Molecular changes during progression from nonmuscle invasive to advanced urothelial carcinoma

Molecular changes occurring during invasion and clinical progression of cancer are difficult to study longitudinally in patient-derived material. A unique feature of urothelial bladder cancer (UBC) is that patients frequently develop multiple nonmuscle invasive tumors, some of which may eventually progress to invade the muscle of the bladder wall. Here, we use a cohort of 73 patients that experienced a total of 357 UBC diagnoses to study the stability or change in detected molecular alterations during cancer progression. The tumors were subtyped by gene expression profiling and analyzed for hotspot mutations in FGFR3, PIK3CA and TERT, the most frequent early driver mutations in this tumor type. TP53 alterations, frequent in advanced UBC, were inferred from p53 staining pattern, and potential genomic alterations were inferred by gene expression pattern

Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair

Basal-like breast cancer (BBC) is a subtype of breast cancer with poor prognosis. Inherited mutations of BRCA1, a cancer susceptibility gene involved in double-strand DNA break (DSB) repair, lead to breast cancers that are nearly always of the BBC subtype; however, the precise molecular lesions and oncogenic consequences of BRCA1 dysfunction are poorly understood. Here we show that heterozygous inactivation of the tumor suppressor gene Pten leads to the formation of basal-like mammary tumors in mice, and that loss of PTEN expression is significantly associated with the BBC subtype in human sporadic and BRCA1-associated hereditary breast cancers. In addition, we identify frequent gross PTEN mutations, involving intragenic chromosome breaks, inversions, deletions and micro copy number aberrations, specifically in BRCA1-deficient tumors. These data provide an example of a specific and recurrent oncogenic consequence of BRCA1-dependent dysfunction in DNA repair and provide insight into the pathogenesis of BBC with therapeutic implications. These findings also argue that obtaining an accurate census of genes mutated in cancer will require a systematic examination for gross gene rearrangements, particularly in tumors with deficient DSB repair

Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

Purpose: Although CD19 chimeric antigen receptor T cells (CAR-T) therapy has shown remarkable success in B-cell malignancies, a substantial fraction of patients do not obtain a long-term clinical response. This could be influenced by the quality of the individual CAR-T infusion product. To shed some light on this, clinical outcome was correlated to characteristics of CAR-T infusion products. Patients and Methods: In this phase II study, patients with B-cell lymphoma (n = 23) or leukemia (n = 1) received one or two infusions of third-generation CD19-directed CAR-Ts (2 × 108/m2). The clinical trial was registered at clinicaltrials.gov: NCT03068416. We investigated the transcriptional profile of individual CD19 CAR-T infusion products using targeted single-cell RNA sequencing and multicolor flow cytometry. Results: Two CAR-T infusions were not better than one in the settings used in this study. As for the CAR-T infusion products, we found that effector-like CD8+CAR-Ts with a high polyfunctionality, high cytotoxic and cytokine production profile, and low dysfunctional signature were associated with clinical response. An extended ex vivo expansion time during CAR-T manufacturing negatively influenced the proportion of effector CD8+CAR-Ts in the infusion product. Conclusions: We identified cell-intrinsic characteristics of effector CD8+CAR-Ts correlating with response that could be used as an indicator for clinical outcome. The results in the study also serve as a guide to CAR-T manufacturing practices.De två första författarna delar förstaförfattarskapetDe två sista författarna delar sistaförfattarskapet</p

Hierarchical clustering of 69 tumor samples with available gene expression data

Clustering was based on 364 genes from the intrinsic gene list published by Sørlie and colleagues [] that matched our cDNA clones. Colored boxes indicate classification of each tumor into subtypes/subgroups. Filled or open boxes indicate the percentage of cells in each tumor positive for the CD44/CD24and CD44/CD24phenotypes as determined by immunohistochemistry. SR, steroid receptor. Hu classification, Hu and colleagues [].<p><b>Copyright information:</b></p><p>Taken from "The CD44/CD24phenotype is enriched in basal-like breast tumors"</p><p>http://breast-cancer-research.com/content/10/3/R53</p><p>Breast Cancer Research : BCR 2008;10(3):R53-R53.</p><p>Published online 17 Jun 2008</p><p>PMCID:PMC2481503.</p><p></p

Immunohistochemical double-staining of human breast tumors for CD44 and CD24

CD44 is stained with Permanent Red and CD24 with diaminobenzidene (DAB). Magnification × 20. A tumor positive for both CD44/CD24(white arrow) and CD44/CD24(black arrow) cancer cells, although the predominant phenotype is CD44/CD24. Almost all cells in this tumor are CD44/CD24. No CD24 staining is seen. A tumor with predominantly CD44/CD24cells. A few CD44/CD24cells are also present (black arrow). A tumor positive for the CD44/CD24phenotype. No CD44 staining is present.<p><b>Copyright information:</b></p><p>Taken from "The CD44/CD24phenotype is enriched in basal-like breast tumors"</p><p>http://breast-cancer-research.com/content/10/3/R53</p><p>Breast Cancer Research : BCR 2008;10(3):R53-R53.</p><p>Published online 17 Jun 2008</p><p>PMCID:PMC2481503.</p><p></p

Supplementary Table S11 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

List of antibodies and dyes used for flow cytometry assays</p

Supplementary Figure S8 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

Supplementary Figure S8. Functional scores amongst the CD8+ CAR-T clusters.</p

Supplementary Figure S7 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

Supplementary Figure S7. Cluster specifications of single-cell RNA sequenced CAR-T infusion products</p

Supplementary Table S5 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

Pearson correlation of genes related to culture time</p

Supplementary Table S12 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients

List of antibodies and dyes used for functionality flow cytometry assays</p