ORCID Profile
0000-0001-5926-3460
Current Organisation
Cell Therapy Manufacturing Center
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Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488762.V1
Abstract: Immune cell analysis by BMI. A. Immunohistochemistry (IHC) analysis for CD8-, CD45RO-, FOXP3-, CD68-, GZMB-, PD-1-, LAG-3-, and CD3-positive cells in overweight/obese (OW/OB) verse normal (NL) tumors as defined by body mass index from the MD Anderson Cancer Center (MDA) cohort. Line represents median +/- interquartile range each dot represents a single tumor. B. IHC analysis for PD-L1-, CD45RO-, FOXP3-, EOMES-, GZMB-, PD-1-, TBET-, and TBET:FOXP3-positive cells in OW/OB verse NL tumors as defined by body mass index from the Gide cohort. Line represents median +/- interquartile range each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488756.V1
Abstract: Direct metabolite measurements from a subset of The Cancer Genome Atlas (TCGA) cohort. Comparison of additional tricarboxylic acid cycle metabolites measured by liquid chromatography/mass spectrometry between metastatic melanoma tumors from overweight/obese (OW/OB) patients by body mass index (BMI) verse normal (NL) BMI from The Cancer Genome Atlas (TCGA). Lines represent mean +/- SEM each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488771
Abstract: Integrated gene set enrichment analysis by body mass index (BMI) with correction for S phase. This figure presents a dotplot of genes differentially up- or downregulated in OW/OB patients versus NL BMI patients. Red indicates upregulation in OW/OB verse NL. The far left column is all patients, and then, an analysis controlling for sex, cohort, and tissue site is shown in the 3 columns to the right.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488750
Abstract: Beta- ersity analysis stratified by sex based on Bray-Curtis dissimilarity represents microbiome s les with metastatic melanoma in terms of the two top principal components (explaining around 17% of variance) obtained from the principal coordinate analysis. Red dots are from overweight/obese (OW/OB) BMI patients, and blue dots are from normal (NL) BMI patients. Shading inside the dots indicates the female gender. This is a subgroup analysis of Figure 5B.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488735.V1
Abstract: Body mass index values by patient ID for all RNASeq cohorts.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488732
Abstract: RNASeq data for the MDA cohort (n=61) with associated clinical info.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488756
Abstract: Direct metabolite measurements from a subset of The Cancer Genome Atlas (TCGA) cohort. Comparison of additional tricarboxylic acid cycle metabolites measured by liquid chromatography/mass spectrometry between metastatic melanoma tumors from overweight/obese (OW/OB) patients by body mass index (BMI) verse normal (NL) BMI from The Cancer Genome Atlas (TCGA). Lines represent mean +/- SEM each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488768
Abstract: Reverse phase protein array of the PI3K pathway expression by BMI. Box plot represents the median bar with the box bounding IQR and whiskers the minimum and maximum values.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488747
Abstract: Inverse Simpson alpha ersity scores of the fecal microbiome by BMI in patients with metastatic melanoma stratified by sex. Box plot represents the median bar with the box bounding the IQR and whiskers the most extreme points within 1.5 x IQR. The red dots represent OW/OB patients and the blue dots represent NL patients by BMI. This is a subgroup analysis of Figure 5C.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488729
Abstract: Supplementary Table 1: Baseline characteristics for patients included in the integrated gene set enrichment analysis (Figure 2-3) by cohort Supplementary Table 6: The most frequent somatic alterations (alts) in patients with regionally metastatic melanoma by body mass index from The Cancer Genome Atlas cohort Supplemental Table 7: Integrated gene set enrichment analysis for pathways associated with fatty acid metabolism by body mass index Supplemental Table 8: Gene expression of selected genes of interest involved in fatty acid metabolism.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488768.V1
Abstract: Reverse phase protein array of the PI3K pathway expression by BMI. Box plot represents the median bar with the box bounding IQR and whiskers the minimum and maximum values.
Publisher: MDPI AG
Date: 22-10-2021
Abstract: Metastatic melanoma is a deadly malignancy with poor outcomes historically. Immuno-oncology (IO) agents, targeting immune checkpoint molecules such as cytotoxic T-lymphocyte associated protein-4 (CTLA-4) and programmed cell death-1 (PD-1), have revolutionized melanoma treatment and outcomes, achieving significant response rates and remarkable long-term survival. Despite these vast improvements, roughly half of melanoma patients do not achieve long-term clinical benefit from IO therapies and there is an urgent need to understand and mitigate mechanisms of resistance. MicroRNAs are key post-transcriptional regulators of gene expression that regulate many aspects of cancer biology, including immune evasion. We used network analysis to define two core microRNA–mRNA networks in melanoma tissues and cell lines corresponding to ‘MITF-low’ and ‘Keratin’ transcriptomic subsets of melanoma. We then evaluated expression of these core microRNAs in pre-PD-1-inhibitor-treated melanoma patients and observed that higher expression of miR-100-5p and miR-125b-5p were associated with significantly improved overall survival. These findings suggest that miR-100-5p and 125b-5p are potential markers of response to PD-1 inhibitors, and further evaluation of these microRNA–mRNA interactions may yield further insight into melanoma resistance to PD-1 inhibitors.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488747.V1
Abstract: Inverse Simpson alpha ersity scores of the fecal microbiome by BMI in patients with metastatic melanoma stratified by sex. Box plot represents the median bar with the box bounding the IQR and whiskers the most extreme points within 1.5 x IQR. The red dots represent OW/OB patients and the blue dots represent NL patients by BMI. This is a subgroup analysis of Figure 5C.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488738.V1
Abstract: Differential gene expression analysis for each subgroup.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488765.V1
Abstract: Integrated gene set enrichment analysis of subgroups by body mass index BMI. This figure compares gene expression between overweight/obese (OW/OB) and normal (NL) BMI patients with metastatic melanoma across subgroups by sex, cohort, and tissue site. Supplementary Figure 2 presents a dotplot of genes differentially up- or downregulated in OW/OB patients versus NL BMI patients by subgroups. Red indicates upregulation in OW/OB verse NL.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2202
DOI: 10.1158/1078-0432.22488759.V1
Abstract: Immune cell analysis by BMI and sex. A. Immunohistochemistry (IHC) analysis of the MDA cohort stratified by BMI and sex. Line represents median +/- interquartile range each dot represents a single tumor. B. IHC analysis of the Gide cohort stratified by BMI and sex. Line represents median +/- interquartile range each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-0023
DOI: 10.1158/1078-0432.22488732.V1
Abstract: RNASeq data for the MDA cohort (n=61) with associated clinical info.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488762
Abstract: Immune cell analysis by BMI. A. Immunohistochemistry (IHC) analysis for CD8-, CD45RO-, FOXP3-, CD68-, GZMB-, PD-1-, LAG-3-, and CD3-positive cells in overweight/obese (OW/OB) verse normal (NL) tumors as defined by body mass index from the MD Anderson Cancer Center (MDA) cohort. Line represents median +/- interquartile range each dot represents a single tumor. B. IHC analysis for PD-L1-, CD45RO-, FOXP3-, EOMES-, GZMB-, PD-1-, TBET-, and TBET:FOXP3-positive cells in OW/OB verse NL tumors as defined by body mass index from the Gide cohort. Line represents median +/- interquartile range each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488765
Abstract: Integrated gene set enrichment analysis of subgroups by body mass index BMI. This figure compares gene expression between overweight/obese (OW/OB) and normal (NL) BMI patients with metastatic melanoma across subgroups by sex, cohort, and tissue site. Supplementary Figure 2 presents a dotplot of genes differentially up- or downregulated in OW/OB patients versus NL BMI patients by subgroups. Red indicates upregulation in OW/OB verse NL.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488771.V1
Abstract: Integrated gene set enrichment analysis by body mass index (BMI) with correction for S phase. This figure presents a dotplot of genes differentially up- or downregulated in OW/OB patients versus NL BMI patients. Red indicates upregulation in OW/OB verse NL. The far left column is all patients, and then, an analysis controlling for sex, cohort, and tissue site is shown in the 3 columns to the right.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488744
Abstract: Differential gene expression analysis for covariates controlled.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488750.V1
Abstract: Beta- ersity analysis stratified by sex based on Bray-Curtis dissimilarity represents microbiome s les with metastatic melanoma in terms of the two top principal components (explaining around 17% of variance) obtained from the principal coordinate analysis. Red dots are from overweight/obese (OW/OB) BMI patients, and blue dots are from normal (NL) BMI patients. Shading inside the dots indicates the female gender. This is a subgroup analysis of Figure 5B.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488735
Abstract: Body mass index values by patient ID for all RNASeq cohorts.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488759
Abstract: Immune cell analysis by BMI and sex. A. Immunohistochemistry (IHC) analysis of the MDA cohort stratified by BMI and sex. Line represents median +/- interquartile range each dot represents a single tumor. B. IHC analysis of the Gide cohort stratified by BMI and sex. Line represents median +/- interquartile range each dot represents a single tumor.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488738
Abstract: Differential gene expression analysis for each subgroup.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.C.6532803
Abstract: AbstractPurpose: Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICI) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient body mass index (BMI). Experimental Design: Associations between BMI [normal (NL 25) or OW/OB (BMI ≥ 25)] and tumor or microbiome characteristics were examined in specimens from 782 patients with metastatic melanoma across 7 cohorts. DNA associations were evaluated in The Cancer Genome Atlas cohort. RNA sequencing from 4 cohorts ( i n /i = 357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients ( i x /i = 36) by LC/MS, and in flow-sorted melanoma tumor cells ( i x /i = 37) and patient-derived melanoma cell lines ( i x /i = 17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort ( i n /i = 371). Results: DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, ersity, and taxonomy of the fecal microbiome did not differ by BMI. Conclusions: These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies. i a href="lincancerres/article/doi/10.1158/1078-0432.CCR-22-3028" target="_blank" See related commentary by Smalley, p. 5 /a /i /
Publisher: Springer Science and Business Media LLC
Date: 09-07-2022
DOI: 10.1038/S41467-022-31510-1
Abstract: Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field.
Publisher: American Association for Cancer Research (AACR)
Date: 12-03-2120
DOI: 10.1158/1078-0432.22488744.V1
Abstract: Differential gene expression analysis for covariates controlled.
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.C.6532803.V1
Abstract: AbstractPurpose: Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICI) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient body mass index (BMI). Experimental Design: Associations between BMI [normal (NL 25) or OW/OB (BMI ≥ 25)] and tumor or microbiome characteristics were examined in specimens from 782 patients with metastatic melanoma across 7 cohorts. DNA associations were evaluated in The Cancer Genome Atlas cohort. RNA sequencing from 4 cohorts ( i n /i = 357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients ( i x /i = 36) by LC/MS, and in flow-sorted melanoma tumor cells ( i x /i = 37) and patient-derived melanoma cell lines ( i x /i = 17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort ( i n /i = 371). Results: DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, ersity, and taxonomy of the fecal microbiome did not differ by BMI. Conclusions: These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies. i a href="lincancerres/article/doi/10.1158/1078-0432.CCR-22-3028" target="_blank" See related commentary by Smalley, p. 5 /a /i /
Publisher: American Association for Cancer Research (AACR)
Date: 27-09-2022
DOI: 10.1158/1078-0432.CCR-22-2661
Abstract: Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICI) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient body mass index (BMI). Associations between BMI [normal (NL & 25) or OW/OB (BMI ≥ 25)] and tumor or microbiome characteristics were examined in specimens from 782 patients with metastatic melanoma across 7 cohorts. DNA associations were evaluated in The Cancer Genome Atlas cohort. RNA sequencing from 4 cohorts (n = 357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients (x = 36) by LC/MS, and in flow-sorted melanoma tumor cells (x = 37) and patient-derived melanoma cell lines (x = 17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort (n = 371). DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, ersity, and taxonomy of the fecal microbiome did not differ by BMI. These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies. See related commentary by Smalley, p. 5
Publisher: American Association for Cancer Research (AACR)
Date: 04-2023
DOI: 10.1158/1078-0432.22488729.V1
Abstract: Supplementary Table 1: Baseline characteristics for patients included in the integrated gene set enrichment analysis (Figure 2-3) by cohort Supplementary Table 6: The most frequent somatic alterations (alts) in patients with regionally metastatic melanoma by body mass index from The Cancer Genome Atlas cohort Supplemental Table 7: Integrated gene set enrichment analysis for pathways associated with fatty acid metabolism by body mass index Supplemental Table 8: Gene expression of selected genes of interest involved in fatty acid metabolism.
Location: United States of America
No related grants have been discovered for Chantale Bernatchez.