ABSTRACT
Unlike other malignancies, therapeutic options in pancreatic ductal adenocarcinoma (PDAC) are largely limited to cytotoxic chemotherapy without the benefit of molecular markers predicting response. Here we report tumor-cell-intrinsic chromatin accessibility patterns of treatment-naïve surgically resected PDAC tumors that were subsequently treated with (Gem)/Abraxane adjuvant chemotherapy. By ATAC-seq analyses of EpCAM+ PDAC malignant epithelial cells sorted from 54 freshly resected human tumors, we show here the discovery of a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identify two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further develop a chromatin accessibility microarray methodology termed "ATAC-array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validate ATAC-array technology in both the original ATAC-seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a low-cost, clinically feasible technology for assessing chromatin accessibility profiles.
Subject(s)
Chromatin Immunoprecipitation Sequencing/methods , Chromatin , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/genetics , Biomarkers, Tumor , Carcinoma, Pancreatic Ductal/diagnosis , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/metabolism , Cell Nucleus , Hepatocyte Nuclear Factor 1-beta/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Kruppel-Like Transcription Factors/genetics , Pancreatic Neoplasms/metabolism , Prognosis , Transcription Factors , Transcriptome , Pancreatic NeoplasmsABSTRACT
CD8 T cells are believed to play a key role in the immune control of human immunodeficiency virus-1 (HIV-1) infection in children as well as in adults. We have used an enhanced EliSpot (AmpliSpot) assay to quantitate CD8 T-cell responses directed to five human leucocyte antigen (HLA)-A2-presented HIV-1 epitopes derived from the key viral antigen Nef. Responses were assayed in one group of 21 children with vertically acquired HIV infection and one group of 19 adult subjects with chronic infection. The paediatric group displayed significantly weaker and more narrowly focused CD8 T-cell responses as compared with the adult subjects. Two epitopes stood out as the most frequently and strongly recognized, suggesting that they should be considered immunodominant in the CD8 T-cell response to HIV-1 Nef. Interestingly, the most frequently and strongly recognized epitope in both adults and children was previously identified in HLA-A2-transgenic mice, demonstrating the usefulness of such mice in finding natural viral epitopes. These findings indicate significant weakness in strength and breadth of the CD8 T-cell response to the target protein Nef in infected children and prompt renewed efforts into the immunology of vertically acquired HIV-1 infection.
Subject(s)
CD8-Positive T-Lymphocytes/immunology , Gene Products, nef/immunology , HIV Infections/transmission , HLA-A2 Antigen/immunology , Infectious Disease Transmission, Vertical , Adult , Animals , Child , Epitopes, T-Lymphocyte/immunology , HIV Infections/immunology , HIV-1/immunology , Humans , Immunity, Cellular , nef Gene Products, Human Immunodeficiency VirusABSTRACT
This cross-sectional study investigated the effect of early highly active antiretroviral therapy (HAART) on human immunodeficiency virus (HIV) type 1-specific CD8 T cell responses in children. HIV-1-specific CD8 T cell responses were quantified using an enzyme-linked immunospot assay to measure interferon-gamma-secreting cells. HIV-1-infected children were classified by time of HAART initiation prior to age 1 year or after age 2 years as early (n=24) or late (n=28) treated. The magnitude and breadth of the HIV-1-specific CD8 T cell response was significantly lower in children receiving early compared with late HAART treatment (P=.0007 and.0001, respectively). However, total CD8 T cell responses in the early HAART treatment group did not differ significantly from those of age-matched non-HAART-treated controls (n=30). Thus, the reduced magnitude and breadth of the HIV-1-specific CD8 T cell response in early HAART-treated children is due to their younger age.
Subject(s)
Anti-HIV Agents/pharmacology , CD8-Positive T-Lymphocytes/drug effects , HIV Infections/drug therapy , HIV Infections/immunology , Adolescent , Anti-HIV Agents/therapeutic use , CD8-Positive T-Lymphocytes/immunology , Child , Child, Preschool , HIV Infections/virology , HIV-1/drug effects , HIV-1/immunology , Humans , InfantABSTRACT
Five cases of methaemoglobinaemia, following exposure to industrial waste, are examined, investigated and managed successfully. The condition is discussed in detail.