Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups

Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-Cre$^{ERT2}$::Smarcb1$^{flox/flox}$ model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway

Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Abstract Background Inflammatory breast cancer (IBC) is the most aggressive form of primary breast cancer. Using a custom-made breast cancer gene sequencing panel, we investigated somatic mutations in IBC to better understand the genomic differences compared with non-IBC and to consider new targeted therapy in IBC patients. Methods Targeted next-generation sequencing (NGS) of 91 candidate breast cancer-associated genes was performed on 156 fresh-frozen breast tumor tissues from IBC patients. Mutational profiles from 197 primary breast tumors from The Cancer Genome Atlas (TCGA) were used as non-IBC controls for comparison analysis. The mutational landscape of IBC was correlated with clinicopathological data and outcomes. Results After genotype calling and algorithmic annotations, we identified 392 deleterious variants in IBC and 320 variants in non-IBC cohorts, respectively. IBC tumors harbored more mutations than non-IBC (2.5 per sample vs. 1.6 per sample, p < 0.0001). Eighteen mutated genes were significantly different between the two cohorts, namely TP53, CDH1, NOTCH2, MYH9, BRCA2, ERBB4, POLE, FGFR3, ROS1, NOTCH4, LAMA2, EGFR, BRCA1, TP53BP1, ESR1, THBS1, CASP8, and NOTCH1. In IBC, the most frequently mutated genes were TP53 (43.0%), PIK3CA (29.5%), MYH9 (8.3%), NOTCH2 (8.3%), BRCA2 (7.7%), ERBB4 (7.1%), FGFR3 (6.4%), POLE (6.4%), LAMA2 (5.8%), ARID1A (5.1%), NOTCH4 (5.1%), and ROS1 (5.1%). After grouping 91 genes on 10 signaling pathways, we found that the DNA repair pathway for the triple-negative breast cancer (TNBC) subgroup, the RTK/RAS/MAPK and cell cycle pathways for the HR–/HER2+ subgroup, the DNA repair, RTK/RAS/MAPK, and NOTCH pathways for the HR+/HER2– subgroup, and the DNA repair, epigenome, and diverse pathways for the HR+/HER2+ subgroup were all significantly differently altered between IBC and non-IBC. PIK3CA mutation was independently associated with worse metastasis-free survival (MFS) in IBC since the median MFS for the PIK3CA mutant type was 26.0 months and for the PIK3CA wild type was 101.1 months (p = 0.002). This association was observed in TNBC (p = 0.04) and the HR–/HER2+ subgroups (p = 0.0003), but not in the HR+/HER2– subgroup of IBC. Conclusions Breast cancer-specific targeted NGS uncovered a high frequency of deleterious somatic mutations in IBC, some of which may be relevant for clinical management

Additional file 3: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Figure S1. Comparison of somatic mutation frequency between IBC and non-IBC in four subgroups. (a) The percentage of samples with somatic mutation in the TNBC subgroup; (b) the percentage of samples with somatic mutation in the HR–/HER2+ subgroup; (c) the percentage of samples with somatic mutation in the HR+/HER2– subgroup; (d) the percentage of samples with somatic mutation in the HR+/HER2+ subgroup. The gray bars indicate non-IBC, the black bars indicate IBC; *p < 0.05, **p < 0.01, ***p < 0.001. (PDF 52 kb

Dichotomy in Neutralizing Antibody Induction to Peptide-Conjugated Vaccine in Squalene Emulsion Contrast With Aluminum Hydroxide Formulation

International audienceW614A-3S peptide is a modified 3S motif of the HIV-gp41 (mutation W614A). We previously detected the presence of natural neutralizing antibodies directed against W614A-3S peptide (NAbs) in long-term non-progressor HIV + patients. Here, we compared the efficacy of W614A-3S peptide formulated in either squalene emulsion (SQE) or in aluminum hydroxide (Alum) in inducing broadly-NAbs (bNAbs). Rabbit and mouse models were used to screen the induction of bNAbs following 4 immunizations. SQE was more efficient than Alum formulation in inducing W614A-3S-specific bNAbs with up to 67%–93% of HIV strains neutralized. We then analyzed the quality of peptide-specific murine B cells by single-cell gene expression by quantitative reverse transcription-PCR and single-cell V(D)J sequencing. We found more frequent germinal center B cells in SQE than in Alum, albeit with a different gene expression profile. The V(D)J sequencing of W614A-3S-specific BCR showed significant differences in BCR sequences and validates the dichotomy between adjuvant formulations. All sixteen BCR sequences which were cloned were specific of peptide. Adjuvant formulations of W614A-3S-peptide-conjugated immunogen impact the quantity and quality of B cell immune responses at both the gene expression level and BCR sequence

Additional file 1: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Table S1. Pathological and clinical characteristics of non-IBC cohorts. (PDF 169 kb

Additional file 4: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Figure S2. Comparison of biological pathway between IBC and non-IBC in four subgroups. (a) The percentage of samples with alteration on 10 biological pathways in the TNBC subgroup; (b) the percentage of samples with alteration on 10 biological pathways in the HR–/HER2+ subgroup; (c) the percentage of samples with alteration on 10 biological pathways in the HR+/HER2– subgroup; (d) the percentage of samples with alteration on 10 biological pathways in the HR+/HER2+ subgroup. The gray bars indicate non-IBC, the black bars indicate IBC; *p < 0.05, **p < 0.01, ***p < 0.001. (PDF 41 kb

Additional file 2: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Table S2. BreastCurie gene panel for targeted NGS. (PDF 411 kb

Additional file 5: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Figure S3. DNA copy number alterations in the IBC cohort. The genes with DNA copy number alterations are grouped along the x axis, the percentage of samples with DNA copy number alterations shown on the y axis, DNA amplifications are indicated by black bars above the x axis, and DNA deletions are indicated by gray bars below the x axis. (PDF 164 kb

Additional file 6: of Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer

Figure S4. MFS curves stratified by PIK3CA mutation in three subgroups of IBC patients. (a) Kaplan-Meier estimates of MFS according to PIK3CA mutations in patients of the HR– subgroup, (b) Kaplan-Meier estimates of MFS according to PIK3CA mutations in patients of the HER2+ subgroup, (c) Kaplan-Meier estimates of MFS according to PIK3CA mutations in patients of the HR+ subgroup. (PDF 42 kb

Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer

International audienceAbstract Although heterogeneity of FAP+ Cancer-Associated Fibroblasts (CAF) has been described in breast cancer, their plasticity and spatial distribution remain poorly understood. Here, we analyze trajectory inference, deconvolute spatial transcriptomics at single-cell level and perform functional assays to generate a high-resolution integrated map of breast cancer (BC), with a focus on inflammatory and myofibroblastic (iCAF/myCAF) FAP+ CAF clusters. We identify 10 spatially-organized FAP+ CAF-related cellular niches, called EcoCellTypes, which are differentially localized within tumors. Consistent with their spatial organization, cancer cells drive the transition of detoxification-associated iCAF (Detox-iCAF) towards immunosuppressive extracellular matrix (ECM)-producing myCAF (ECM-myCAF) via a DPP4- and YAP-dependent mechanism. In turn, ECM-myCAF polarize TREM2+ macrophages, regulatory NK and T cells to induce immunosuppressive EcoCellTypes, while Detox-iCAF are associated with FOLR2+ macrophages in an immuno-protective EcoCellType. FAP+ CAF subpopulations accumulate differently according to the invasive BC status and predict invasive recurrence of ductal carcinoma in situ (DCIS), which could help in identifying low-risk DCIS patients eligible for therapeutic de-escalation