Project description:The metastatic form of Melanoma has a reported ten-year survival rate of approximately 15%. Clinical trials have shown modest success in a subset of patients. Particularly, combinational therapy using checkpoint blockade has shown the most success, but many patients do not respond. The patients that do respond to treatments often have a pre-existing antitumor immunity. To generate an optimal anti-tumor immune response, we have previously created a dendritic cell (DC) based adenovirus vaccine targeted against three common melanoma associated antigens: Tyrosinase, MART-1, and MAGE-A6 (TMM2). The vaccine was used in a Phase 1 clinical trial (NCT01622933) , where 35 patients were enrolled. Immature DC (iDC) were generated from patient monocytes (GM-CSF + IL-4), matured (mDC) using IFNG + LPS, and transduced with the adenovirus vaccine (AdVTMM2 DC). Patients received three intradermal injections of the vaccine over the course of one month. Human genome RNA microarray was used to analyze the gene expression profiles of the DC vaccine for each patient.
Project description:Gene expression profile in Locally Advanced Cervical Cancer patients The RNA total samples were obtain from 89 biopsies of patients with locally advanced cervical cancer (staged).
Project description:Extracorporeal photochemotherapy (ECP) is widely used to treat cutaneous T cell lymphoma, graft versus host disease and allografted organ rejection. Its clinical and experimental efficacy in both cancer immunotherapy and autoreactive disorders suggests a novel mechanism. This study reveals that ECP induces a high percentage of processed monocytes to enter the dendritic antigen presenting cell (DC) differentiation pathway, as determined by expression of relevant genes. The resulting DC are capable of processing and presentation of exogenous antigen and are largely maturationally synchronized, as assessed by the level of expression of co-stimulatory surface molecules. Principal component analysis of the ECP-induced monocyte transcriptome indicates that activation or suppression of more than 3500 genes produces a reproducible distinctive molecular signature. Pathway analysis suggests that DC maturation may be triggered by transient adherence of passaged monocytes to plasma proteins coating the ECP plastic ultraviolet exposure plate. Co-incubation with lymphocytes, simultaneously induced by ECP to undergo apoptosis, may accelerate conversion of monocytes to DC. The efficiency with which ECP induces new functional DC supports the possibility that these cells participate prominently in the clinical successes of the treatment. ECP may offer a practical source of DC for use in a spectrum of immunotherapeutic trials. We have used microarrays to analyze the expression of genes modulated by ECP treatment. Samples were obtained pre-treatment, after ECP on day 0 and after overnight incubation of the ECP product on 3 cutaneous T cell lymphoma patients, 3 graft-versus host disease patients and 6 normals.
Project description:Extracorporeal photochemotherapy (ECP) is widely used to treat cutaneous T cell lymphoma, graft versus host disease and allografted organ rejection. Its clinical and experimental efficacy in both cancer immunotherapy and autoreactive disorders suggests a novel mechanism. This study reveals that ECP induces a high percentage of processed monocytes to enter the dendritic antigen presenting cell (DC) differentiation pathway, as determined by expression of relevant genes. The resulting DC are capable of processing and presentation of exogenous antigen and are largely maturationally synchronized, as assessed by the level of expression of co-stimulatory surface molecules. Principal component analysis of the ECP-induced monocyte transcriptome indicates that activation or suppression of more than 3500 genes produces a reproducible distinctive molecular signature. Pathway analysis suggests that DC maturation may be triggered by transient adherence of passaged monocytes to plasma proteins coating the ECP plastic ultraviolet exposure plate. Co-incubation with lymphocytes, simultaneously induced by ECP to undergo apoptosis, may accelerate conversion of monocytes to DC. The efficiency with which ECP induces new functional DC supports the possibility that these cells participate prominently in the clinical successes of the treatment. ECP may offer a practical source of DC for use in a spectrum of immunotherapeutic trials. We have used microarrays to analyze the expression of genes modulated by ECP treatment.
Project description:Affymetrix oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged.
Project description:Natural killer (NK) cells are innate cytotoxic and immunoregulatory lymphocytes that have a central role in anti-tumor immunity and play a critical role in mediating cellular immunity in advanced cancer immunotherapies, such as dendritic cell (DC) vaccines. Our group recently tested a novel recombinant adenovirus-transduced autologous DC-based vaccine that simultaneously induces T cell responses against three melanoma-associated antigens for advanced melanoma patients. We examined the impact of this vaccine on the NK cell profile in melanoma patients. Relative immune cell population abundance was evaluated as previously described (Danaher et al. JITC, 2017). The abundance of the CD56dim NK cell gene signature was compared between pattients with better and worse outcome.
Project description:Expression profiling of tumor samples obtained during CA209-038 (ClinicalTrials.gov Identifier: NCT01621490). The purpose of this study is to evaluate pharmacodynamic changes of nivolumab and nivolumab in combination with ipilimumab treatment on the biomarkers measured in the peripheral blood and tumor tissues of subjects with advanced melanoma (unresectable or advanced). Samples are rumor core needle biopsies obtained at trial enrolment (i.e. Screen) and/or at Cycle 1 Day 29 (i.e.Week 4) from Subjects With Advanced Melanoma (Unresectable or Metastatic) treated with nivolumab (BMS-936558,MDX-1106) 3 mg/kg solution intravenously every 2 weeks on Bristol-Myers Squibb clinical trial protocol CA209-038 Part 1 . Cohort 2 patients have progressed on anti-CTLA4 (ipilimumab) monoclonal antibody therapy. Values are from an interim lock of the trial data in July 2014. Best overall response (BOR) was defined using RECIST 1.1 criteria: tumor assessments between date of first dose and the date of first objectively documented progression, or the date of non-missing subsequent anti-cancer therapy (whichever occurs first) were used to derive BOR. MPCT is Maximum reduction in tumor size (index lesions only) up to first progression, and is the value typically shown on a waterfall plot.
Project description:Immunotherapy improves the survival of patients with advanced melanoma, 40% of whom become long-term responders. However, not all patients respond to immunotherapy. Further knowledge about the processes involved in response and resistance to immunotherapy is still needed. In this study, clinical paraffin samples from fifty-two advanced melanoma patients treated with anti-PD1 inhibitors were assessed by high-throughput proteomics and RNA-seq. The obtained proteomics and transcriptomics data were analyzed using network analyses based on probabilistic graphical models to identify those biological processes involved in response to immunotherapy. Additionally, proteins related to overall survival were studied.
Project description:The monocyte-macrophage-dendritic cell (DC) (MMD) system exerts crucial functions that may modulate fibrogenesis in nonalcoholic steatohepatitis (NASH). We explored the cell characteristics, distribution and developmental trajectory of the liver MMD system in NASH mice with fibrosis using single-cell RNA sequensing (scRNA-seq).
Project description:Melanoma is the most serious and deadly form of skin cancer and with progression to advanced melanoma, the intrinsically disordered protein α-synuclein is upregulated to high levels; and while toxic to dopaminergic neurons in Parkinson’s disease, it is highly beneficial for primary and metastatic melanoma cells. To gain detailed insights, both at the level of the proteome and the transcriptome, into this exact opposite role of α-synuclein in advanced melanoma, we performed proteome and transcriptome studies of high-level α-synuclein-expressing primary and metastatic human melanoma cell lines and metastatic human melanoma xenografts treated with the small-molecule diphenyl-pyrazole compound anle138b, which binds to and interferes with the oligomeric structure of α-synuclein. Our data demonstrate that interfering with oligomerized α-synuclein in these melanoma cells and tumor xenografts leads to a substantial upregulation of major histocompatibility complex (MHC) proteins, which are important for enhancing anti-melanoma immune responses.