Analyse de la relation dose-réponse pour les risques de mortalité par cancer et par maladie de l'appareil circulatoire chez les mineurs d'uranium

The relation between lung cancer risk and radon exposure has been clearly established, especially from the studies on uranium miner cohorts. But the association between radon exposure and extrapulmonary cancers and non-cancer diseases remains not well known. Moreover, the health risks associated with the other mining-related ionizing radiation exposures are still under consideration. The aim of this thesis is to contribute to the estimation of the radio-induced health risks at low-doses through the analysis of the kidney cancer and Circulatory System Disease (CSD) mortality risks among uranium miners.Kidney cancer mortality risk analyses were performed from the French cohort of uranium miners (n=5086; follow-up period: 1946-2007), the post-55 cohort (n=3,377; follow-up period: 1957-2007) and the German cohort of the Wismut (n=58,986; follow-up period: 1946-2003) which included 24, 11 and 174 deaths from kidney cancer, respectively. The exposures to radon and its short-lived progeny (expressed in Working Level Month WLM), to uranium ore dust (kBqh.m-3) and to external gamma rays (mSv) were estimated for each miners and the equivalent kidney dose was calculated. The dose-response relation was refined considering two responses: the instantaneous risk of kidney cancer mortality (corresponding to the classical analysis, Cause-specific Hazard Ratio (CSHR) estimated with the Cox model) and its occurrence probability during the follow-up (Subdistribution Hazard Ratio (SHR) estimated with the Fine & Gray model). An excess of kidney cancer mortality was observed only in the French cohort (SMR = 1.62 CI95%[1.04; 2.41]). In the Wismut cohort, a decrease of the kidney cancer mortality was observed (0.89 [0.78; 0.99]). For these three cohorts, the occupational radiological exposures (or the equivalent kidney dose) were significantly associated neither with the risk of kidney cancer mortality (e.g. CSHRWismut_radon/100WLM=1.023 [0.993; 1.053]), nor with its occurrence probability during the follow-up (e.g. SHRWismut_radon /100WLM=1.012 [0.983; 1.042]).CSD mortality risk analyses in the French cohort showed a significant increase of the risks of mortality from CSD (n=442, CSHR/100WLM=1.11 [1.01; 1.22]) and from CerebroVascular Disease (MCeV, n=105, CSHR/100WLM=1.25 [1.09; 1.43]) with radon exposure. A case-control study nested in the French cohort was set up to collect the information related to CSD risk factors (overweight, hypertension, diabetes...) from the medical records of 313 miners (76 deaths from CSD (including 26 from Ischemic Heart Disease (IHD) and 16 from MCeV) and 237 controls). For the three radiological exposures, the exposure-risk relation was analyzed in a pseudo-cohort (n=1,644 pseudo-individuals, obtained from the weighting of the observations by their inverse selection probability) with the Cox model, adjusted for the CSD risk factors. The association between the radiological exposure and the risk of mortality from CSD, IHD or MCeV was not significant (e.g. CSHRCSD_radon/100WLM=1.43 [0.71; 2.87]). The adjustment for CSD risk factors did not substantially change the exposure-risk relation.The lack of a significant dose-response relation suggests that the excess of kidney cancer mortality among the French uranium miners may be induced by other risk factors, unavailable for this study. The small change of the coefficients observed after adjustment for CSD risk factors in the nested case-control study supports the assumption of the existence of the MCeV mortality risk increase associated with radon exposure in the French cohort of uranium miners. Future analyses based on further follow-up updates should allow to confirm or not these results.La relation entre le risque de décès par cancer du poumon et l’exposition au radon est aujourd’hui établie, notamment à partir des études conduites chez les mineurs d’uranium. Mais de nombreuses interrogations persistent sur les risques de cancers extra-pulmonaires et de maladies non-cancéreuses, et sur l'impact sur la santé des autres expositions radiologiques professionnelles. L’objectif général de cette thèse est de contribuer à l’estimation des risques radio-induits aux faibles débits de dose au travers de l'analyse des risques de décès par cancer du rein et par Maladie de l'Appareil Circulatoire (MAC) chez les mineurs d’uranium.Les analyses du risque de décès par cancer du rein ont été réalisées au sein de la cohorte française des mineurs d'uranium (n=5 086 ; période de suivi : 1946-2007), la cohorte post-55 (n=3 377 ; période de suivi : 1957-2007) et la cohorte allemande de la Wismut (n=58 986; période de suivi : 1946-2003) au sein desquelles sont respectivement répertoriés 24, 11 et 174 décès par cancer du rein. L’exposition au radon et à ses descendants à vie courte (exprimée en Working Level Month WLM), aux poussières d’uranium (kBqh.m-3) et aux rayonnements gamma (mSv) a été estimée individuellement et la dose absorbée au rein a été calculée. La relation dose-réponse a été affinée par rapport à l'analyse classique en considérant deux types de réponse : le risque instantané de décès par cancer du rein (analyse classique, Cause-specific Hazard Ratio (CSHR) estimé avec le modèle de Cox) et sa probabilité d'occurrence au cours du suivi (Subdistribution Hazard Ratio (SHR) estimé avec le modèle de Fine & Gray). Un excès de mortalité par cancer du rein était observé dans la cohorte française (SMR = 1,62 IC95%[1,04; 2,41]), mais pas dans la cohorte post-55. Dans la cohorte de la Wismut, un déficit de mortalité par cancer du rein était observé (0,89 [0,78; 0,99]). Pour ces trois populations, aucune relation n'a pu être mise en évidence entre les expositions radiologiques (ou la dose au rein) et le risque de décès par cancer du rein (ex : CSHRWismut_radon/100WLM=1,023 [0,993; 1,053]), ni avec sa probabilité d'occurrence au cours du suivi (ex : SHRWismut_radon /100WLM=1,012 [0,983; 1,042]).L’étude du risque de décès par MAC dans la cohorte française a montré une augmentation significative du risque de décès par MAC (n=442, CSHR/100WLM=1,11 [1,01; 1,22]) et par Maladie CérébroVasculaire (MCeV, n=105, CSHR/100WLM=1,25 [1,09; 1,43]) avec l’exposition au radon. Une enquête cas-témoins nichée au sein de la cohorte a été mise en place pour recueillir dans les dossiers médicaux les facteurs de risque classiques de MAC (surpoids, hypertension, diabète...) pour 313 mineurs (76 décès par MAC (dont 26 par Cardiopathie Ischémique (CI) et 16 par MCeV) et 237 témoins). Pour les trois expositions radiologiques, la relation exposition-risque a été analysée au sein d'une pseudo-cohorte (obtenue en pondérant les observations par l'inverse de la probabilité de sélection, n=1 644 pseudo-individus) avec le modèle de Cox, en ajustant sur les différents facteurs de risque. L’association entre les expositions radiologiques et le risque de décès par MAC, CI ou MCeV n'était pas significative (ex : CSHRMAC_radon/100WLM=1,43 [0,71; 2,87]). La prise en compte des facteurs de risque ne modifiait pas sensiblement cette association.L'absence de relation dose-réponse significative suggère que l'excès de mortalité par cancer du rein chez les mineurs français serait induit par d'autres facteurs, non-disponibles pour cette analyse. La faible variation des coefficients avec l'ajustement sur les facteurs de risque de MAC dans l'enquête cas-témoins nichée soutient l'hypothèse de l'existence d'une augmentation du risque de MCeV dans la cohorte française associée à l’exposition au radon. La poursuite du suivi de la cohorte permettra d'affiner ces résultats

Tumor infiltrating lymphocyte stratification of prognostic staging of early-stage triple negative breast cancer

The importance of integrating biomarkers into the TNM staging has been emphasized in the 8 th Edition of the American Joint Committee on Cancer (AJCC) Staging system. In a pooled analysis of 2148 TNBC-patients in the adjuvant setting, TILs are found to strongly up and downstage traditional pathological-staging in the Pathological and Clinical Prognostic Stage Groups from the AJJC 8 th edition Cancer Staging System. This suggest that clinical and research studies on TNBC should take TILs into account in addition to stage, as for example patients with stage II TNBC and high TILs have a better outcome than patients with stage I and low TILs.Peer reviewe

Tumor-Infiltrating Lymphocytes and Prognosis: A Pooled Individual Patient Analysis of Early-Stage Triple-Negative Breast Cancers

PURPOSE: The aim of the current study was to conduct a pooled analysis of studies that have investigated the prognostic value of tumor-infiltrating lymphocytes (TILs) in early-stage triple negative breast cancer (TNBC). METHODS: Participating studies had evaluated the percentage infiltration of stromally located TILs (sTILs) that were quantified in the same manner in patient diagnostic samples of early-stage TNBC treated with anthracycline-based chemotherapy with or without taxanes. Cox proportional hazards regression models stratified by trial were used for invasive disease-free survival (iDFS; primary end point), distant disease-free survival (D-DFS), and overall survival (OS), fitting sTILs as a continuous variable adjusted for clinicopathologic factors. RESULTS: We collected individual data from 2,148 patients from nine studies. Average age was 50 years (range, 22 to 85 years), and 33% of patients were node negative. The average value of sTILs was 23% (standard deviation, 20%), and 77% of patients had 1% or more sTILs. sTILs were significantly lower with older age ( P = .001), larger tumor size ( P = .01), more nodal involvement ( P = .02), and lower histologic grade ( P = .001). A total of 736 iDFS and 548 D-DFS events and 533 deaths were observed. In the multivariable model, sTILs added significant independent prognostic information for all end points (likelihood ratio \u3c72, 48.9 iDFS; P < .001; \u3c72, 55.8 D-DFS; P < .001; \u3c72, 48.5 OS; P < .001). Each 10% increment in sTILs corresponded to an iDFS hazard ratio of 0.87 (95% CI, 0.83 to 0.91) for iDFS, 0.83 (95% CI, 0.79 to 0.88) for D-DFS, and 0.84 (95% CI, 0.79 to 0.89) for OS. In node-negative patients with sTILs 65 30%, 3-year iDFS was 92% (95% CI, 89% to 98%), D-DFS was 97% (95% CI, 95% to 99%), and OS was 99% (95% CI, 97% to 100%). CONCLUSION: This pooled data analysis confirms the strong prognostic role of sTILs in early-stage TNBC and excellent survival of patients with high sTILs after adjuvant chemotherapy and supports the integration of sTILs in a clinicopathologic prognostic model for patients with TNBC. This model can be found at www.tilsinbreastcancer.org

Nox2-deficient Tregs improve heart transplant outcomes via their increased graft recruitment and enhanced potency.

Nox2 is a ROS-generating enzyme, deficiency of which increases suppression by Tregs in vitro and in an in vivo model of cardiac remodelling. Since Tregs have emerged as a candidate therapy in autoimmunity and transplantation, we hypothesised that Nox2 deficiency in Tregs in recipient mice may improve outcomes in a heart transplant model. A novel B6129 mouse model with Treg-targeted Nox2 deletion (Nox2fl/flFoxP3Cre+) was generated and transplanted with hearts from CB6F1 donors. As compared to littermate controls, Nox2fl/flFoxP3Cre+ mice had lower plasma levels of alloantibodies and troponin-I, reduced levels of IFN-γ in heart allograft homogenates and diminished cardiomyocyte necrosis and allograft fibrosis. Single cell analyses of allografts revealed higher absolute numbers of Tregs and lower CD8+ T cell infiltration in Nox2-deficient recipients compared to Nox2-replete mice. Mechanistically, in addition to a greater suppression of CD8+CD25- T effector cell proliferation and IFN-γ production, Nox2-deficient Tregs expressed higher levels of CCR4 and CCR8, driving cell migration to allografts; this was associated with increased expression of miR214-3p. These data indicate that Nox2 deletion in Tregs enhances their suppressive ability and migration to heart allografts. Therefore, Nox2 inhibition in Tregs may be a useful approach to improve their therapeutic efficacy

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Funder: Breast Cancer Research Foundation (BCRF); doi: https://doi.org/10.13039/100001006Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting

Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Funder: U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)Funder: National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University.Funder: Susan G Komen Foundation (CCR CCR18547966) and a Young Investigator Grant from the Breast Cancer Alliance.Funder: The Canadian Cancer SocietyFunder: Breast Cancer Research Foundation (BCRF), Grant No. 17-194Abstract: Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring

Analyse de la relation dose-réponse pour les risques de mortalité par cancer et par maladie de l'appareil circulatoire chez les mineurs d'uranium

The relation between lung cancer risk and radon exposure has been clearly established, especially from the studies on uranium miner cohorts. But the association between radon exposure and extrapulmonary cancers and non-cancer diseases remains not well known. Moreover, the health risks associated with the other mining-related ionizing radiation exposures are still under consideration. The aim of this thesis is to contribute to the estimation of the radio-induced health risks at low-doses through the analysis of the kidney cancer and Circulatory System Disease (CSD) mortality risks among uranium miners.Kidney cancer mortality risk analyses were performed from the French cohort of uranium miners (n=5086; follow-up period: 1946-2007), the post-55 cohort (n=3,377; follow-up period: 1957-2007) and the German cohort of the Wismut (n=58,986; follow-up period: 1946-2003) which included 24, 11 and 174 deaths from kidney cancer, respectively. The exposures to radon and its short-lived progeny (expressed in Working Level Month WLM), to uranium ore dust (kBqh.m-3) and to external gamma rays (mSv) were estimated for each miners and the equivalent kidney dose was calculated. The dose-response relation was refined considering two responses: the instantaneous risk of kidney cancer mortality (corresponding to the classical analysis, Cause-specific Hazard Ratio (CSHR) estimated with the Cox model) and its occurrence probability during the follow-up (Subdistribution Hazard Ratio (SHR) estimated with the Fine & Gray model). An excess of kidney cancer mortality was observed only in the French cohort (SMR = 1.62 CI95%[1.04; 2.41]). In the Wismut cohort, a decrease of the kidney cancer mortality was observed (0.89 [0.78; 0.99]). For these three cohorts, the occupational radiological exposures (or the equivalent kidney dose) were significantly associated neither with the risk of kidney cancer mortality (e.g. CSHRWismut_radon/100WLM=1.023 [0.993; 1.053]), nor with its occurrence probability during the follow-up (e.g. SHRWismut_radon /100WLM=1.012 [0.983; 1.042]).CSD mortality risk analyses in the French cohort showed a significant increase of the risks of mortality from CSD (n=442, CSHR/100WLM=1.11 [1.01; 1.22]) and from CerebroVascular Disease (MCeV, n=105, CSHR/100WLM=1.25 [1.09; 1.43]) with radon exposure. A case-control study nested in the French cohort was set up to collect the information related to CSD risk factors (overweight, hypertension, diabetes...) from the medical records of 313 miners (76 deaths from CSD (including 26 from Ischemic Heart Disease (IHD) and 16 from MCeV) and 237 controls). For the three radiological exposures, the exposure-risk relation was analyzed in a pseudo-cohort (n=1,644 pseudo-individuals, obtained from the weighting of the observations by their inverse selection probability) with the Cox model, adjusted for the CSD risk factors. The association between the radiological exposure and the risk of mortality from CSD, IHD or MCeV was not significant (e.g. CSHRCSD_radon/100WLM=1.43 [0.71; 2.87]). The adjustment for CSD risk factors did not substantially change the exposure-risk relation.The lack of a significant dose-response relation suggests that the excess of kidney cancer mortality among the French uranium miners may be induced by other risk factors, unavailable for this study. The small change of the coefficients observed after adjustment for CSD risk factors in the nested case-control study supports the assumption of the existence of the MCeV mortality risk increase associated with radon exposure in the French cohort of uranium miners. Future analyses based on further follow-up updates should allow to confirm or not these results.La relation entre le risque de décès par cancer du poumon et l’exposition au radon est aujourd’hui établie, notamment à partir des études conduites chez les mineurs d’uranium. Mais de nombreuses interrogations persistent sur les risques de cancers extra-pulmonaires et de maladies non-cancéreuses, et sur l'impact sur la santé des autres expositions radiologiques professionnelles. L’objectif général de cette thèse est de contribuer à l’estimation des risques radio-induits aux faibles débits de dose au travers de l'analyse des risques de décès par cancer du rein et par Maladie de l'Appareil Circulatoire (MAC) chez les mineurs d’uranium.Les analyses du risque de décès par cancer du rein ont été réalisées au sein de la cohorte française des mineurs d'uranium (n=5 086 ; période de suivi : 1946-2007), la cohorte post-55 (n=3 377 ; période de suivi : 1957-2007) et la cohorte allemande de la Wismut (n=58 986; période de suivi : 1946-2003) au sein desquelles sont respectivement répertoriés 24, 11 et 174 décès par cancer du rein. L’exposition au radon et à ses descendants à vie courte (exprimée en Working Level Month WLM), aux poussières d’uranium (kBqh.m-3) et aux rayonnements gamma (mSv) a été estimée individuellement et la dose absorbée au rein a été calculée. La relation dose-réponse a été affinée par rapport à l'analyse classique en considérant deux types de réponse : le risque instantané de décès par cancer du rein (analyse classique, Cause-specific Hazard Ratio (CSHR) estimé avec le modèle de Cox) et sa probabilité d'occurrence au cours du suivi (Subdistribution Hazard Ratio (SHR) estimé avec le modèle de Fine & Gray). Un excès de mortalité par cancer du rein était observé dans la cohorte française (SMR = 1,62 IC95%[1,04; 2,41]), mais pas dans la cohorte post-55. Dans la cohorte de la Wismut, un déficit de mortalité par cancer du rein était observé (0,89 [0,78; 0,99]). Pour ces trois populations, aucune relation n'a pu être mise en évidence entre les expositions radiologiques (ou la dose au rein) et le risque de décès par cancer du rein (ex : CSHRWismut_radon/100WLM=1,023 [0,993; 1,053]), ni avec sa probabilité d'occurrence au cours du suivi (ex : SHRWismut_radon /100WLM=1,012 [0,983; 1,042]).L’étude du risque de décès par MAC dans la cohorte française a montré une augmentation significative du risque de décès par MAC (n=442, CSHR/100WLM=1,11 [1,01; 1,22]) et par Maladie CérébroVasculaire (MCeV, n=105, CSHR/100WLM=1,25 [1,09; 1,43]) avec l’exposition au radon. Une enquête cas-témoins nichée au sein de la cohorte a été mise en place pour recueillir dans les dossiers médicaux les facteurs de risque classiques de MAC (surpoids, hypertension, diabète...) pour 313 mineurs (76 décès par MAC (dont 26 par Cardiopathie Ischémique (CI) et 16 par MCeV) et 237 témoins). Pour les trois expositions radiologiques, la relation exposition-risque a été analysée au sein d'une pseudo-cohorte (obtenue en pondérant les observations par l'inverse de la probabilité de sélection, n=1 644 pseudo-individus) avec le modèle de Cox, en ajustant sur les différents facteurs de risque. L’association entre les expositions radiologiques et le risque de décès par MAC, CI ou MCeV n'était pas significative (ex : CSHRMAC_radon/100WLM=1,43 [0,71; 2,87]). La prise en compte des facteurs de risque ne modifiait pas sensiblement cette association.L'absence de relation dose-réponse significative suggère que l'excès de mortalité par cancer du rein chez les mineurs français serait induit par d'autres facteurs, non-disponibles pour cette analyse. La faible variation des coefficients avec l'ajustement sur les facteurs de risque de MAC dans l'enquête cas-témoins nichée soutient l'hypothèse de l'existence d'une augmentation du risque de MCeV dans la cohorte française associée à l’exposition au radon. La poursuite du suivi de la cohorte permettra d'affiner ces résultats

Dose-response Relationship Analysis for Cancer and Circulatory System Disease Mortality Risks Among Uranium Miners

La relation entre le risque de décès par cancer du poumon et l’exposition au radon est aujourd’hui établie, notamment à partir des études conduites chez les mineurs d’uranium. Mais de nombreuses interrogations persistent sur les risques de cancers extra-pulmonaires et de maladies non-cancéreuses, et sur l'impact sur la santé des autres expositions radiologiques professionnelles. L’objectif général de cette thèse est de contribuer à l’estimation des risques radio-induits aux faibles débits de dose au travers de l'analyse des risques de décès par cancer du rein et par Maladie de l'Appareil Circulatoire (MAC) chez les mineurs d’uranium.Les analyses du risque de décès par cancer du rein ont été réalisées au sein de la cohorte française des mineurs d'uranium (n=5 086 ; période de suivi : 1946-2007), la cohorte post-55 (n=3 377 ; période de suivi : 1957-2007) et la cohorte allemande de la Wismut (n=58 986; période de suivi : 1946-2003) au sein desquelles sont respectivement répertoriés 24, 11 et 174 décès par cancer du rein. L’exposition au radon et à ses descendants à vie courte (exprimée en Working Level Month WLM), aux poussières d’uranium (kBqh.m-3) et aux rayonnements gamma (mSv) a été estimée individuellement et la dose absorbée au rein a été calculée. La relation dose-réponse a été affinée par rapport à l'analyse classique en considérant deux types de réponse : le risque instantané de décès par cancer du rein (analyse classique, Cause-specific Hazard Ratio (CSHR) estimé avec le modèle de Cox) et sa probabilité d'occurrence au cours du suivi (Subdistribution Hazard Ratio (SHR) estimé avec le modèle de Fine & Gray). Un excès de mortalité par cancer du rein était observé dans la cohorte française (SMR = 1,62 IC95%[1,04; 2,41]), mais pas dans la cohorte post-55. Dans la cohorte de la Wismut, un déficit de mortalité par cancer du rein était observé (0,89 [0,78; 0,99]). Pour ces trois populations, aucune relation n'a pu être mise en évidence entre les expositions radiologiques (ou la dose au rein) et le risque de décès par cancer du rein (ex : CSHRWismut_radon/100WLM=1,023 [0,993; 1,053]), ni avec sa probabilité d'occurrence au cours du suivi (ex : SHRWismut_radon /100WLM=1,012 [0,983; 1,042]).L’étude du risque de décès par MAC dans la cohorte française a montré une augmentation significative du risque de décès par MAC (n=442, CSHR/100WLM=1,11 [1,01; 1,22]) et par Maladie CérébroVasculaire (MCeV, n=105, CSHR/100WLM=1,25 [1,09; 1,43]) avec l’exposition au radon. Une enquête cas-témoins nichée au sein de la cohorte a été mise en place pour recueillir dans les dossiers médicaux les facteurs de risque classiques de MAC (surpoids, hypertension, diabète...) pour 313 mineurs (76 décès par MAC (dont 26 par Cardiopathie Ischémique (CI) et 16 par MCeV) et 237 témoins). Pour les trois expositions radiologiques, la relation exposition-risque a été analysée au sein d'une pseudo-cohorte (obtenue en pondérant les observations par l'inverse de la probabilité de sélection, n=1 644 pseudo-individus) avec le modèle de Cox, en ajustant sur les différents facteurs de risque. L’association entre les expositions radiologiques et le risque de décès par MAC, CI ou MCeV n'était pas significative (ex : CSHRMAC_radon/100WLM=1,43 [0,71; 2,87]). La prise en compte des facteurs de risque ne modifiait pas sensiblement cette association.L'absence de relation dose-réponse significative suggère que l'excès de mortalité par cancer du rein chez les mineurs français serait induit par d'autres facteurs, non-disponibles pour cette analyse. La faible variation des coefficients avec l'ajustement sur les facteurs de risque de MAC dans l'enquête cas-témoins nichée soutient l'hypothèse de l'existence d'une augmentation du risque de MCeV dans la cohorte française associée à l’exposition au radon. La poursuite du suivi de la cohorte permettra d'affiner ces résultats.The relation between lung cancer risk and radon exposure has been clearly established, especially from the studies on uranium miner cohorts. But the association between radon exposure and extrapulmonary cancers and non-cancer diseases remains not well known. Moreover, the health risks associated with the other mining-related ionizing radiation exposures are still under consideration. The aim of this thesis is to contribute to the estimation of the radio-induced health risks at low-doses through the analysis of the kidney cancer and Circulatory System Disease (CSD) mortality risks among uranium miners.Kidney cancer mortality risk analyses were performed from the French cohort of uranium miners (n=5086; follow-up period: 1946-2007), the post-55 cohort (n=3,377; follow-up period: 1957-2007) and the German cohort of the Wismut (n=58,986; follow-up period: 1946-2003) which included 24, 11 and 174 deaths from kidney cancer, respectively. The exposures to radon and its short-lived progeny (expressed in Working Level Month WLM), to uranium ore dust (kBqh.m-3) and to external gamma rays (mSv) were estimated for each miners and the equivalent kidney dose was calculated. The dose-response relation was refined considering two responses: the instantaneous risk of kidney cancer mortality (corresponding to the classical analysis, Cause-specific Hazard Ratio (CSHR) estimated with the Cox model) and its occurrence probability during the follow-up (Subdistribution Hazard Ratio (SHR) estimated with the Fine & Gray model). An excess of kidney cancer mortality was observed only in the French cohort (SMR = 1.62 CI95%[1.04; 2.41]). In the Wismut cohort, a decrease of the kidney cancer mortality was observed (0.89 [0.78; 0.99]). For these three cohorts, the occupational radiological exposures (or the equivalent kidney dose) were significantly associated neither with the risk of kidney cancer mortality (e.g. CSHRWismut_radon/100WLM=1.023 [0.993; 1.053]), nor with its occurrence probability during the follow-up (e.g. SHRWismut_radon /100WLM=1.012 [0.983; 1.042]).CSD mortality risk analyses in the French cohort showed a significant increase of the risks of mortality from CSD (n=442, CSHR/100WLM=1.11 [1.01; 1.22]) and from CerebroVascular Disease (MCeV, n=105, CSHR/100WLM=1.25 [1.09; 1.43]) with radon exposure. A case-control study nested in the French cohort was set up to collect the information related to CSD risk factors (overweight, hypertension, diabetes...) from the medical records of 313 miners (76 deaths from CSD (including 26 from Ischemic Heart Disease (IHD) and 16 from MCeV) and 237 controls). For the three radiological exposures, the exposure-risk relation was analyzed in a pseudo-cohort (n=1,644 pseudo-individuals, obtained from the weighting of the observations by their inverse selection probability) with the Cox model, adjusted for the CSD risk factors. The association between the radiological exposure and the risk of mortality from CSD, IHD or MCeV was not significant (e.g. CSHRCSD_radon/100WLM=1.43 [0.71; 2.87]). The adjustment for CSD risk factors did not substantially change the exposure-risk relation.The lack of a significant dose-response relation suggests that the excess of kidney cancer mortality among the French uranium miners may be induced by other risk factors, unavailable for this study. The small change of the coefficients observed after adjustment for CSD risk factors in the nested case-control study supports the assumption of the existence of the MCeV mortality risk increase associated with radon exposure in the French cohort of uranium miners. Future analyses based on further follow-up updates should allow to confirm or not these results

A benchmark study of scoring methods for non-coding mutations

Motivation: Detailed knowledge of coding sequences has led to different candidate models for pathogenic variant prioritization. Several deleteriousness scores have been proposed for the non-coding part of the genome, but no large-scale comparison has been realized to date to assess their performance. Results: We compared the leading scoring tools (CADD, FATHMM-MKL, Funseq2 and GWAVA) and some recent competitors (DANN, SNP and SOM scores) for their ability to discriminate assumed pathogenic variants from assumed benign variants (using the ClinVar, COSMIC and 1000 genomes project databases). Using the ClinVar benchmark, CADD was the best tool for detecting the pathogenic variants that are mainly located in protein coding gene regions. Using the COSMIC benchmark, FATHMM-MKL, GWAVA and SOMliver outperformed the other tools for pathogenic variants that are typically located in lincRNAs, pseudogenes, and other parts of the non-coding genome. However, all tools had low precision, which could potentially be improved by future non-coding genome feature discoveries. These results may have been influenced by the presence of potential benign variants in the COSMIC database. The development of a gold standard as consistent as ClinVar for these regions will be necessary to confirm our tool ranking. Availability and Implementation: The Snakemake, C ++ and R codes are freely available from https://github.com/Oncostat/BenchmarkNCVTools and supported on Linux. Contact: [email protected]. Supplementary information: Supplementary results are available at Bioinformatics online