16 research outputs found
Analyses in-silico d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers pour le diagnostic et le choix de traitement
No full textCe travail est consacré à l'analyse d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers dans un contexte clinique et de la mise en place d'un outil de diagnostic. La première partie de la thèse décrit le déficit en recombinaison homologue (HRD) et les motifs d'aberration génomique dans les tumeurs qui émergent lors de ce déficit. La recombinaison homologue (HR) est une voie de réparation de l'ADN qui peut réparer les cassures double brin en utilisant une chromatide soeur et un chromosome soeur comme matrice. Les tumeurs inactivées pour certains gènes majeurs impliqués dans HR tels que BRCA1, BRCA2, RAD51C et PALB2 se sont avérées présenter une instabilité génomique élevée. La détection de l'inactivation de la voie HR dans les tumeurs est aujourd'hui devenue extrêmement importante en raison de nouvelles options thérapeutiques ciblant l'HRD (inhibiteurs de PARP) et des pratiques cliniques pour la surveillance génétique familiale. Les tests complets d'inactivation des gènes HR sont compliqués en raison de la diversité des mécanismes d'inactivation, y compris les mutations germinales et somatiques, la méthylation du promoteur et les variants structurelles. Des signatures génomiques basées sur les profils d'aberrations spécifiques des tumeurs HRD ont été développées. Un nouvel outil shallowHRD pour évaluer le HRD dans les tumeurs est présenté. ShallowHRD est basée sur le séquençage du génome entier à faible couverture (TpG. Son inactivation dans les tumeurs a été systématiquement associée à un taux élevé de mutations CpG>TpG et a marqué une réponse à l'immunothérapie. Les résultats du criblage de la cohorte de 1093 ADN germinaux de patients UM non apparentés et de 193 tumeurs UM pour la mutation MBD4 sont présentés. Des mutations germinales inactivant MBD4 ont été trouvées dans 0,7% des cas d'UM et MBD4 a été prouvé prédisposant à l'UM avec un risque relatif de 9. L'étude a conclu que MBD4 doit être inclus dans les panels de gènes pour les tests cliniques et doit être exploré davantage dans l'UM et d'autres maladies.This work is devoted to the analysis of cancer genomic instability and DNA repair deficiency as a part of clinical investigation and implementation of a diagnostic tool. The first part of the thesis describes Homologous Recombination Deficiency (HRD) and the genomic aberration patterns in tumors which emerge upon this deficiency. Homologous Recombination (HR) is a DNA repair pathway that can fix double-strand breaks by using a sister chromatid and sister chromosome as a DNA template. Tumors inactivated for some major genes involved in HR such as BRCA1, BRCA2, RAD51C and PALB2 were shown to present high genomic instability. Detecting inactivation of HR pathway in tumors nowadays became extremely important because of new therapeutic options targeting HRD (PARP inhibitors) and established clinical practice of familial genetic supervision. The comprehensive testing for HR gene inactivation is complicated because of the diversity of inactivation mechanisms including germline and somatic mutations, promoter methylation and structural variants. Genomic signatures based on the specific aberration profiles of HRD tumors have been developed. These signatures capturing tumor BRCAness or genomic HRD covering all possible causes are described. A new tool called shallowHRD to evaluate HRD in tumors is presented. shallowHRD is based on low-coverage Whole Genome Sequencing ( TpG mutations and its inactivation in tumors was consistently associated with high rate of CpG > TpG mutations and marked the response to immunotherapy. The results of screening of the cohort of 1093 germline DNA of unrelated UM patient and 193 UM tumors for MBD4 mutation are presented. MBD4 germline inactivating mutations were found in 0.7% of UM cases and MBD4 is proved to be an UM predisposing gene with a 10-fold relative risk. The study concluded that MBD4 must be included into cancer gene panel for clinical testing and further explored in UM and other diseases
Analyses in-silico d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers pour le diagnostic et le choix de traitement
No full textThis work is devoted to the analysis of cancer genomic instability and DNA repair deficiency as a part of clinical investigation and implementation of a diagnostic tool. The first part of the thesis describes Homologous Recombination Deficiency (HRD) and the genomic aberration patterns in tumors which emerge upon this deficiency. Homologous Recombination (HR) is a DNA repair pathway that can fix double-strand breaks by using a sister chromatid and sister chromosome as a DNA template. Tumors inactivated for some major genes involved in HR such as BRCA1, BRCA2, RAD51C and PALB2 were shown to present high genomic instability. Detecting inactivation of HR pathway in tumors nowadays became extremely important because of new therapeutic options targeting HRD (PARP inhibitors) and established clinical practice of familial genetic supervision. The comprehensive testing for HR gene inactivation is complicated because of the diversity of inactivation mechanisms including germline and somatic mutations, promoter methylation and structural variants. Genomic signatures based on the specific aberration profiles of HRD tumors have been developed. These signatures capturing tumor BRCAness or genomic HRD covering all possible causes are described. A new tool called shallowHRD to evaluate HRD in tumors is presented. shallowHRD is based on low-coverage Whole Genome Sequencing ( TpG mutations and its inactivation in tumors was consistently associated with high rate of CpG > TpG mutations and marked the response to immunotherapy. The results of screening of the cohort of 1093 germline DNA of unrelated UM patient and 193 UM tumors for MBD4 mutation are presented. MBD4 germline inactivating mutations were found in 0.7% of UM cases and MBD4 is proved to be an UM predisposing gene with a 10-fold relative risk. The study concluded that MBD4 must be included into cancer gene panel for clinical testing and further explored in UM and other diseases.Ce travail est consacré à l'analyse d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers dans un contexte clinique et de la mise en place d'un outil de diagnostic. La première partie de la thèse décrit le déficit en recombinaison homologue (HRD) et les motifs d'aberration génomique dans les tumeurs qui émergent lors de ce déficit. La recombinaison homologue (HR) est une voie de réparation de l'ADN qui peut réparer les cassures double brin en utilisant une chromatide soeur et un chromosome soeur comme matrice. Les tumeurs inactivées pour certains gènes majeurs impliqués dans HR tels que BRCA1, BRCA2, RAD51C et PALB2 se sont avérées présenter une instabilité génomique élevée. La détection de l'inactivation de la voie HR dans les tumeurs est aujourd'hui devenue extrêmement importante en raison de nouvelles options thérapeutiques ciblant l'HRD (inhibiteurs de PARP) et des pratiques cliniques pour la surveillance génétique familiale. Les tests complets d'inactivation des gènes HR sont compliqués en raison de la diversité des mécanismes d'inactivation, y compris les mutations germinales et somatiques, la méthylation du promoteur et les variants structurelles. Des signatures génomiques basées sur les profils d'aberrations spécifiques des tumeurs HRD ont été développées. Un nouvel outil shallowHRD pour évaluer le HRD dans les tumeurs est présenté. ShallowHRD est basée sur le séquençage du génome entier à faible couverture (TpG. Son inactivation dans les tumeurs a été systématiquement associée à un taux élevé de mutations CpG>TpG et a marqué une réponse à l'immunothérapie. Les résultats du criblage de la cohorte de 1093 ADN germinaux de patients UM non apparentés et de 193 tumeurs UM pour la mutation MBD4 sont présentés. Des mutations germinales inactivant MBD4 ont été trouvées dans 0,7% des cas d'UM et MBD4 a été prouvé prédisposant à l'UM avec un risque relatif de 9. L'étude a conclu que MBD4 doit être inclus dans les panels de gènes pour les tests cliniques et doit être exploré davantage dans l'UM et d'autres maladies
Analyses in-silico d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers pour le diagnostic et le choix de traitement
No full textThis work is devoted to the analysis of cancer genomic instability and DNA repair deficiency as a part of clinical investigation and implementation of a diagnostic tool. The first part of the thesis describes Homologous Recombination Deficiency (HRD) and the genomic aberration patterns in tumors which emerge upon this deficiency. Homologous Recombination (HR) is a DNA repair pathway that can fix double-strand breaks by using a sister chromatid and sister chromosome as a DNA template. Tumors inactivated for some major genes involved in HR such as BRCA1, BRCA2, RAD51C and PALB2 were shown to present high genomic instability. Detecting inactivation of HR pathway in tumors nowadays became extremely important because of new therapeutic options targeting HRD (PARP inhibitors) and established clinical practice of familial genetic supervision. The comprehensive testing for HR gene inactivation is complicated because of the diversity of inactivation mechanisms including germline and somatic mutations, promoter methylation and structural variants. Genomic signatures based on the specific aberration profiles of HRD tumors have been developed. These signatures capturing tumor BRCAness or genomic HRD covering all possible causes are described. A new tool called shallowHRD to evaluate HRD in tumors is presented. shallowHRD is based on low-coverage Whole Genome Sequencing ( TpG mutations and its inactivation in tumors was consistently associated with high rate of CpG > TpG mutations and marked the response to immunotherapy. The results of screening of the cohort of 1093 germline DNA of unrelated UM patient and 193 UM tumors for MBD4 mutation are presented. MBD4 germline inactivating mutations were found in 0.7% of UM cases and MBD4 is proved to be an UM predisposing gene with a 10-fold relative risk. The study concluded that MBD4 must be included into cancer gene panel for clinical testing and further explored in UM and other diseases.Ce travail est consacré à l'analyse d'instabilités génomiques et de déficiences de réparation de l'ADN dans les cancers dans un contexte clinique et de la mise en place d'un outil de diagnostic. La première partie de la thèse décrit le déficit en recombinaison homologue (HRD) et les motifs d'aberration génomique dans les tumeurs qui émergent lors de ce déficit. La recombinaison homologue (HR) est une voie de réparation de l'ADN qui peut réparer les cassures double brin en utilisant une chromatide soeur et un chromosome soeur comme matrice. Les tumeurs inactivées pour certains gènes majeurs impliqués dans HR tels que BRCA1, BRCA2, RAD51C et PALB2 se sont avérées présenter une instabilité génomique élevée. La détection de l'inactivation de la voie HR dans les tumeurs est aujourd'hui devenue extrêmement importante en raison de nouvelles options thérapeutiques ciblant l'HRD (inhibiteurs de PARP) et des pratiques cliniques pour la surveillance génétique familiale. Les tests complets d'inactivation des gènes HR sont compliqués en raison de la diversité des mécanismes d'inactivation, y compris les mutations germinales et somatiques, la méthylation du promoteur et les variants structurelles. Des signatures génomiques basées sur les profils d'aberrations spécifiques des tumeurs HRD ont été développées. Un nouvel outil shallowHRD pour évaluer le HRD dans les tumeurs est présenté. ShallowHRD est basée sur le séquençage du génome entier à faible couverture (TpG. Son inactivation dans les tumeurs a été systématiquement associée à un taux élevé de mutations CpG>TpG et a marqué une réponse à l'immunothérapie. Les résultats du criblage de la cohorte de 1093 ADN germinaux de patients UM non apparentés et de 193 tumeurs UM pour la mutation MBD4 sont présentés. Des mutations germinales inactivant MBD4 ont été trouvées dans 0,7% des cas d'UM et MBD4 a été prouvé prédisposant à l'UM avec un risque relatif de 9. L'étude a conclu que MBD4 doit être inclus dans les panels de gènes pour les tests cliniques et doit être exploré davantage dans l'UM et d'autres maladies
Objective Binaural Loudness Balancing Based on 40-Hz Auditory Steady-State Responses. Part I: Normal Hearing
No full textPsychophysical procedures are used to balance loudness across the ears. However, they can be difficult and require active cooperation. We investigated whether 40-Hz auditory steady-state response (ASSR) amplitudes can be used to objectively estimate the balanced loudness across the ears for a group of young, normal-hearing participants. The 40-Hz ASSRs were recorded using monaural stimuli with carrier frequencies of 500, 1000, or 2000 Hz over a range of levels between 40 and 80 dB SPL. Behavioral loudness balancing was performed for at least one reference level of the left ear. ASSR amplitude growth functions were listener dependent, but median across-ear ratios in ASSR amplitudes were close to 1. The differences between the ASSR-predicted balanced levels and the behaviorally found balanced levels were smaller than 5 dB in 59% of cases and smaller than 10 dB in 85% of cases. The differences between the ASSR-predicted balanced levels and the reference levels were smaller than 5 dB in 54% of cases and smaller than 10 dB in 87% of cases. No clear hemispheric lateralization was found for 40-Hz ASSRs, with the exception of responses evoked by stimulus levels of 40 to 60 dB SPL at 2000 Hz.sponsorship: The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: Funding of the first author was provided by a Strategic Basic Research grant from the Agency for Innovation by Science and Technology in Flanders (IWT number 131106). (Agency for Innovation by Science and Technology in Flanders (IWT)|131106)status: Publishe
Auditory steady-state responses as neural correlates of loudness growth
No full textThe aim of this study was to find an objective estimate of individual, complete loudness growth functions based on auditory steady-state responses. Both normal-hearing and hearing-impaired listeners were involved in two behavioral loudness growth tasks and one EEG recording session. Behavioral loudness growth was measured with Absolute Magnitude Estimation and a Graphic Rating Scale with loudness categories. Stimuli were sinusoidally amplitude-modulated sinusoids with carrier frequencies of either 500 Hz or 2000 Hz, a modulation frequency of 40 Hz, a duration of 1 s, and presented at intensities encompassing the participants' dynamic ranges. Auditory steady-state responses were evoked by the same stimuli using durations of at least 5 min. Results showed that there was a good correspondence between the relative growth of the auditory steady-state response amplitudes and the behavioral loudness growth responses for each participant of both groups of listeners. This demonstrates the potential for a more individual, objective, and automatic fitting of hearing aids in future clinical practice.sponsorship: The authors would like to thank all participants for volunteering. We would also like to thank Marit Schroyen, Julie De Winter, and Ellen Van Avondt for their assistance in recruiting hearing impaired participants, and Astrid Buelens, Roosmarij Clercx, and Thuur Schilders for their assistance with data collection. We appreciate the help of Dimitar Spirrov in implementing the loudness models. Finally, we are grateful to Brian C.J. Moore and two anonymous reviewers for their valuable remarks to improve the manuscript. The first author was supported by a PhD grant for Strategic Basic Research by the Agency for Innovation by Science and Technology in Flanders (IWT, 131106). (PhD grant for Strategic Basic Research by the Agency for Innovation by Science and Technology in Flanders (IWT)|131106)status: Publishe
Stability of auditory steady-state responses over time
No full textOBJECTIVES: Auditory steady state responses (ASSRs) are used in clinical practice for objective hearing assessments. The response is called steady state because it is assumed to be stable over time, and because it is evoked by a stimulus with a certain periodicity, which will lead to discrete frequency components that are stable in amplitude and phase over time. However, the stimuli commonly used to evoke ASSRs are also known to be able to induce loudness adaptation behaviorally. Researchers and clinicians using ASSRs assume that the response remains stable over time. This study investigates (1) the stability of ASSR amplitudes over time, within one recording, and (2) whether loudness adaptation can be reflected in ASSRs. DESIGN: ASSRs were measured from 14 normal-hearing participants. The ASSRs were evoked by the stimuli that caused the most loudness adaptation in a previous behavioral study, that is, mixed-modulated sinusoids with carrier frequencies of either 500 or 2000 Hz, a modulation frequency of 40 Hz, and a low sensation level of 30 dB SL. For each carrier frequency and participant, 40 repetitions of 92 sec recordings were made. Two types of analyses were used to investigate the ASSR amplitudes over time: with the more traditionally used Fast Fourier Transform and with a novel Kalman filtering approach. Robust correlations between the ASSR amplitudes and behavioral loudness adaptation ratings were also calculated. RESULTS: Overall, ASSR amplitudes were stable. Over all individual recordings, the median change of the amplitudes over time was -0.0001 μV/s. Based on group analysis, a significant but very weak decrease in amplitude over time was found, with the decrease in amplitude over time around -0.0002 μV/s. Correlation coefficients between ASSR amplitudes and behavioral loudness adaptation ratings were significant but low to moderate, with r = 0.27 and r = 0.39 for the 500 and 2000 Hz carrier frequency, respectively. CONCLUSIONS: The decrease in amplitude of ASSRs over time (92 sec) is small. Consequently, it is safe to use ASSRs in clinical practice, and additional correction factors for objective hearing assessments are not needed. Because only small decreases in amplitudes were found, loudness adaptation is probably not reflected by the ASSRs.sponsorship: The authors thank all participants. Special thanks to Steffi Tilkens for her help in acquiring the data. The first author was supported by a PhD grant for Strategic Basic Research by the Agency for Innovation by Science and Technology in Flanders (IWT, 131106). (Agency for Innovation by Science and Technology in Flanders (IWT)|131106)status: Publishe
ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing
No full textInternational audienceWe introduce shallowHRD, a software tool to evaluate tumor homologous recombination deficiency (HRD) based on whole genome sequencing (WGS) at low coverage (shallow WGS or sWGS; $1X coverage). The tool, based on mining copy number alterations profile, implements a fast and straightforward procedure that shows 87.5% sensitivity and 90.5% specificity for HRD detection. shallowHRD could be instrumental in predicting response to poly(ADP-ribose) polymerase inhibitors, to which HRD tumors are selectively sensitive. shallowHRD displays efficiency comparable to most state-of-art approaches, is cost-effective, generates low-storable outputs and is also suitable for fixed-formalin paraffin embedded tissues
Germline MBD4 Mutations and Predisposition to Uveal Melanoma
No full textInternational audienceBackground: Uveal melanoma (UM) arises from malignant transformation of melanocytes in the uveal tract of the eye. This rare tumor has a poor outcome with frequent chemo-resistant liver metastases. BAP1 is the only known predisposing gene for UM. UMs are generally characterized by low tumor mutation burden, but some UMs display a high level of CpG>TpG mutations associated with MBD4 inactivation. Here, we explored the incidence of germline MBD4 variants in a consecutive series of 1093 primary UM case patients and a series of 192 UM tumors with monosomy 3 (M3). Methods: We performed MBD4 targeted sequencing on pooled germline (n ¼ 1093) and tumor (n ¼ 192) DNA samples of UM patients. MBD4 variants (n ¼ 28) were validated by Sanger sequencing. We performed whole-exome sequencing on available tumor samples harboring MBD4 variants (n ¼ 9). Variants of unknown pathogenicity were further functionally assessed. Results: We identified 8 deleterious MBD4 mutations in the consecutive UM series, a 9.15-fold (95% confidence interval ¼ 4.24-fold to 19.73-fold) increased incidence compared with the general population (Fisher exact test, P ¼ 2.00 Â 10-5 , 2-sided), and 4 additional deleterious MBD4 mutations in the M3 cohort, including 3 germline and 1 somatic mutations. Tumors carrying deleterious MBD4 mutations were all associated with high tumor mutation burden and a CpG>TpG hypermutator phenotype. Conclusions: We demonstrate that MBD4 is a new predisposing gene for UM associated with hypermutated M3 tumors. The tumor spectrum of this predisposing condition will likely expand with the addition of MBD4 to diagnostic panels. Tumors arising in such a context should be recognized because they may respond to immunotherapy
Lack of evidence for CDK12 as an ovarian cancer predisposing gene
No full textInternational audienceCDK12 variants were investigated as a genetic susceptibility to ovarian cancer in a series of 416 unrelated and consecutive patients with ovarian carcinoma and who carry neither germline BRCA1 nor BRCA2 pathogenic variant. The presence of CDK12 variants was searched in germline DNA by massive parallel sequencing on pooled DNAs. The lack of detection of deleterious variants and the observed proportion of missense variants in the series of ovarian carcinoma patients as compared with all human populations strongly suggests that CDK12 is not an ovarian cancer predisposing gene
Oral Etoposide and Trastuzumab Use for HER2-Positive Metastatic Breast Cancer: A Retrospective Study from the Institut Curie Hospitals
No full textSIMPLE SUMMARY: Oral etoposide (VP16), an inhibitor of topoisomerase-II, has demonstrated clinical activity in metastatic breast cancer (MBC). To our knowledge, oral VP16 combined with trastuzumab (VP16-T) in HER2+ MBC has not been evaluated before. This combination is biologically relevant, as TOP2A, the gene encoding topoisomerase II, is often co-amplified with ERBB2. We report a retrospective analysis of the impact of oral VP16-trastuzumab on HER2+ MBC patients, together with TOP2A/ERBB2 co-amplification status, assessed through shallow whole genome sequencing. In addition to its low cost and convenience, the oral VP16-trastuzumab regimen has shown a satisfactory activity and excellent tolerability. ABSTRACT: Background: The TOP2A and ERBB2 genes are co-amplified in about 40% of HER2 positive (HER2+) breast cancers. Oral etoposide (VP16), an inhibitor of topoisomerase-II (encoded by TOP2A), has demonstrated clinical activity in metastatic breast cancer (MBC). The benefit of oral VP16 combined with trastuzumab (VP16-T) in HER2+ MBC has not yet been evaluated. Methods: Patients treated at the Institut Curie Hospitals with VP16-T for HER2+ MBC were retrieved by an in silico search. Progression-free survival (PFS), overall survival (OS), response rate, prolonged PFS (defined as at least 6 months), clinical benefit, and toxicity were assessed. The co-amplification of ERBB2 and TOP2A was assessed by shallow whole genome sequencing on tumor tissue whenever available. Results: Forty-three patients received VP16-T after a median number of six prior treatment lines for HER2+ MBC. Median PFS and OS were 2.9 months (95% CI [2.4–4.7]) and 11.3 months (95% CI [8.3–25.0]), respectively. Three patients had a complete response, while 12/40 (30%) experienced clinical benefit. Only three patients stopped treatment for toxicity. Seven (35%) patients displayed a TOP2A/ERBB2 co-amplification. No statistically significant correlation was found between outcome and TOP2A/ERBB2 co-amplification. Conclusion: Our analysis suggests a favorable efficacy and toxicity profile for VP16-T in patients with heavily pretreated HER2+ MBC
