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This article introduces a novel collaborative optimal motion planning framework for parallel aerial 3D printing. The proposed novel framework is efficiently capable of handling conflicts between the utilized Unmanned Aerial Vehicles (UAVs), as they follow predefined paths, allowing for a seamless enhancement of aerial 3D printing capabilities by employing multiple UAVs to collaborate in a parallel printing process. The established approach ingeniously formulates UAVs’ motion planning as a multi-constraint optimization problem, ensuring minimal adjustments to their velocities within specified limits. This guarantees smooth and uninterrupted printing while preventing collisions and adhering to the requirements of aerial printing. To substantiate the effectiveness of our proposed motion planning algorithm, an extensive array of simulation studies have been undertaken, encompassing scenarios where multiple UAVs engage in the fabrication of diverse construction shapes. The overall novel concept is being extensively validated in simulations, while the obtained results promise for enhancing the viability and advancing the landscape of aerial additive manufacturing., Validerad;2024;Nivå 2;2024-01-22 (signyg);Full text license: CC BY-4.0

This article introduces a novel collaborative optimal motion planning framework for parallel aerial 3D printing. The proposed novel framework is efficiently capable of handling conflicts between the utilized Unmanned Aerial Vehicles (UAVs), as they follow predefined paths, allowing for a seamless enhancement of aerial 3D printing capabilities by employing multiple UAVs to collaborate in a parallel printing process. The established approach ingeniously formulates UAVs’ motion planning as a multi-constraint optimization problem, ensuring minimal adjustments to their velocities within specified limits. This guarantees smooth and uninterrupted printing while preventing collisions and adhering to the requirements of aerial printing. To substantiate the effectiveness of our proposed motion planning algorithm, an extensive array of simulation studies have been undertaken, encompassing scenarios where multiple UAVs engage in the fabrication of diverse construction shapes. The overall novel concept is being extensively validated in simulations, while the obtained results promise for enhancing the viability and advancing the landscape of aerial additive manufacturing., Validerad;2024;Nivå 2;2024-01-22 (signyg);Full text license: CC BY-4.0

Background: Somatic and germline genetic alterations are significant drivers of cancer. Increasing integration of new technologies which profile these alterations requires timely, equitable and high-quality genetic counselling to facilitate accurate diagnoses and informed decision-making by patients and their families in preventive and clinical settings. This article aims to provide an overview of genetic counselling legislation and practice across European Union (EU) Member States to serve as a foundation for future European recommendations and action. Methods: National legislative databases of all 27 Member States were searched using terms relevant to genetic counselling, translated as appropriate. Interviews with relevant experts from each Member State were conducted to validate legislative search results and provide detailed insights into genetic counselling practice in each country. Results: Genetic counselling is included in national legislative documents of 22 of 27 Member States, with substantial variation in legal mechanisms and prescribed details (i.e. the ‘who, what, when and where’ of counselling). Practice is similarly varied. Workforce capacity (25 of 27 Member States) and genetic literacy (all Member States) were common reported barriers. Recognition and/or better integration of genetic counsellors and updated legislation and were most commonly noted as the ‘most important change’ which would improve practice. Conclusions: This review highlights substantial variability in genetic counselling across EU Member States, as well as common barriers notwithstanding this variation. Future recommendations and action should focus on addressing literacy and capacity challenges through legislative, regulatory and/or strategic approaches at EU, national, regional and/or local levels.

Aerial 3D printing is a pioneering technology yet in its conceptual stage that combines frontiers of 3D printing and Unmanned aerial vehicles (UAVs) aiming to construct large-scale structures in remote and hard-to-reach locations autonomously. The envisioned technology will enable a paradigm shift in the construction and manufacturing industries by utilizing UAVs as precision flying construction workers. However, the limited payload-carrying capacity of the UAVs, along with the intricate dexterity required for manipulation and planning, imposes a formidable barrier to overcome. Aiming to surpass these issues, a novel aerial decomposition-based and scheduling 3D printing framework is presented in this article, which considers a near-optimal decomposition of the original 3D shape of the model into smaller, more manageable sub-parts called chunks. This is achieved by searching for planar cuts based on a heuristic function incorporating necessary constraints associated with the interconnectivity between subparts, while avoiding any possibility of collision between the UAV’s extruder and generated chunks. Additionally, an autonomous task allocation framework is presented, which determines a priority-based sequence to assign each printable chunk to a UAV for manufacturing. The efficacy of the proposed framework is demonstrated using the physics-based Gazebo simulation engine, where various primitive CAD-based aerial 3D constructions are established, accounting for the nonlinear UAVs dynamics, associated motion planning and reactive navigation through Model predictive control., Validerad;2024;Nivå 2;2024-04-02 (marisr);Full text license: CC BY

Aerial 3D printing is a pioneering technology yet in its conceptual stage that combines frontiers of 3D printing and Unmanned aerial vehicles (UAVs) aiming to construct large-scale structures in remote and hard-to-reach locations autonomously. The envisioned technology will enable a paradigm shift in the construction and manufacturing industries by utilizing UAVs as precision flying construction workers. However, the limited payload-carrying capacity of the UAVs, along with the intricate dexterity required for manipulation and planning, imposes a formidable barrier to overcome. Aiming to surpass these issues, a novel aerial decomposition-based and scheduling 3D printing framework is presented in this article, which considers a near-optimal decomposition of the original 3D shape of the model into smaller, more manageable sub-parts called chunks. This is achieved by searching for planar cuts based on a heuristic function incorporating necessary constraints associated with the interconnectivity between subparts, while avoiding any possibility of collision between the UAV’s extruder and generated chunks. Additionally, an autonomous task allocation framework is presented, which determines a priority-based sequence to assign each printable chunk to a UAV for manufacturing. The efficacy of the proposed framework is demonstrated using the physics-based Gazebo simulation engine, where various primitive CAD-based aerial 3D constructions are established, accounting for the nonlinear UAVs dynamics, associated motion planning and reactive navigation through Model predictive control., Validerad;2024;Nivå 2;2024-04-02 (marisr);Full text license: CC BY

Purpose Primary mediastinal large B-cell lymphoma (PMBCL) is a rare aggressive lymphoma predominantly affecting young female patients. Large-scale genomic investigations and genetic markers for risk stratification are lacking. Patients and Methods To elucidate the full spectrum of genomic alterations, samples from 340 patients with previously untreated PMBCL were investigated by whole-genome (n = 20), whole-exome (n = 78), and targeted (n = 308) sequencing. Statistically significant prognostic variables were identified using a multivariable Cox regression model and confirmed by L1/L2 regularized regressions. Results Whole-genome sequencing revealed a commonly disrupted p53 pathway with nonredundant somatic structural variations (SVs) in TP53-related genes (TP63, TP73, and WWOX) and identified novel SVs facilitating immune evasion (DOCK8 and CD83). Integration of mutation and copy-number data expanded the repertoire of known PMBCL alterations (eg, ARID1A, P2RY8, and PLXNC1) with a previously unrecognized role for epigenetic/chromatin modifiers. Multivariable analysis identified six genetic lesions with significant prognostic impact. CD58 mutations (31%) showed the strongest association with worse PFS (hazard ratio [HR], 2.52 [95% CI, 1.50 to 4.21]; P < .001) and overall survival (HR, 2.33 [95% CI, 1.14 to 4.76]; P = .02). IPI high-risk patients with mutated CD58 demonstrated a particularly poor prognosis, with 5-year PFS and OS rates of 41% and 58%, respectively. The adverse prognostic significance of the CD58 mutation status was predominantly observed in patients treated with nonintensified regimens, indicating that dose intensification may, to some extent, mitigate the impact of this high-risk marker. By contrast, DUSP2-mutated patients (24%) displayed durable responses (PFS: HR, 0.2 [95% CI, 0.07 to 0.55]; P = .002) and prolonged OS (HR, 0.11 [95% CI, 0.01 to 0.78]; P = .028). Upon CHOP-like treatment, these patients had very favorable outcome, with 5-year PFS

Profound immune dysregulation and impaired response to the SARS-CoV-2 vaccine put patients with chronic lymphocytic leukemia (CLL) at risk of severe COVID-19. We compared humoral memory and T-cell responses after booster dose vaccination or breakthrough infection. (Green) Quantitative determination of anti-Spike specific antibodies. Booster doses increased seroconversion rate and antibody titers in all patient categories, ultimately generating humoral responses similar to those observed in the postinfection cohort. In detail, humoral response with overscale median antibody titers arose in >80% of patients in watch and wait, off-therapy in remission, or under treatment with venetoclax single-agent. Anti-CD20 antibodies and active treatment with BTK inhibitors (BTKi) represent limiting factors of humoral response, still memory mounted in ~40% of cases following booster doses or infection. (Blue) Evaluation of SARS-CoV-2-specific T-cell responses. Number of T-cell functional activation markers documented in each patient. The vast majority of patients, including those seronegative, developed T-cell responses, qualitatively similar between treatment groups or between vaccination alone and infection cases. These data highlight the efficacy of booster doses in eliciting T-cell immunity independently of treatment status and support the use of additional vaccination boosters to stimulate humoral immunity in patients on active CLL-directed treatments., The project was supported in part by Fondazione Veronesi (ID 1852164), Janssen (IBR-I-20-EMEA-014-V01/54179060CLL4024; NOPRODCLL4001), and MH CZ—DRO (FNBr, 65269705).

Antibodies are major molecules of the immune system raised in response to invading pathogens. They are characterised by their high binding affinity and specificity, as well as their vast antigen binding diversity. These characteristics have made antibodies attractive for the development of new therapeutics against diseases such as cancers, autoimmune disorders or infectious diseases. A better understanding of the characteristics of antibodies and their target antigens can therefore help in the development of new antibody-based therapeutics, as well as a better understanding of B-cell associated leukemias. This PhD thesis presents the results of multiple computational analyses performed on antibody and antigen data, and in particular in the context of SARS-CoV-2 and chronic lymphocytic leukemia (CLL).First, following a rigorous and independent benchmark, we showed that conformational B-cell epitope prediction methods are in general no better than random. We concluded that the B-cell epitope prediction task is probably ill-posed, and that it is likely that almost all protein surfaces can be bound by some antibody. Second, we performed an analysis of 83 neutralising antibodies with known 3D structures targeting the spike protein in the context of the SARS-CoV-2 pandemic. By comparing our computational analysis with experimental data, our results supported the existence of an immunodominant subset of antibodies, and indicated that they are characterized by an intermediate overlap with the binding interface of the ACE2 receptor, the entry point to the host cells, and, chiefly, by their ability to bind the closed conformation of the spike protein. On the basis of these results, we improved SpikePro, an in-house SARS-CoV-2 variant fitness prediction model based on the impact of the mutations on the spike protein's stability, binding affinity with ACE2 and binding affinity against an updated panel of immunodominant-only antibodies. SpikePro has been made freely and easily a, Doctorat en Sciences de l'ingénieur et technologie, info:eu-repo/semantics/nonPublished

This article introduces an experimental emulation of a novel chunk-based flexible multi-DoF aerial 3D printing framework. The experimental demonstration of the overall autonomy focuses on precise motion planning and task allocation for a UAV, traversing through a series of planned space-filling paths involved in the aerial 3D printing process without physically depositing the overlaying material. The flexible multi-DoF aerial 3D printing is a newly developed framework and has the potential to strategically distribute the envisioned 3D model to be printed into small, manageable chunks suitable for distributed 3D printing. Moreover, by harnessing the dexterous flexibility due to the 6 DoF motion of UAV, the framework enables the provision of integrating the overall autonomy stack, potentially opening up an entirely new frontier in additive manufacturing. However, it's essential to note that the feasibility of this pioneering concept is still in its very early stage of development, which yet needs to be experimentally verified. Towards this direction, experimental emulation serves as the crucial stepping stone, providing a pseudo mockup scenario by virtual material deposition, helping to identify technological gaps from simulation to reality. Experimental emulation results, supported by critical analysis and discussion, lay the foundation for addressing the technological and research challenges to significantly push the boundaries of the state-of-the-art 3D printing mechanism., Comment: This paper has been accepted for publication at IEEE International Conference on Robotics and Automation (ICRA) 2024

Through an uncertainty quantification (UQ) perspective, we show that score-based generative models (SGMs) are provably robust to the multiple sources of error in practical implementation. Our primary tool is the Wasserstein uncertainty propagation (WUP) theorem, a model-form UQ bound that describes how the $L^2$ error from learning the score function propagates to a Wasserstein-1 ($\mathbf{d}_1$) ball around the true data distribution under the evolution of the Fokker-Planck equation. We show how errors due to (a) finite sample approximation, (b) early stopping, (c) score-matching objective choice, (d) score function parametrization expressiveness, and (e) reference distribution choice, impact the quality of the generative model in terms of a $\mathbf{d}_1$ bound of computable quantities. The WUP theorem relies on Bernstein estimates for Hamilton-Jacobi-Bellman partial differential equations (PDE) and the regularizing properties of diffusion processes. Specifically, PDE regularity theory shows that stochasticity is the key mechanism ensuring SGM algorithms are provably robust. The WUP theorem applies to integral probability metrics beyond $\mathbf{d}_1$, such as the total variation distance and the maximum mean discrepancy. Sample complexity and generalization bounds in $\mathbf{d}_1$ follow directly from the WUP theorem. Our approach requires minimal assumptions, is agnostic to the manifold hypothesis and avoids absolute continuity assumptions for the target distribution. Additionally, our results clarify the trade-offs among multiple error sources in SGMs.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.

(English) This thesis records the evolution of the container throughput dynamics of the European port system from 2001-2020, analyses the dynamics of the European container port hierarchy with methodologies that have not been used in that context, applies network analysis on the liner shipping networks of individual shipping companies and proposes a model for short-term forecasts of container throughput and their accompanying prediction intervals. Chapter 2 explores the dynamics of container throughput in the European port system from 2001-2020 at the level both of groups of ports and individual ports (Notteboom, 2010). The evolution of the container throughput is examined by the application of concentration indicators. The market share of port groups or ports in the total throughput of the system, the normalized Herfindahl–Hirschman Index and a customized form of shift-share analysis are used for this purpose. The influence of the two crises that occurred during the examined period, the global financial crisis of 2009 and the health crisis of 2020, on the container throughput dynamics is explored. The dynamics of the European container port hierarchy are analyzed in chapter 3 by the application of 3 methodologies. First, two types of rank-size models are used in order to investigate the formation of the hierarchies and the dynamics of container throughput distribution. Second, a methodology based on the principals of Analytic Hierarchy Process (AHP) combined with an allometric growth model is introduced in order to explore the relative growth of large ports as a group upon groups of medium-sized and small ports. Third, a Markov chain modeling is applied in order to investigate the mobility of ports within the hierarchy of the European container port system. The dataset that is used in all the methodologies consists of the annual container port throughputs in TEUs of the top-100 European container ports for every year between 2001 and 2020. Chapter 4 analyzes the co, (Español) Esta tesis a) registra la evolución de la dinámica del tráfico de contenedores del sistema portuario europeo desde 2001-2020 b) analiza la dinámica de la jerarquía portuaria de contenedores europea con metodologías que no se han utilizado en ese contexto c) aplica el análisis de redes en las redes de transporte marítimo de línea de compañías navieras individuales y d) propone un modelo de pronósticos del movimiento de contenedores a corto plazo y de los intervalos de predicción correspondientes. El capítulo 2 explora la dinámica del tráfico de contenedores en el sistema portuario europeo entre 2001 y 2020, tanto a nivel de conjuntos de puertos como de casos individuales (Notteboom, 2010). La evolución del movimiento de contenedores se examina mediante la aplicación de indicadores de concentración. Para este propósito, se utiliza la cuota del mercado de los grupos portuarios o puertos en el rendimiento total del sistema, el índice Herfindahl-Hirschman normalizado y una forma de “shift-share” análisis adaptada. Se explora también la influencia en la dinámica del tráfico de contenedores de los dos crisis que ocurrieron durante el periodo examinado, es decir la crisis financiera mundial de 2009 y la crisis de salud de 2020. En el capítulo 3 se analiza la dinámica de la jerarquía portuaria europea de contenedores mediante la aplicación de 3 metodologías. En primer lugar, se utilizan dos tipos de modelos de tamaño de rango para investigar la formación de las jerarquías y la dinámica de la distribución del rendimiento de los contenedores. En segundo lugar, se introduce una metodología basada en los principios del Proceso Jerárquico Analítico (AHP) combinado con un modelo de crecimiento alométrico para explorar el crecimiento relativo de los puertos grandes como grupo sobre grupos de puertos medianos y pequeños. En tercer lugar, se aplica un modelo de cadena de Markov para investigar la movilidad de los puertos dentro de la jerarquía del sistema portuario europeo, Postprint (published version)

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Background: Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. Experimental design: TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Results: Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Conclusions: Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.

Background: Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. Experimental design: TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Results: Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Conclusions: Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

Background: Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. Experimental design: TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Results: Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Conclusions: Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

01 augustus 2023, Item does not contain fulltext

Contains fulltext : 296673.pdf (Publisher’s version ) (Open Access), Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality-NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon-based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.

Background: Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. Experimental design: TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Results: Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Conclusions: Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.

Motivation The fast and accurate detection of similar geometrical arrangements of protein residues, known as 3D structural motifs, is highly relevant for many applications such as binding region and catalytic site detection, drug discovery and structure conservation analyses. With the recent publication of new protein structure prediction methods, the number of available protein structures is exploding, which makes efficient and easy-to-use tools for identifying 3D structural motifs essential. Results We present an open-source Python package that enables the search for both exact and mutated motifs with position-specific residue substitutions. The tool is efficient, flexible, accurate, and suitable to run both on computer clusters and personal laptops. Two successful applications of pyScoMotif for catalytic site identification are showcased. Availability and implementation The pyScoMotif package can be installed from the PyPI repository and is also available at https://github.com/3BioCompBio/pyScoMotif. It is free to use for non-commercial purposes., info:eu-repo/semantics/published

The neutron-induced fission cross section of 230 Th has been measured at the neutron time-of-flight facility n_TOF located at CERN. The experiment was performed at the experimental area EAR-1 with a neutron flight path of 185 m, using Micromegas detectors for the detection of the fission fragments. The 230 Th(n, f ) cross section was determined relative to the 235 U(n, f ) one, covering the energy range from the fission threshold up to 400 MeV. The results from the present work are compared with existing cross-section datasets and the observed discrepancies are discussed and analyzed. Finally, using the code EMPIRE 3.2.3 a theoretical study, based on the statistical model, was performed leading to a satisfactory reproduction of the experimental results with the proper tuning of the respective parameters, while for incident neutron energy beyond 200 MeV the fission of 230 Th was described by Monte Carlo simulations.

Le mélanome est la forme la plus agressive et la plus mortelle des cancers de la peau. Une mutation activatrice dans les gènes BRAF ou NRAS est présente dans 95% des cas de mélanomes humains. L'importance de l'inflammation chronique et du microenvironnement tumoral dans le développement, la progression et le potentiel métastatique de cette maladie est bien établie. Les molécules chimioattractantes comme la chémérine jouent dans ce contexte un rôle clé via le recrutement sélectif de populations leucocytaires spécifiques exprimant le récepteur ChemR23. Lors de ma thèse, nous avons étudié le rôle de la chémérine, dans les différentes étapes de la carcinogenèse. Elle possède des propriétés antitumorales, et notamment dans le mélanome. Cependant, les mécanismes de base de son action in vivo restent à déterminer.Suite aux études sur le modèle murin, nous avons choisi d’utiliser le poisson-zèbre afin d’investiguer in vivo les fonctions de la chémérine dans la biologie du mélanome. En effet, les résultats chez le poisson-zèbre obtenus au sein de notre laboratoire, suggèrent que l'axe chémérine/ChemR23 est hautement conservé à travers le phylum des vertébrés. Pour évaluer les propriétés antitumorales de la chémérine, j’ai utilisé différentes stratégies préalablement établies et validées chez le poisson-zèbre :un modèle mosaïque utilisant le système MiniCoopR exprimant l'oncogène NRASQ61L, un modèle génétique stable de mélanome faisant intervenir l’oncogène BRAF sur fond d’absence d’une protéine p53 fonctionnelle, et un modèle de xénogreffe de tumeurs. Mes analyses comparant l’apparition et la progression tumorale entre des animaux invalidés pour le cluster b de la chémérine ou pour son récepteur cmklr1.1 et leurs contrôles WT démontrent de manière non ambigüe que les propriétés antitumorales du système chémérine/ChemR23 sont conservées chez le poisson-zèbre.En ouvrant la voie à l’utilisation du poisson-zèbre pour l’étude des mécanismes clés par lesquels la chémérine agit sur, Doctorat en Sciences biomédicales et pharmaceutiques (Médecine), info:eu-repo/semantics/nonPublished

Following their discovery at the end of the 20th century, extracellular vesicles (EVs) ranging from 50-1,000 nm have proven to be paramount in the progression of many cancers, including hematological malignancies. EVs are a heterogeneous group of cell-derived membranous structures that include small EVs (commonly called exosomes) and large EVs (microparticles). They have been demonstrated to participate in multiple physiological and pathological processes by allowing exchange of biological material (including among others proteins, DNA and RNA) between cells. They are therefore a crucial way of intercellular communication. In this context, malignant cells can release these extracellular vesicles that can influence their microenvironment, induce the formation of a tumorigenic niche, and prepare and establish distant niches facilitating metastasis by significantly impacting the phenotypes of surrounding cells and turning them toward supportive roles. In addition, EVs are also able to manipulate the immune response and to establish an immunosuppressive microenvironment. This in turn allows for ideal conditions for heightened chemoresistance and increased disease burden. Here, we review the latest findings and reports studying the effects and therapeutic potential of extracellular vesicles in various hematological malignancies. The study of extracellular vesicles remains in its infancy; however, rapid advances in the analysis of these vesicles in the context of disease allow us to envision prospects to improve the detection and treatment of hematological malignancies., SCOPUS: re.j, info:eu-repo/semantics/published

The neutron-induced fission cross section of 230 Th has been measured at the neutron time-of-flight facility n_TOF located at CERN. The experiment was performed at the experimental area EAR-1 with a neutron flight path of 185 m, using Micromegas detectors for the detection of the fission fragments. The 230 Th(n, f ) cross section was determined relative to the 235 U(n, f ) one, covering the energy range from the fission threshold up to 400 MeV. The results from the present work are compared with existing cross-section datasets and the observed discrepancies are discussed and analyzed. Finally, using the code EMPIRE 3.2.3 a theoretical study, based on the statistical model, was performed leading to a satisfactory reproduction of the experimental results with the proper tuning of the respective parameters, while for incident neutron energy beyond 200 MeV the fission of 230 Th was described by Monte Carlo simulations., This project received funding from the Euratom “Support safe operation of nuclear systems” program 2014–2018 under Grant Agreement No. 847552 (SANDA) and by the funding agencies of the participating institutes. This research is imple- mented through the IKY scholarships program and cofinanced by the European Union (European Social Fund ’ESF) and Greek national funds through the action entitled “Reinforce- ment of Postdoctoral Researchers - 2nd call (MIS 5033021)”, in the framework of the Operational Programme “Human Resources Development Program, Education and Lifelong Learning” of the National Strategic Reference Framework., Article signat per 137 autors/es: V. Michalopoulou, A. Stamatopoulos, M. Diakaki, A. Tsinganis, R. Vlastou, M. Kokkoris, N. Patronis, Z. Eleme, D. Macina, L. Tassan-Got, N. Colonna, E. Chiaveri, A. Ventura, P. Schillebeeckx, J. Heyse, G. Sibbens, G. Alaerts, A. Borella, A. Moens, D. Vanleeuw, O. Aberle, V. Alcayne, S. Amaducci, J. Andrzejewski, L. Audouin, V. Babiano-Suarez, M. Bacak, M. Barbagallo, S. Bennett, E. Berthoumieux, J. Billowes, D. Bosnar, A. Brown, M. Busso, M. Caamaño, L. Caballero, F. Calviño, M. Calviani, D. Cano-Ott, A. Casanovas, F. Cerutti, G. Cortés, M. A. Cortés-Giraldo, L. Cosentino, S. Cristallo, L. A. Damone, P. J. Davies, M. Dietz, C. Domingo-Pardo, R. Dressler, Q. Ducasse, E. Dupont, I. Durán, B. Fernández-Domínguez, A. Ferrari, P. Finocchiaro, V. Furman, K. Göbel, R. Garg, A. Gawlik-Ramiega, S. Gilardoni, I. F. Gonçalves, E. González-Romero, C. Guerrero, F. Gunsing, H. Harada, S. Heinitz, D. G. Jenkins, A. Junghans, F. Käppeler, Y. Kadi, A. Kimura, I. Knapová, Y. Kopatch, M. Krticka, D. Kurtulgil, I. Ladarescu, C. Lederer-Woods, H. Leeb, J. Lerendegui-Marco, S. J. Lonsdale, A. Manna, T. Martínez, A. Masi, C. Massimi, P. Mastinu, M. Mastromarco, E. A. Maugeri, A. Mazzone, E. Mendoza, A. Mengoni, P. M. Milazzo, F. Mingrone, J. Moreno-Soto, A. Musumarra, A. Negret, R. Nolte, F. Ogállar, A. Oprea, A. Pavlik, J. Perkowski, C. Petrone, L. Piersanti, E. Pirovano, I. Porras, J. Praena, J. M. Quesada, D. Ramos-Doval, T. Rauscher, R. Reifarth, D. Rochman, Y. Romanets, C. Rubbia, M. Sabaté-Gilarte, A. Saxena, D. Schumann, A. Sekhar, A. G. Smith, N. V. Sosnin, P. Sprung, G. Tagliente, J. L. Tain, A. Tarifeño-Saldivia, Th. Thomas, P. Torres-Sánchez, J. Ulrich, S. Urlass, S. Valenta, G. Vannini, V. Variale, P. Vaz, D. Vescovi, V. Vlachoudis, A. Wallner, P. J. Woods, T. Wright, and P. Žugec., Postprint (published version)

T cell large granular lymphocyte (T-LGL) lymphoproliferations constitute a disease spectrum ranging from poly/oligo to monoclonal. Boundaries within this spectrum of proliferations are not well established. T-LGL lymphoproliferations co-occur with a wide variety of other diseases ranging from autoimmune disorders, solid tumors, hematological malignancies, post solid organ, and hematopoietic stem cell transplantation, and can therefore arise as a consequence of a wide variety of antigenic triggers. Persistence of a dominant malignant T-LGL clone is established through continuous STAT3 activation. Using next-generation sequencing, we profiled a cohort of 27 well-established patients with T-LGL lymphoproliferations, aiming to identify the subclonal architecture of the T-cell receptor beta (TRB) chain gene repertoire. Moreover, we searched for associations between TRB gene repertoire patterns and clinical manifestations, with the ultimate objective of discriminating between T-LGL lymphoproliferations developing in different clinical contexts and/or displaying distinct clinical presentation. Altogether, our data demonstrates that the TRB gene repertoire of patients with T-LGL lymphoproliferations is context-dependent, displaying distinct clonal architectures in different settings. Our results also highlight that there are monoclonal T-LGL cells with or without STAT3 mutations that cause symptoms such as neutropenia on one end of a spectrum and reactive oligoclonal T-LGL lymphoproliferations on the other. Longitudinal analysis revealed temporal clonal dynamics and showed that T-LGL cells might arise as an epiphenomenon when co-occurring with other malignancies, possibly reactive toward tumor antigens.

Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality–NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon–based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.

Le cancer du pancréas est l'une des formes de cancer les plus mortelles à travers le monde et le traitement de cette maladie demeure un défi majeur. Il a été rapporté que des exosomes dérivés de fibroblastes de peau de souris et chargés d’un siARN ciblant le proto-oncogène KRAS peuvent supprimer le cancer du pancréas dans des modèles de souris et augmenter significativement la survie globale. Le but de ce travail de thèse est d'évaluer la faisabilité d’utiliser les vésicules extracellulaires (VEs) dérivées de cellules stromales mésenchymateuses (CSM) humaines obtenues à partir du cordon ombilical comme transporteurs de siRNA et/ou drogues pour cibler spécifiquement les cellules cancéreuses pancréatiques. Le cordon ombilical a été choisi comme source de CSM car il présente plusieurs avantages par rapport à d'autres sources :déchet médical, grande disponibilité, collecte facile, autorenouvellement rapide, faible immunogénicité et absence de tumorigénicité. Les CSM obtenues par une méthode explant et leur expansion in vitro permet d’obtenir des VEs. Après leur purification par ultracentrifugation, leur identification et leur caractérisation biologique, les vésicules sont chargées en siRNA et/ou de drogue. Leur cinétique d’intégration et les effets biologiques in vitro de ces VEs naturelles ou chargées ont été évalués sur différentes lignées cellulaires humaines pancréatiques et intestinales présentant ou non la mutation KRASG12D. Différents paramètres ont été évalués :prolifération, apoptose, migration, invasion mais aussi l’expression de KRAS par qPCR. Les VEs chargées du siARN KRASG12D ont permis une réduction significative de la prolifération, de la viabilité et de la migration des lignées cellulaire KRASG12D par rapport aux VEs chargées en siARN scramble. Une méthode de chargement endogène de VEs a été appliquée pour obtenir des VEs chargées en DOXO. Ces VEs chargées sont rapidement intégrées par les cellules cancéreuses et ont un effet supérieur à la drogue libre., Doctorat en Sciences biomédicales et pharmaceutiques (Médecine), info:eu-repo/semantics/nonPublished

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide. Treatment of PDAC remains a major challenge. This study aims to evaluate, in vitro, the use of human umbilical cord mesenchymal stromal cell (UC-MSC)-derived EVs to specifically target pancreatic cancer cells. EVs were isolated from the FBS-free supernatants of the cultured UC-MSCs by ultracentrifugation and characterized by several methods. EVs were loaded with scramble or KRASG12D-targeting siRNA by electroporation. The effects of control and loaded EVs on different cell types were evaluated by assessing cell proliferation, viability, apoptosis and migration. Later, the ability of EVs to function as a drug delivery system for doxorubicin (DOXO), a chemotherapeutic drug, was also evaluated. Loaded EVs exhibited different kinetic rates of uptake by three cell lines, namely, BxPC-3 cells (pancreatic cancer cell line expressing KRASwt), LS180 cells (colorectal cell line expressing KRASG12D) and PANC-1 cells (pancreatic cell line expressing KRASG12D). A significant decrease in the relative expression of the KRASG12D gene after incubation with KRAS siRNA EVs was observed by real-time PCR. KRASG12D siRNA EVs significantly reduced the proliferation, viability and migration of the KRASG12D cell lines compared to scramble siRNA EVs. An endogenous EV production method was applied to obtain DOXO-loaded EVs. Briefly, UC-MSCs were treated with DOXO. After 24 h, UC-MSCs released DOXO-loaded EVs. DOXO-loaded EVs were rapidly taken up by PANC-1 cells and induced apoptotic cell death more efficiently than free DOXO. In conclusion, the use of UC-MSC-derived EVs as a drug delivery system for siRNAs or drugs could be a promising approach for the targeted treatment of PDAC., SCOPUS: ar.j, info:eu-repo/semantics/published

Dysregulation of mRNA translation, including preferential translation of mRNA with complex 5'-UTRs such as the MYC oncogene, is recognized as an important mechanism in cancer. In this study, we show that both human and murine chronic lymphocytic leukemia (CLL) cells display a high translation rate, which can be inhibited by the synthetic flavagline FL3, a prohibitin (PHB)-binding drug. A multiomics analysis consisting of pulsed SILAC, RNA sequencing and polysome profiling performed in CLL patient samples and cell lines treated with FL3 revealed the decreased translation of the MYC oncogene and of proteins involved in cell cycle and metabolism. Furthermore, inhibition of translation was associated with a block of proliferation and a profound rewiring of MYC-driven metabolism. Interestingly, contrary to other models, the RAS-RAF-(PHBs)-MAPK pathway is neither impaired by FL3 nor implicated in translation regulation in CLL cells. Here, we rather show that PHBs are directly associated with the translation initiation complex and can be targeted by FL3. Knock-down of PHBs resembled FL3 treatment. Importantly, inhibition of translation was efficient in controlling CLL development in vivo either alone or combined with immunotherapy. Finally, high expression of translation initiation-related genes and PHBs genes correlated with poor survival and unfavorable clinical parameters in CLL patients. In conclusion, we demonstrated that translation inhibition is a valuable strategy to control CLL development by blocking the translation of several oncogenic pathways including MYC. We also unraveled a new and direct role of PHBs in translation initiation, thus creating new therapeutic opportunities for CLL patients., SCOPUS: ar.j, info:eu-repo/semantics/published

Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.

The somatic hypermutation (SHM) status of the clonotypic, rearranged immunoglobulin heavy variable (IGHV) gene is an established prognostic and predictive marker in chronic lymphocytic leukemia (CLL). Analysis of SHM is generally performed by polymerase chain reaction (PCR)-amplification of clonal IGHV-IGHD-IGHJ gene rearrangements followed by sequencing to identify IGHV gene sequences and germline identity. Targeted-hybridization next-generation sequencing (NGS) can simultaneously assess clonality and other genetic aberrations. However, it has limitations for SHM analysis due to sequence similarity between different IGHV genes and mutations introduced by SHM, which can affect alignment efficiency and accuracy. We developed a novel SHM assessment strategy using a targeted-hybridization NGS approach (EuroClonality- NDC assay) and applied it to 331 samples of lymphoproliferative disorder (LPD). Our strategy focuses on analyzing the sequence downstream to the clonotypic, rearranged IGHJ gene up to the IGHM enhancer (IGHJ-E) which provides more accurate alignment. Overall, 84/95 (88.4%) CLL cases with conventional SHM data showed concordant SHM status, increasing to 91.6% when excluding borderline cases. Additionally, IGHJ-E mutation analysis in a wide range of pre- and post-germinal center LPD showed significant correlation with differentiation and lineage status, suggesting that IGHJ-E analysis is a promising surrogate marker enabling SHM to be reported using NGS-capture strategies and whole genome sequencing.

Peptide receptor radionuclide therapy with 177Lu-DOTATATE improves the outcome of patients with somatostatin receptor (SSTR)-expressing neuroendocrine tumours. Nevertheless, stable disease has been the main response pattern observed, with some rare complete responses. Lu-177 exerts about two-thirds of its biological effects via the indirect effects of ionizing radiation that generate reactive oxygen species, eventually leading to oxidative damage and cell death. This provides a rationale for targeting the antioxidant defence system in combination with 177Lu-DOTATATE. In the present study, the radiosensitizing potential and the safety of depleting glutathione (GSH) levels using buthionine sulfoximine (BSO) during 177Lu-DOTATATE therapy were assessed in vitro and in vivo using a xenograft mouse model. In vitro, the combination resulted in a synergistic effect in cell lines exhibiting a BSO-mediated GSH decrease. In vivo, BSO neither influenced 177Lu-DOTATATE biodistribution nor induced liver, kidney or bone marrow toxicity. In terms of efficacy, the combination resulted in reduced tumour growth and metabolic activity. Our results showed that disturbing the cell redox balance using a GSH synthesis inhibitor increased 177Lu-DOTATATE efficacy without additional toxicity. Targeting the antioxidant defence system opens new safe treatment combination opportunities with 177Lu-DOTATATE., SCOPUS: ar.j, info:eu-repo/semantics/published

In the nervous system, glial cells coexist and collaborate with neurons to process information and generate adaptive responses. However, how neurons and glia in the nervous system communicate with each other to properly perform their functions is an underexplored research topic. The survival of neurons depends on glia making it difficult to analyze intercellular communication. Here, I used the nematode Caenorhabditis elegans to circumvent these obstacles and study neuron-glial communication. Taking advantage of the invariant anatomy of C. elegans, I selected as a model a sensory organ composed of 12 ciliated neurons and two glial cells. This organ serves as a model to explore how neurons and glia communicate in the context of tissues within a living animal.Cilia are sensory projections present on several types of cells and used to detect external stimuli. The ciliated sensory neurons of C. elegans have been widely used as a model to understand cilia biology. Ciliary traffic homeostasis is key in cilia biology, and several diseases, collectively referred to as ciliopathies, are caused by dysfunctional cilia. In C. elegans, cilia dysfunction disrupts sensory responses to odors, food, repellent molecules, and temperature changes. In addition to their sensory function, cilia are believed to aid in the communication between cells and individuals by excreting extracellular vesicles larger than 100 nm, called ectosomes.First, I show how ectosomes bud from the ciliary membrane of ciliated neurons of hermaphroditic animals, a mechanism thought to be exclusive to the male ciliated neurons of C. elegans. To describe how and which ciliated sensory neurons produce ectosomes, I selected potential cargoes of ciliated ectosomes that were marked by transgenesis or knock-in. These new ectosome markers include tetraspanins TSP-6, 7 and 4, as well as other membrane receptors or sensory machinery proteins. Ciliary distribution and entry into ectosomes of these markers have been studied, Doctorat en Sciences biomédicales et pharmaceutiques (Médecine), info:eu-repo/semantics/nonPublished

Intercellular communication, through direct and indirect cell contact, is mandatory in multicellular organisms. These last years, the microenvironment, and in particular, transfer by extracellular vesicles (EVs), has emerged as a new communication mechanism. Different biological fluids and cell types are common sources of EVs. EVs play different roles, acting as signalosomes, biomarkers, and therapeutic agents. As therapeutic agents, MSC-derived EVs display numerous advantages: they are biocompatible, non-immunogenic, and stable in circulation, and they are able to cross biological barriers. Furthermore, EVs have a great potential for drug delivery. Different EV isolation protocols and loading methods have been tested and compared. Published and ongoing clinical trials, and numerous preclinical studies indicate that EVs are safe and well tolerated. Moreover, the latest studies suggest their applications as nanocarriers. The current review will describe the potential for MSC-derived EVs as drug delivery systems (DDS) in disease treatment, and their advantages. Thereafter, we will outline the different EV isolation methods and loading techniques, and analyze relevant preclinical studies. Finally, we will describe ongoing and published clinical studies. These elements will outline the benefits of MSC-derived EV DDS over several aspects., SCOPUS: re.j, info:eu-repo/semantics/published

Background: Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. Experimental design: TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Results: Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Conclusions: Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3–9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3–9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

[Background]: Patients with chronic lymphocytic leukemia (CLL) have a higher risk of developing other malignancies (OMs) compared to the general population. However, the impact of CLL-related risk factors and CLL-directed treatment is still unclear and represents the focus of this work., [Methods]: We conducted a retrospective international multicenter study to assess the incidence of OMs and detect potential risk factors in 19,705 patients with CLL, small lymphocytic lymphoma, or high-count CLL-like monoclonal B-cell lymphocytosis, diagnosed between 2000 and 2016. Data collection took place between October 2020 and March 2022., [Findings]: In 129,254 years of follow-up after CLL diagnosis, 3513 OMs were diagnosed (27.2 OMs/1000 person-years). The most common hematological OMs were Richter transformation, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Non-melanoma skin (NMSC) and prostate cancers were the most common solid tumors (STs). The only predictor for MDS and AML development was treatment with fludarabine and cyclophosphamide with/without rituximab (FC ± R) (OR = 3.7; 95% CI = 2.79–4.91; p < 0.001). STs were more frequent in males and patients with unmutated immunoglobulin heavy variable genes (OR = 1.77; 95% CI = 1.49–2.11; p < 0.001/OR = 1.89; 95% CI = 1.6–2.24; p < 0.001). CLL-directed treatment was associated with non-melanoma skin and prostate cancers (OR = 1.8; 95% CI = 1.36–2.41; p < 0.001/OR = 2.11; 95% CI = 1.12–3.97; p = 0.021). In contrast, breast cancers were more frequent in untreated patients (OR = 0.17; 95% CI = 0.08–0.33; p < 0.001). Patients with CLL and an OM had inferior overall survival (OS) than those without. AML and MDS conferred the worst OS (p < 0.001)., [Interpretation]: OMs in CLL impact on OS. Treatment for CLL increased the risk for AML/MDS, prostate cancer, and NMSC. FCR was associated with increased risk for AML/MDS.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3–9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Neutron cross section measurements are often made relative to a neutron cross section standard. Thus, the accuracy of the neutron standards determines the best possible accuracy of the neutron measurements. The U-235(n,f) cross section is widely used as reference, while it is considered a standard at thermal point and between 0.15 to 200 MeV. For this reason, additional cross section data for the U-235(n,f) reaction are useful in order to improve the accuracy and to extend the energy range of the standard. In this work, preliminary results of the measurement of the 235U(n,f) cross-section relative to the standard (10) B(n,a) reaction are presented. The high accuracy measurement was performed at the experimental area EAR-1 of the n_TOF facility at CERN, aiming at covering the energy range from the thermal region up to approximately 100 keV. The samples were produced at JRC-Geel in Belgium, while the experimental setup was based on Micromegas detectors.

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

The future of 3D printing utilizing unmanned aerial vehicles (UAVs) presents a promising capability to revolutionize manufacturing and to enable the creation of large-scale structures in remote and hard- to-reach areas e.g. in other planetary systems. Nevertheless, the limited payload capacity of UAVs and the complexity in the 3D printing of large objects pose significant challenges. In this article we propose a novel chunk-based framework for distributed 3D printing using UAVs that sets the basis for a fully collaborative aerial 3D printing of challenging structures. The presented framework, through a novel proposed optimisation process, is able to divide the 3D model to be printed into small, manageable chunks and to assign them to a UAV for partial printing of the assigned chunk, in a fully autonomous approach. Thus, we establish the algorithms for chunk division, allocation, and printing, and we also introduce a novel algorithm that efficiently partitions the mesh into planar chunks, while accounting for the inter-connectivity constraints of the chunks. The efficiency of the proposed framework is demonstrated through multiple physics based simulations in Gazebo, where a CAD construction mesh is printed via multiple UAVs carrying materials whose volume is proportionate to a fraction of the total mesh volume., Comment: This paper has been accepted for publication at 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2023)

Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B-and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-To-end workflow for simultaneous detection of B-and T-cell clonality, translocations, CNAs, and sequence variants.