1.71 +/- 0.17 A, when the structured core of the protein (residues 11-103) is considered. The solution structure of p13MTCP1 consists of an orthogonal beta-barrel, composed of eight antiparallel beta-strands which present an original arrangement. The two beta-pleated loops which emerge from this barrel might constitute the interaction surface with a potential molecular partner.

Crystal structure of p14TCL1, an oncogene product involved in T-cell prolymphocytic leukemia, reveals a novel beta-barrel topology

BACKGROUND

Chromosome rearrangements are frequently involved in the generation of hematopoietic tumors. One type of T-cell leukemia, T-cell prolymphocytic leukemia, is consistently associated with chromosome rearrangements characterized by the juxtaposition of the TCRA locus on chromosome 14q11 and either the TCL1 gene on 14q32.1 or the MTCP1 gene on Xq28. The TCL1 gene is preferentially expressed in cells of early lymphoid lineage; its product is a 14 kDa protein (p14TCL1), expressed in the cytoplasm. p14TCL1 has strong sequence similarity with one product of the MTCP1 gene, p13MTCP1 (41% identical and 61% similar). The functions of the TCL1 and MTCP1 genes are not known yet. They have no sequence similarity to any other published sequence, including those of well-documented oncogene families responsible for leukemia. In order to gain a more fundamental insight into the role of this particular class of oncogenes, we have determined the three-dimensional structure of p14TCL1.

RESULTS

The crystal structure of p14TCL1 has been determined at 2.5 A resolution. The structure was solved by molecular replacement using the solution structure of p13MTCP1, revealing p14TCL1 to be an all-beta protein consisting of an eight-stranded antiparallel beta barrel with a novel topology. The barrel consists of two four-stranded beta-meander motifs, related by a twofold axis and connected by a long loop. This internal pseudo-twofold symmetry was not expected on basis of the sequence alone, but structure-based sequence analysis of the two motifs shows that they are related. The structures of p13MTCP1 and p14TCL1 are very similar, diverging only in regions that are either flexible and/or involved in crystal packing. p14TCL1 forms a tight crystallographic dimer, probably corresponding to the 28 kDa species identified in solution by gel filtration experiments.

CONCLUSIONS

Structural similarities between p14TCL1 and p13MTCP1 suggest that their (unknown) function may be analogous. This is confirmed by the fact that these proteins are implicated in analogous diseases. Their structure does not show similarity to other oncoproteins of known structure, confirming their classification as a novel class of oncoproteins.

Solution structure of human p8MTCP1, a cysteine-rich protein encoded by the MTCP1 oncogene, reveals a new alpha-helical assembly motif

MTCP1 (for Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8(MTCP1) protein encoded by the MTCP1 oncogene was determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After sequence specific assignments, a total of 931 distance restraints and 57 dihedral restraints were collected. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of p8(MTCP1) is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol with the AMBER force field. The r.m.s.d. values with respect to the mean structure for the backbone and all heavy atoms for a family of 30 structures are 0.73(+/-0.28) and 1.17(+/-0.23) A, when the structured core of the protein (residues 5 to 63) is considered. The solution structure of p8(MTCP1) reveals an original scaffold consisting of three alpha helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an alpha-hairpin which resembles an antiparallel coiled-coil. The third helix is oriented roughly parallel to the plane defined by the alpha-antiparallel motif and its axis forms an angle of approximately 60 degrees with respect to the main axis of this motif.

Alternative origin of p13MTCP1-encoding transcripts in mature T-cell proliferations with t(X;14) translocations

The MTCP1 gene is involved in the t(X;14)(q28;q11) translocation associated with T-cell prolymphocytic leukemia and related conditions. This gene is unusual in that it codes for two distinct proteins: a small mitochondrial protein, p8MTCP1, and a putative oncogenic protein, p13MTCP1. Scarcity of material from t(X;14)-associated proliferations and very low levels of mRNA expression have so far prevented a thorough description of p13MTCP1-encoding transcripts. Here, we characterize two additional t(X;14) bearing leukemias allowing this analysis. In one case, with a breakpoint located 5' to the MTCP1 gene, the level of transcription of previously described p13MTCP1-encoding transcripts is enhanced. In the second case, with a breakpoint within the MTCP1 intron I, an alternative transcription initiation site is demonstrated in the tumor cells at 229 bp upstream to exon II. The identification of this internal promoter, together with the similarity between TCL1 and MTCP1 genomic structures, allow us to propose a model in which the duplication of an ancestral gene was followed by the insertion of one copy within the intron of a p8-encoding gene, accounting for the unusual feature of the MTCP1 gene.

[Oncogenesis of T-cell prolymphocytic leukemia]

The molecular characterization of the recurrent chromosomal translocations associated with T-cell prolymphocytic leukemia recently led to the identification of two putative oncogenes: TCL1 located on chromosome 14q32.1, and MTCP1 located on chromosome Xq28. These genes code for two homologous small cytoplasmic proteins lacking similarity with other known proteins. Uncovering the function of these proteins will be the next step toward an understanding of pathogenesis of the T-cell prolymphocytic leukemia.

Multiple tumor-suppressor gene 1 inactivation is the most frequent genetic alteration in T-cell acute lymphoblastic leukemia

No constant genetic alteration has yet been unravelled in T-cell acute lymphoblastic leukemia (T-ALL), and, to date, the most frequent alteration, the SIL-TAL1 deletion, is found in approximately 20% of cases. Recently, two genes have been identified, the multiple tumor-suppressor gene 1 (MTS1) and multiple tumor-suppressor gene 2 (MTS2), whose products inhibit cell cycle progression. A characterization of the MTS locus organization allowed to determine the incidence of MTS1 and MTS2 inactivation in T-ALL. MTS1 and MTS2 configurations were determined by Southern blotting using 8 probes in 59 patients with T-ALL (40 children and 19 adults). Biallelic MTS1 inactivation by deletions and/or rearrangements was observed in 45 cases (76%). Monoallelic alterations were found in 6 cases (10%). The second MTS1 allele was studied in the 4 cases with available material. A point mutation was found in 2 cases. The lack of MTS1 mRNA expression was observed by Northern blot analysis in a third case. A normal single-strand conformation polymorphism pattern of MTS1 exons 1alpha and 2 was found and MTS1 RNA was detected in the fourth case, but a rearrangement occurring 5' to MTS1 exon 1 alpha deleting MTS1 exon 1Beta was documented. One case presented a complex rearrangement. Germline configuration for MTS1 and MTS2 was found in only 7 cases. The localization of the 17 breakpoints occurring in the MTS locus were determined. Ten of them (59%) are clustered in a 6-kb region located 5 kb downstream to the newly identified MTS1 exon 1Beta. No rearrangement disrupting MTS2 was detected and more rearrangements spared MTS2 than MTS1 (P<.01). MTS1 but not MTS2 RNA was detected by Northern blotting in the human thymus. These data strongly suggest that MTS1 is the functional target of rearrangements in T-ALL. MTS1 inactivation, observed in at least 80% of T-ALL, is the most consistent genetic defect found in this disease to date.

Expression of p13MTCP1 is restricted to mature T-cell proliferations with t(X;14) translocations

T-cell prolymphocytic leukemia (T-PLL), a rare form of mature T-cell leukemias, and ataxia telangiectasia clonal proliferation, a related condition occurring in patients suffering from ataxia telangiectasia, have been associated to translocations involving the 14q32.1 or Xq28 regions, where are located the TCL1 and MTCP1 putative oncogenes, respectively. The MTCP1 gene is involved in the t(X;14)(q28;q11) translocation associated with these T-cell proliferations. Alternative splicing generates type A and B transcripts that potentially encode two entirely distinct proteins; type A transcripts code for a small mitochondrial protein, p8MTCP1, and type B transcripts, containing an additional open reading frame, may code for 107 amino-acid protein, p13MTCP1. The recently cloned TCL1 gene, also involved in translocations and inversions associated with T-cell proliferations, codes for a 14-kD protein that displays significant homology with p13MTCP1. We have generated rabbit antisera against this putative p13MTCP1 protein and screened for expression of p13MTCP1 normal lymphoid tissues and 33 cases of immature and mature lymphoid T-cell proliferations using a sensitive Western blot assay. We also investigated the MTCP1 locus configuration by Southern blot analysis. The p13MTCP1 protein was detected in the three T-cell proliferations with MTCP1 rearrangements because of t(X;14) translocations, but neither in normal resting and activated lymphocytes nor in the other T-cell leukemias. Our data support the hypothesis that p13MTCP1 and p14TCL1 form a new protein family that plays a key role in the pathogenesis of T-PLL and related conditions.

The 8 kD product of the putative oncogene MTCP-1 is a mitochondrial protein

An unusually small (8 kD) protein (p8MTCP-1) is coded by the putative oncogene MTCP-1 (also called c6.1B), involved in the translocation t(X;14)(q28;q11) associated with some mature T-cell proliferations. Here, we show by subcellular fractionation and by confocal microscopy that this protein is located in the mitochondria. This localization orientates toward a role of p8MTCP-1 in the mitochondrial metabolism which may be relevant for the oncogenic process.

The MTCP-1/c6.1B gene encodes for a cytoplasmic 8 kD protein overexpressed in T cell leukemia bearing a t(X;14) translocation

The t(X;14)(q28;q11.2) translocation is associated with mature T-cell proliferations. Recently this translocation has been shown to implicate the MTCP-1/c6.1B gene on chromosome Xq28, leading to aberrant or overexpressed MTCP-1 transcripts. The potential coding role of this gene was made uncertain by the lack of a long open reading frame in its major transcripts. However, a short 204 bases open reading frame is potentially coding for a 68 amino-acid protein. Here, we show that this open reading frame sequence and the deduced product are well conserved in mouse. A 8 kD protein (p8), which corresponds to the predicted molecular weight was revealed in transient transfectants and in cell lines by Western blotting, using a rabbit antiserum. This product was absent in lymphoblastoid cell lines with deletions of the MTCP-1/c6.1B locus. A dramatic overexpression of p8 was found in leukemic cells from a patient with a t(X;14). This small protein was localized in the cytoplasm by immunofluorescence. In conclusion, MTCP-1 encodes for a cytoplasmic 8 kD product. Its potential role in leukemogenesis is supported by its overexpression in leukemia with t(X;14), but its function remains unknown.

MTCP-1: a novel gene on the human chromosome Xq28 translocated to the T cell receptor alpha/delta locus in mature T cell proliferations

T-cell lymphoproliferative diseases are often associated with recurrent chromosomal translocations involving T cell receptor genes (TCR) and genes that are thought to play a role in the pathogenesis of these diseases. Whereas numerous such genes have already been identified in acute T cell leukemias, no candidate gene has yet been identified to play a role in the heterogeneous group of T cell proliferations with a mature phenotype. We here report the molecular cloning of two examples of the rare but recurrent t(X;14) translocation. The first translocation was associated with a benign clonal proliferation in an ataxia telangiectasia patient and the second with a T cell prolymphocytic leukemia. Both translocations implicated the TCR alpha/delta locus and a common breakpoint region on chromosome Xq28. A previously unidentified gene, abnormally transcribed in both T cell proliferations, was characterized in the immediate proximity of the breakpoints. This Xq28 gene has no homology with known sequences, uses a complex alternative splicing pattern and demonstrates two short open reading frames. This gene, named MTCP-1 (Mature T Cell Proliferation-1) is the first candidate gene potentially involved in the leukemogenic process of mature T cell proliferations.

Ataxia telangiectasia: a model for T-cell leukemogenesis

Ataxia telangiectasia is a complex genetic disease which includes a high risk to develop lymphoid malignancies. In approximately 10% of the patients, clonal translocations are observed in large T lymphocytes populations, with generally no consequences for the patient. Cytological and biological studies of these cell populations have shown striking similarities with T-cell prolymphocytic leukemia. Clonal chromosomal aberrations are constituted by the translocation of one TCR gene to either the 14q32.1 band or the Xq28 band. Whereas no gene candidate is yet identified on the 14q32.1 region, we have recently identified a new gene on Xq28 that may play a role in leukemogenesis.

Hybrid T cell receptor genes formed by interlocus recombination in normal and ataxia-telangiectasis lymphocytes

In this paper, using polymerase chain reaction (PCR), we demonstrated the occurrence of hybrid genes formed by interlocus recombination between T cell receptor gamma (TCR-gamma) variable (V) regions and TCR-beta joining (J) regions in the peripheral blood lymphocytes (PBL) from normal individuals and patients with ataxia-telangiectasia (AT). Sequence analysis of the PCR-derived hybrid genes confirmed that site-specific V gamma-J beta recombination had occurred and showed that 10 of 23 genomic hybrid genes maintained a correct open reading frame. By dilution analysis, the frequency of these hybrid genes was 8 +/- 1/10(5) cells in normal PBL and 587 +/- 195/10(5) cells in AT PBL. These frequencies and the approximately 70-fold difference between the normal and AT samples are consistent with previous cytogenetic data examining the occurrence of an inversion of chromosome 7 in normal and AT PBL. We also demonstrated expression of these hybrid genes by PCR analysis of first-strand cDNA prepared from both normal and AT PBL. Sequence analysis of the PCR-amplified transcripts showed that, in contrast to the genomic hybrid genes, 19 of 22 expressed genes maintained a correct open reading frame at the V-J junction and correctly spliced the hybrid V-J exon to a TCR-beta constant region, thus allowing translation into a potentially functional hybrid TCR protein. Another type of hybrid TCR transcript was found in a which a rearranged TCR-gamma V-J exon was correctly spliced to a TCR-beta constant region. This form of hybrid gene may be formed by trans-splicing. These hybrid TCR genes may serve to increase the repertoire of the immune response. In addition, studies of their mechanism of formation and its misregulation in AT may provide insight into the nature of the chromosomal instability syndrome associated with AT. The mechanism underlying hybrid gene formation may be analogous to the mechanism underlying rearrangements between putative growth-affecting genes and the antigen receptor loci, which are associated with AT lymphocyte clones and lymphoid malignancies.

Mapping of human chromosome 22 by in situ hybridization

The second smallest chromosome of the human karyotype, i.e., chromosome 22, is involved in many congenital or acquired structural aberrations. This variety can be taken advantage of to determine the exact linear order, from centromere to telomere, of cloned probes and chromosomal breakpoints. Eleven probes were localized with respect to breakpoints of 11 der(22) of independent cell lines using in situ hybridization on metaphasic spreads. The deduced order of the tested probes and that of the breakpoints are in complete agreement with the published genetic map and the karyotypic analysis, respectively. This approach enables a correlation of the genetic map with the chromosomal banding.

Analysis of positive cultures from endodontically treated teeth: a retrospective study

A study of 12,150 endodontically treated teeth from 11,797 patients in a private patient setup revealed an incidence of 10.2% positive cultures obtained just before obturation of the root canal. Streptococcal predominance was reflected by a presence of nearly 60% in the pure culture and nearly 98% in the mixed cultures. No significant changes in microbial predominance or bacterial sensitivities were detected over the 7-year period of study. Ampicillin, cephalothin, erythromycin, and penicillin were the most effective antibiotics against the viridans streptococci, the most prevalent organism in the infected teeth.

Inversion of chromosome 7 in ataxia telangiectasia is generated by a rearrangement between T-cell receptor beta and T-cell receptor gamma genes

Specific and recurrent chromosomal rearrangements are often observed in the karyotypes of phytohemagglutinin-stimulated lymphocytes. The percentage of cells demonstrating these rearrangements is dramatically increased in the genetic disease ataxia telangiectasia. Inversion of chromosome 7 represents approximately half of the chromosomal rearrangements in this disease. Because the chromosomal locations of the inv(7) breakpoints coincide precisely with those of the T-cell antigen receptor (TCR) beta and gamma genes, it has been hypothesized that this rearrangement may occur by recombination between those two loci. Here, we present direct evidence that inversion of chromosome 7 in ataxia telangiectasia is generated by site-specific recombination between a TCR gamma variable segment and a TCR beta joining segment.

T-cell nonmalignant clonal proliferation in ataxia telangiectasia: a cytological, immunological, and molecular characterization

Cytogenetically abnormal T-cell nonmalignant clones are a characteristic feature of ataxia telangiectasia (AT). Here, we study a t(14;14) clone from a patient with AT, and provide a cytological, immunological, and molecular characterization. This cellular population is clonal at the molecular level, but is phenotypically heterogeneous, with CD4+CD8+ and CD4-CD8+ cells. Although these cells do not divide in the peripheral blood, a majority of them are found in G1 phase and express the membrane antigen 4F2, a very early marker of activation. Many similarities are found between this nonmalignant AT clone and T-cell prolymphocytic leukemia at the morphologic, cytogenetic, and immunologic levels, despite the different clinical courses associated with these proliferations. We hypothesize that the t(14;14) translocation is linked to the abnormal morphology and immunophenotype of the AT clone cells, but that this translocation confers only a preactivated state to the cells. A complete malignant transformation would then be due to secondary events.

Molecular characterization of ataxia telangiectasia T cell clones. III. Mapping the 14q32.1 distal breakpoint

To delimit the 14q32.1 recurrent breakpoint of ataxia telangiectasia clones, we performed an in situ hybridization study with various probes located on the 14q32 band. We thus mapped this breakpoint between the D14S1 and Pi loci. Furthermore, an interstitial duplication including D14S1 and a part of the IgH locus was demonstrated on a t(14;14) clone.

Molecular characterization of ataxia telangiectasia T cell clones. II. The clonal inv(14) in ataxia telangiectasia differs from the inv(14) in T cell lymphoma

We compared inversions of chromosome 14 in an ataxia telangiectasia clone and in a malignant T cell line (SUP-T1). The R-banding chromosome analysis showed a clear difference between the distal breakpoint of the two inversions. Fine mapping of the distal breakpoint in the ataxia telangiectasia inv(14) was performed by in situ hybridization. We conclude that this breakpoint is centromeric to the immunoglobulin heavy chain locus and to the D14S1 anonymous locus. Our results favor the existence of an unknown oncogene in band 14q32.1.

Molecular characterization of different ataxia telangiectasia T-cell clones. I. A common breakpoint at the 14q11.2 band splits the T-cell receptor alpha-chain gene

Using in situ chromosomal hybridization we have mapped the gene for the T-cell receptor alpha-chain in three different non-malignant T-cell clones occurring in ataxia telangiectasia. The constant region was translocated in each of the three clones. The variable region remained in its original position in two cases and was deleted in one clone which lost the derivative chromosome 14. We have therefore demonstrated that the T-cell receptor alpha-gene is split in at least two of these translocations. To our knowledge, this is the first direct evidence of the involvement of a gene from the immunoglobulin superfamily in chromosomal rearrangements in ataxia telangiectasia.

[Anti-centromere antibody, biological marker of the CREST syndrome as distinct from scleroderma]

Using HEp2 cells to study antinuclear antibodies has resulted in the discovery of the anti-centromere antibody which is thought to separate the CREST syndrome from progressive systemic sclerosis (scleroderma). This antibody seems to be exceptional in healthy subjects and are in patients with connective tissue diseases, except for scleroderma. It has also been found in CREST syndrome associated with other diseases, such as primary cirrhosis and neoplasias. In our study, the sensitivity of the anti-centromere antibody was 89.1% and its specificity 92.3% which shows that it is worth looking for.

Isolation and characterization of inflammatory cells from the human periapical granuloma

Twelve histologically-confirmed periapical granulomas were evaluated by conventional immunologic rosette assays for the presence of T-lymphocytes and complement receptor-bearing lymphocytes. A technique for dispersing the granuloma cells into suspensions was adopted to facilitate performance of the assays which were not applicable to tissue sections. Differential cell counts by an acridine orange vital dye method disclosed that the cell suspensions contained 30% macrophages, 44% lymphocytes, 15% plasma cells, and 12% neutrophils. Complement receptor-bearing cells comprised 17.9%, and T cells comprised 34.5% of the unseparated inflammatory cells. This study provides the first direct evidence of a predominance of thymic-derived lymphocytes in the lymphocyte compartment of the periapical granuloma. Analysis of the data shows that cell-mediated immunity most likely plays a role in the pathogenesis of the periapical granuloma.

The role of biliary scintigraphy and ultrasonography in the diagnosis of cholecystitis

The scintigraphic and sonographic findings in 70 patients with pathologically confirmed gallbladder disease are described. Fifty-two patients were found to have had acute cholecystitis. All 52 patients (100%) had non-visualized of the gallbladder on scintigraphy. Of these patients, 71% had abnormal ultrasound examinations and 29% had normal ultrasound examination. Eighteen patients were proven to have chronic cholecystitis. All 18 (100%) had an abnormal ultrasound examination. Four patients (22%) had non-visualization of the gallbladder on scintigraphy producing a false-positive incidence of approximately 6% for acute cholecystitis. The predictive value of scintigraphy in the patient with suspected acute cholecystitis was 94%. A combination of ultrasound and scintigraphy yielded a sensitivity of 100% in the detection of gallbladder disease in the 70 patients.