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10 result(s) for "Demangel, Delphine"
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Whole-Exome Sequencing-Based Linkage Analysis of Multiple Myeloma (MM) and Monoclonal Gammopathy of Undetermined Significance (MGUS) Pedigrees
Background/Objectives: Family history is a known risk factor for multiple myeloma (MM) and its precursor condition, monoclonal gammopathy of undetermined significance (MGUS). Previous genome-wide association studies (GWASs) have identified 35 common loci associated with MM risk and 21 associated with MGUS. The objective of this study was to identify less common and rare genetic loci predisposing to MM/MGUS through whole-exome sequencing (WES)-based linkage analysis. Methods:Multipoint linkage analysis was conducted using the Multipoint Engine for Rapid Likelihood Inference (MERLIN) with the Lander–Green algorithm on germline WES data from 79 pedigrees with 2 or more affected relatives (120 MM, 86 MGUS, and 21 unaffected). Genome-wide linkage was evaluated using 12,946 independent single-nucleotide variants (linkage disequilibrium r2 < 0.05). Results: Significant linkage was observed at chromosome 6q22.33–q24.2 by the non-parametric model (logarithm-of-odds (LOD) = 3.3) and suggestive linkage by the dominant parametric model (heterogeneity LOD (HLOD) = 2.5). Fourteen rare variants within this region were prioritized using family-specific partial LOD scores and in silico functional prediction tools. Nine of these variants, REPS1, THEMIS, TAAR6, AHI1, VNN1, VNN3, MTFR2/FAM54A, LAMA2, and PHACTR2, overlapped immune-regulatory regions in blood cell lines and were not previously identified in GWASs. Conclusions: This study demonstrates the utility of applying a linkage analysis framework to familial WES data for identifying genomic regions and candidate genes that may contribute to MM/MGUS predisposition. These findings provide new insight into the inherited risk and etiology of familial MM and MGUS.
Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk
The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.
Whole-Exome Sequencing-Based Linkage Analysis of Multiple Myeloma Pedigrees
People with relatives who have multiple myeloma or its early condition, monoclonal gammopathy of undetermined significance, face higher risk. Most research has focused on common DNA changes, but these do not explain all inherited risk. We studied 79 families with two or more affected relatives and examined their protein-coding DNA to find regions that are passed down together with disease. We found strong evidence that a stretch of chromosome 6 (q22.33–q24.2) is linked to risk. Within this region, we highlighted 14 rare variants predicted to affect gene function; nine reside in areas that regulate immune cells. This work shows that family-based DNA linkage can uncover risk regions missed by previous approaches and points to new genes and pathways that may help explain—and ultimately predict—risk for multiple myeloma and its precursor.
Genetically determined telomere length and multiple myeloma risk and outcome
Telomeres are involved in processes like cellular growth, chromosomal stability, and proper segregation to daughter cells. Telomere length measured in leukocytes (LTL) has been investigated in different cancer types, including multiple myeloma (MM). However, LTL measurement is prone to heterogeneity due to sample handling and study design (retrospective vs. prospective). LTL is genetically determined; genome-wide association studies identified 11 SNPs that, combined in a score, can be used as a genetic instrument to measure LTL and evaluate its association with MM risk. This approach has been already successfully attempted in various cancer types but never in MM. We tested the “teloscore” in 2407 MM patients and 1741 controls from the International Multiple Myeloma rESEarch (IMMeNSE) consortium. We observed an increased risk for longer genetically determined telomere length (gdTL) (OR = 1.69; 95% CI 1.36–2.11; P = 2.97 × 10−6 for highest vs. lowest quintile of the score). Furthermore, in a subset of 1376 MM patients we tested the relationship between the teloscore and MM patients survival, observing a better prognosis for longer gdTL compared with shorter gdTL (HR = 0.93; 95% CI 0.86–0.99; P = 0.049). In conclusion, we report convincing evidence that longer gdTL is a risk marker for MM risk, and that it is potentially involved in increasing MM survival.
Sensitivity and gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868
Purpose The need for new treatment options for acute myeloid leukemia (AML) is increasing. AS602868 is a novel investigational drug with reported activity on AML cells. Methods We studied gene expression profiles in AML blasts exposed to AS602868 in order to better understand its mechanism of action. We analyzed the in vitro cytotoxicity of AS602868 alone or in combination with daunorubicin, etoposide or cytarabine. To document AS602868-induced IKK2 inhibition in fresh AML cells, a flow cytometry analysis of IκB was performed. Finally, the effect of AS602868 on gene expression in fresh AML cells was analyzed. Results The results show that AML cells are globally as sensitive to AS602868 as they are to cytarabine, with large interindividual variations. Combinations with conventional antileukemic agents showed enhanced cytotoxic activity in subsets of patients. IKK2 appeared to be effectively inhibited by 100 μM AS602868 in fresh leukemic cells. Gene expression profiling and gene ontology analyses identified several groups of genes induced/inhibited by exposure to AS602868 and/or exhibiting a correlation with sensitivity to this agent in vitro. Of note, the expression of several genes related to immune function was found to be significantly altered after exposure to AS602868. Conclusion These data suggest that AS602868 is cytotoxic against fresh human AML blasts and provide insights regarding the mechanisms of cytotoxicity.
Sensitivity and gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868
PURPOSE: The need for new treatment options for acute myeloid leukemia (AML) is increasing. AS602868 is a novel investigational drug with reported activity on AML cells. METHODS: We studied gene expression profiles in AML blasts exposed to AS602868 in order to better understand its mechanism of action. We analyzed the in vitro cytotoxicity of AS602868 alone or in combination with daunorubicin, etoposide or cytarabine. To document AS602868-induced IKK2 inhibition in fresh AML cells, a flow cytometry analysis of IκB was performed. Finally, the effect of AS602868 on gene expression in fresh AML cells was analyzed. RESULTS: The results show that AML cells are globally as sensitive to AS602868 as they are to cytarabine, with large interindividual variations. Combinations with conventional antileukemic agents showed enhanced cytotoxic activity in subsets of patients. IKK2 appeared to be effectively inhibited by 100 μM AS602868 in fresh leukemic cells. Gene expression profiling and gene ontology analyses identified several groups of genes induced/inhibited by exposure to AS602868 and/or exhibiting a correlation with sensitivity to this agent in vitro. Of note, the expression of several genes related to immune function was found to be significantly altered after exposure to AS602868. CONCLUSION: These data suggest that AS602868 is cytotoxic against fresh human AML blasts and provide insights regarding the mechanisms of cytotoxicity.
Novel pedigree analysis implicates DNA repair and chromatin remodeling in Multiple Myeloma risk
The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance, a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691*, p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly, p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.
Electron Backscatter Diffraction and Transmission Kikuchi Diffraction Analysis of an Austenitic Stainless Steel Subjected to Surface Mechanical Attrition Treatment and Plasma Nitriding
Austenitic 316L stainless steel can be used for orthopedic implants due to its biocompatibility and high corrosion resistance. Its range of applications in this field could be broadened by improving its wear and friction properties. Surface properties can be modified through surface hardening treatments. The effects of such treatments on the microstructure of the alloy were investigated here. Surface Mechanical Attrition Treatment (SMAT) is a surface treatment that enhances mechanical properties of the material surface by creating a thin nanocrystalline layer. After SMAT, some specimens underwent a plasma nitriding process to further enhance their surface properties. Using electron backscatter diffraction, transmission Kikuchi diffraction, energy dispersive spectroscopy, and transmission electron microscopy, the microstructural evolution of the stainless steel after these different surface treatments was characterized. Microstructural features investigated include thickness of the nanocrystalline layer, size of the grains within the nanocrystalline layer, and depth of diffusion of nitrogen atoms within the material.
Electrophoretic Deposition of Hydroxyapatite and 58S Bioactive Glass Coatings on the Ti6Al4V Alloy Subjected to Surface Mechanical Attrition Treatment
Hydroxyapatite (HAP) and 58S Bioactive Glasses (BG) coatings are successfully synthesized by Electrophoretic Deposition (EPD) on Ti6Al4V alloy subjected to Surface Mechanical Attrition Treatment (SMAT). This process uses steel balls impacts on the Ti6Al4V surface to improve its mechanical properties. However when the Ti6Al4V substrate is treated by SMAT the industrial plasma spray technique is not efficient to obtain adherent HAP coatings. This problem is mainly related to the modifications of the Ti6Al4V surface topography due to the SMAT process. Therefore, in this work we demonstrate that EPD offers an efficient solution to solve this technical problem. Indeed we obtain a homogeneous and adherent HAP coating on the SMATed Ti6Al4V surface from a suspension of nanoparticles in ethanol. Moreover EPD is successfully employed to produce a 58S BG coating on the SMATed Ti6Al4V surface. Scanning Electron Microscopy (SEM) associated to Energy Dispersive X-Ray Spectroscopy (EDXS) reveals that the coatings obtained by EPD are adherent and compact without alteration of their chemical composition.