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1.
Nat Commun ; 11(1): 1395, 2020 03 13.
Article in English | MEDLINE | ID: mdl-32170083

ABSTRACT

Oncolytic viruses offer an in situ vaccination approach to activate tumor-specific T cell responses. However, the upregulation of PD-L1 expression on tumor cells and immune cells leads to tumor resistance to oncolytic immunotherapy. In this study, we generate an engineered oncolytic virus that coexpresses a PD-L1 inhibitor and GM-CSF. We find that the oncolytic virus is able to secrete the PD-L1 inhibitor that systemically binds and inhibits PD-L1 on tumor cells and immune cells. Importantly, the intratumoral injection with the oncolytic virus overcomes PD-L1-mediated immunosuppression during both the priming and effector phases, provokes systemic T cell responses against dominant and subdominant neoantigen epitopes derived from mutations, and leads to an effective rejection of both virus-injected and distant tumors. In summary, this engineered oncolytic virus is able to activate tumor neoantigen-specific T cell responses, providing a potent, individual tumor-specific oncolytic immunotherapy for cancer patients, especially those resistant to PD-1/PD-L1 blockade therapy.


Subject(s)
B7-H1 Antigen/antagonists & inhibitors , Oncolytic Virotherapy , Oncolytic Viruses/genetics , Oncolytic Viruses/metabolism , Animals , Antigens, Neoplasm/metabolism , Antineoplastic Agents , B7-H1 Antigen/genetics , B7-H1 Antigen/metabolism , CD8-Positive T-Lymphocytes/immunology , Cell Line, Tumor , Disease Models, Animal , Genetic Engineering , Granulocyte-Macrophage Colony-Stimulating Factor/immunology , HEK293 Cells , Humans , Immunosuppression Therapy , Immunotherapy , Mice , Mice, Inbred C57BL , Oncolytic Viruses/immunology , Recombinant Proteins
2.
Cancers (Basel) ; 11(12)2019 Dec 01.
Article in English | MEDLINE | ID: mdl-31805690

ABSTRACT

Dendritic cells (DCs) are potent antigen-presenting cells that play a critical role in activating cellular and humoral immune responses. DC-based tumor vaccines targeting tumor-associated antigens (TAAs) have been extensively tested and demonstrated to be safe and potent in inducing anti-TAA immune responses in cancer patients. Sipuleucel-T (Provenge), a cancer vaccine of autologous DCs loaded with TAA, was approved by the United States Food and Drug Administration (FDA) for the treatment of castration-resistant prostate cancer. Sipuleucel-T prolongs patient survival, but has little or no effect on clinical disease progression or biomarker kinetics. Due to the overall limited clinical efficacy of tumor vaccines, there is a need to enhance their potency. PD-L1 is a key immune checkpoint molecule and is frequently overexpressed on tumor cells to evade antitumor immune destruction. Repeated administrations of PD-L1 or PD-1 antibodies have induced sustained tumor regression in a fraction of cancer patients. In this study, we tested whether vaccinations with DCs, loaded with a PD-L1 immunogen (PDL1-Vax), are able to induce anti-PD-L1 immune responses. We found that DCs loaded with PDL1-Vax induced anti-PD-L1 antibody and T cell responses in immunized mice and that PD-L1-specific CTLs had cytolytic activities against PD-L1+ tumor cells. We demonstrated that vaccination with PDL1-Vax DCs potently inhibited the growth of PD-L1+ tumor cells. In summary, this study demonstrates for the first time the principle and feasibility of DC vaccination (PDL1-Vax) to actively induce anti-PD-L1 antibody and T cell responses capable of inhibiting PD-L1+ tumor growth. This novel anti-PD-L1 vaccination strategy could be used for cancer treatment and prevention.

3.
Nat Med ; 25(6): 947-953, 2019 06.
Article in English | MEDLINE | ID: mdl-31011207

ABSTRACT

Anti-CD19 chimeric antigen receptor (CAR) T cell therapies can cause severe cytokine-release syndrome (CRS) and neurotoxicity, impeding their therapeutic application. Here we generated a new anti-CD19 CAR molecule (CD19-BBz(86)) derived from the CD19-BBz prototype bearing co-stimulatory 4-1BB and CD3ζ domains. We found that CD19-BBz(86) CAR T cells produced lower levels of cytokines, expressed higher levels of antiapoptotic molecules and proliferated more slowly than the prototype CD19-BBz CAR T cells, although they retained potent cytolytic activity. We performed a phase 1 trial of CD19-BBz(86) CAR T cell therapy in patients with B cell lymphoma (ClinicalTrials.gov identifier NCT02842138 ). Complete remission occurred in 6 of 11 patients (54.5%) who each received a dose of 2 × 108-4 × 108 CD19-BBz(86) CAR T cells. Notably, no neurological toxicity or CRS (greater than grade 1) occurred in any of the 25 patients treated. No significant elevation in serum cytokine levels after CAR T cell infusion was detected in the patients treated, including in those who achieved complete remission. CD19-BBz(86) CAR T cells persistently proliferated and differentiated into memory cells in vivo. Thus, therapy with the new CD19-BBz(86) CAR T cells produces a potent and durable antilymphoma response without causing neurotoxicity or severe CRS, representing a safe and potent anti-CD19 CAR T cell therapy.


Subject(s)
Antigens, CD19/immunology , Immunotherapy, Adoptive/methods , Lymphoma, B-Cell/immunology , Lymphoma, B-Cell/therapy , Receptors, Chimeric Antigen/immunology , Adult , Aged , Antigens, CD19/genetics , Cytokines/blood , Female , Humans , Immunotherapy, Adoptive/adverse effects , Lymphoma, B-Cell/diagnostic imaging , Male , Middle Aged , Positron Emission Tomography Computed Tomography , Remission Induction , T-Lymphocytes/immunology , Treatment Outcome , Young Adult
4.
JCI Insight ; 3(3)2018 02 08.
Article in English | MEDLINE | ID: mdl-29415891

ABSTRACT

BACKGROUND: DC-based tumor vaccines have had limited clinical success thus far. SOCS1, a key inhibitor of inflammatory cytokine signaling, is an immune checkpoint regulator that limits DC immunopotency. METHODS: We generated a genetically modified DC (gmDC) vaccine to perform immunotherapy. The adenovirus (Ad-siSSF) delivers two tumor-associated antigens (TAAs), survivin and MUC1; secretory bacterial flagellin for DC maturation; and an RNA interference moiety to suppress SOCS1. A 2-stage phase I trial was performed for patients with relapsed acute leukemia after allogenic hematopoietic stem cell transplantation: in stage 1, we compared the safety and efficacy between gmDC treatment (23 patients) and standard donor lymphocyte infusion (25 patients); in stage 2, we tested the efficacy of the gmDC vaccine for 12 acute myeloid leukemia (AML) patients with early molecular relapse. RESULTS: gmDCs elicited potent TAA-specific CTL responses in vitro, and the immunostimulatory activity of gmDC vaccination was demonstrated in rhesus monkeys. A stage 1 study established that this combinatory gmDC vaccine is safe in acute leukemia patients and yielded improved survival rate. In stage 2, we observed a complete remission rate of 83% in 12 relapsed AML patients. Overall, no grade 3 or grade 4 graft-versus-host disease incidence was detected in any of the 35 patients enrolled. CONCLUSIONS: This study, with combinatory modifications in DCs, demonstrates the safety and efficacy of SOCS1-silenced DCs in treating relapsed acute leukemia. TRIAL REGISTRATION: ClinicalTrials.gov NCT01956630. FUNDING: National Institute of Health (R01CA90427); the Key New Drug Development and Manufacturing Program of the "Twelfth Five-Year Plan" of China (2011ZX09102-001-29); and Clinical Application Research of Beijing (Z131107002213148).


Subject(s)
Cancer Vaccines/administration & dosage , Dendritic Cells/immunology , Leukemia, Myeloid, Acute/therapy , Neoplasm Recurrence, Local/therapy , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Adenoviridae/genetics , Adolescent , Adult , Antigens, Neoplasm/genetics , Antigens, Neoplasm/immunology , Cancer Vaccines/adverse effects , Cancer Vaccines/genetics , Cancer Vaccines/immunology , Cell Engineering/methods , Child , Dendritic Cells/transplantation , Female , Follow-Up Studies , Genetic Vectors/genetics , Graft vs Host Disease/epidemiology , Graft vs Host Disease/immunology , Hematopoietic Stem Cell Transplantation/adverse effects , Humans , Immunotherapy, Adoptive/methods , Leukemia, Myeloid, Acute/immunology , Leukemia, Myeloid, Acute/mortality , Lymphocyte Transfusion , Male , Middle Aged , Neoplasm Recurrence, Local/immunology , Neoplasm Recurrence, Local/mortality , Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology , Precursor Cell Lymphoblastic Leukemia-Lymphoma/mortality , Survival Analysis , Transplantation, Autologous , Treatment Outcome , Young Adult
5.
Sci Rep ; 6: 33519, 2016 09 19.
Article in English | MEDLINE | ID: mdl-27641744

ABSTRACT

Circulating tumor DNA (ctDNA) in peripheral blood is a "liquid biopsy" that contains representative tumor information including gene mutations. Additionally, repeated ctDNA samples can be easily obtained to monitor response to treatment and disease progression, which may be especially valuable to lung cancer patients with tumors that cannot be easily biopsied or removed. To investigate the changes in ctDNA after surgical tumor resection, tumor and blood samples obtained before and after surgery were collected prospectively from 41 non-small lung cancer (NSCLC) patients. Somatic driver mutations in tumor DNA (tDNA) and pre- and post-op plasma ctDNA sample pairs were identified by targeted sequencing in several genes including EGFR, KRAS, and TP53 with an overall study concordance of 78.1% and sensitivity and specificity of 69.2% and 93.3%, respectively. Importantly, the frequency of 91.7% of ctDNA mutations decreased after surgery and these changes were observed as little as 2 days post-op. Moreover, the presence of ctDNA had a higher positive predictive value than that of six tumor biomarkers in current clinical use. This study demonstrates the use of targeted sequencing to reliably identify ctDNA changes in response to treatment, indicating a potential utility of this approach in the clinical management of NSCLC.


Subject(s)
Circulating Tumor DNA/blood , Lung Neoplasms/blood , Lung Neoplasms/surgery , Adult , Aged , Biomarkers, Tumor/blood , Carcinoma, Non-Small-Cell Lung/blood , Carcinoma, Non-Small-Cell Lung/surgery , Female , Humans , Male , Middle Aged , Mutation/genetics , Mutation Rate
6.
Sci Rep ; 6: 31985, 2016 08 24.
Article in English | MEDLINE | ID: mdl-27555497

ABSTRACT

Circulating tumor DNA (ctDNA) isolated from peripheral blood has recently been shown to be an alternative source to detect gene mutations in primary tumors; however, most previous studies have focused on advanced stage cancers, and few have evaluated ctDNA detection in early-stage lung cancer. In the present study, blood and tumor samples were collected prospectively from 58 early-stage non-small lung cancer (NSCLC) patients (stages IA, IB, and IIA) and a targeted sequencing approach was used to detect somatic driver mutations in matched tumor DNA (tDNA) and plasma ctDNA. We identified frequent driver mutations in plasma ctDNA and tDNA in EGFR, KRAS, PIK3CA, and TP53, and less frequent mutations in other genes, with an overall study concordance of 50.4% and sensitivity and specificity of 53.8% and 47.3%, respectively. Cell-free (cfDNA) concentrations were found to be significantly associated with some clinical features, including tumor stage and subtype. Importantly, the presence of cfDNA had a higher positive predictive value than that of currently used protein tumor biomarkers. This study demonstrates the feasibility of identifying plasma ctDNA mutations in the earliest stage lung cancer patients via targeted sequencing, demonstrating a potential utility of targeted sequencing of ctDNA in the clinical management of NSCLC.


Subject(s)
Carcinoma, Non-Small-Cell Lung/pathology , Circulating Tumor DNA/blood , Lung Neoplasms/pathology , Adult , Aged , Aged, 80 and over , Antigens, Tumor-Associated, Carbohydrate/blood , Biomarkers, Tumor/blood , CA-125 Antigen/blood , Carcinoma, Non-Small-Cell Lung/genetics , Circulating Tumor DNA/chemistry , Class I Phosphatidylinositol 3-Kinases/genetics , DNA, Neoplasm/blood , DNA, Neoplasm/chemistry , ErbB Receptors/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/genetics , Male , Membrane Proteins/blood , Middle Aged , Mutation , Neoplasm Staging , Proto-Oncogene Proteins p21(ras)/genetics , Sequence Analysis, DNA , Tumor Suppressor Protein p53/genetics
7.
Cancer Lett ; 370(2): 324-31, 2016 Jan 28.
Article in English | MEDLINE | ID: mdl-26582655

ABSTRACT

Non-small cell lung cancers (NSCLC) have unique mutation patterns, and some of these mutations may be used to predict prognosis or guide patient treatment. Mutation profiling before and during treatment often requires repeated tumor biopsies, which is not always possible. Recently, cell-free, circulating tumor DNA (ctDNA) isolated from blood plasma has been shown to contain genetic mutations representative of those found in the primary tumor tissue DNA (tDNA), and these samples can readily be obtained using non-invasive techniques. However, there are still no standardized methods to identify mutations in ctDNA. In the current study, we used a targeted sequencing approach with a semi-conductor based next-generation sequencing (NGS) platform to identify gene mutations in matched tDNA and ctDNA samples from 42 advanced-stage NSCLC patients from China. We identified driver mutations in matched tDNA and ctDNA in EGFR, KRAS, PIK3CA, and TP53, with an overall concordance of 76%. In conclusion, targeted sequencing of plasma ctDNA may be a feasible option for clinical monitoring of NSCLC in the near future.


Subject(s)
Carcinoma, Non-Small-Cell Lung/genetics , DNA, Neoplasm/blood , Lung Neoplasms/genetics , Adult , Aged , Carcinoma, Non-Small-Cell Lung/pathology , Female , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/pathology , Male , Middle Aged , Mutation , Neoplasm Staging
8.
Sci Rep ; 5: 13755, 2015 Sep 08.
Article in English | MEDLINE | ID: mdl-26348977

ABSTRACT

B cell-mediated antibody response plays critical roles in protective immunity, as well as in the pathogenesis of allergic and autoimmune diseases. Epigenetic histone and DNA modifications regulate gene transcription and immunity; however, so far, little is known about the role of epigenetic regulation in antibody responses. In this study, we found that mice deficient in the histone H2A deubiquitinase MYSM1, despite their severe defect in B cell development, exhibit an enhanced antibody response against both T cell-dependent and independent antigens. We revealed that MYSM1 intrinsically represses plasma cell differentiation and antibody production. Mechanistic studies demonstrated that MYSM1 is a transcriptional activator of Pax5, the repressors of plasma cell differentiation, by facilitating key transcriptional factor recruitment and coordinating histone modifications at the Pax5 loci. Hence, this study uncovers a critical role for MYSM1 in epigenetically repressing plasma cell differentiation and antibody production, in addition to its opposing, active role in B cell development. Importantly, this study further provides a new target and strategy to modulate antibody production and responses with profound therapeutic implications.


Subject(s)
Antibody Formation/genetics , Endopeptidases/genetics , Epigenesis, Genetic , Gene Expression Regulation , Animals , B-Lymphocytes/cytology , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , Cell Differentiation/genetics , Cell Differentiation/immunology , DNA-Binding Proteins/genetics , Immunoglobulins/blood , Immunoglobulins/immunology , Immunologic Memory , Lymphocyte Activation/immunology , Mice , Mice, Knockout , PAX5 Transcription Factor/genetics , Plasma Cells/cytology , Plasma Cells/immunology , Plasma Cells/metabolism , Positive Regulatory Domain I-Binding Factor 1 , Protein Binding , Proto-Oncogene Proteins/metabolism , Regulatory Factor X Transcription Factors , Trans-Activators/metabolism , Transcription Factors/genetics , Ubiquitin-Specific Proteases
9.
Cancer Inform ; 14: 83-93, 2015.
Article in English | MEDLINE | ID: mdl-26244006

ABSTRACT

Lung cancer remains the most prevalent malignancy and the primary cause of cancer-related deaths worldwide. Unique mutations patterns can be found in lung cancer subtypes, in individual cancers, or within a single tumor, and drugs that target these genetic mutations and signal transduction pathways are often beneficial to patients. In this study, we used the Ion Torrent AmpliSeq Cancer Panel to sequence 737 loci from 45 cancer-related genes and oncogenes to identify genetic mutations in 48 formalin-fixed, paraffin-embedded (FFPE) human lung cancer samples from Chinese patients. We found frequent mutations in EGFR, KRAS, PIK3CA, and TP53 genes. Moreover, we observed that a portion of the lung cancer samples harbored two or more mutations in these key genes. This study demonstrates the feasibility of using the Ion Torrent sequencing to efficiently identify genetic mutations in individual tumors for targeted lung cancer therapy.

10.
J Hum Genet ; 60(10): 589-96, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26134512

ABSTRACT

Colorectal cancer (CRC) is widespread with significant mortality. Both inherited and sporadic mutations in various signaling pathways influence the development and progression of the cancer. Identifying genetic mutations in CRC is important for optimal patient treatment and many approaches currently exist to uncover these mutations, including next-generation sequencing (NGS) and commercially available kits. In the present study, we used a semiconductor-based targeted DNA-sequencing approach to sequence and identify genetic mutations in 91 human rectal cancer samples. Analysis revealed frequent mutations in KRAS (58.2%), TP53 (28.6%), APC (16.5%), FBXW7 (9.9%) and PIK3CA (9.9%), and additional mutations in BRAF, CTNNB1, ERBB2 and SMAD4 were also detected at lesser frequencies. Thirty-eight samples (41.8%) also contained two or more mutations, with common combination mutations occurring between KRAS and TP53 (42.1%), and KRAS and APC (31.6%). DNA sequencing for individual cancers is of clinical importance for targeted drug therapy and the advantages of such targeted gene sequencing over other NGS platforms or commercially available kits in sensitivity, cost and time effectiveness may aid clinicians in treating CRC patients in the near future.


Subject(s)
High-Throughput Nucleotide Sequencing , Neoplasm Proteins/genetics , Rectal Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Mutation
11.
Hum Genomics ; 9: 2, 2015 Feb 08.
Article in English | MEDLINE | ID: mdl-25757876

ABSTRACT

Breast cancer is the most common malignancy in women and the leading cause of cancer deaths in women worldwide. Breast cancers are heterogenous and exist in many different subtypes (luminal A, luminal B, triple negative, and human epidermal growth factor receptor 2 (HER2) overexpressing), and each subtype displays distinct characteristics, responses to treatment, and patient outcomes. In addition to varying immunohistochemical properties, each subtype contains a distinct gene mutation profile which has yet to be fully defined. Patient treatment is currently guided by hormone receptor status and HER2 expression, but accumulating evidence suggests that genetic mutations also influence drug responses and patient survival. Thus, identifying the unique gene mutation pattern in each breast cancer subtype will further improve personalized treatment and outcomes for breast cancer patients. In this study, we used the Ion Personal Genome Machine (PGM) and Ion Torrent AmpliSeq Cancer Panel to sequence 737 mutational hotspot regions from 45 cancer-related genes to identify genetic mutations in 80 breast cancer samples of various subtypes from Chinese patients. Analysis revealed frequent missense and combination mutations in PIK3CA and TP53, infrequent mutations in PTEN, and uncommon combination mutations in luminal-type cancers in other genes including BRAF, GNAS, IDH1, and KRAS. This study demonstrates the feasibility of using Ion Torrent sequencing technology to reliably detect gene mutations in a clinical setting in order to guide personalized drug treatments or combination therapies to ultimately target individual, breast cancer-specific mutations.


Subject(s)
Breast Neoplasms/genetics , High-Throughput Nucleotide Sequencing/methods , Mutation/genetics , Receptor, ErbB-2/genetics , Adult , Aged , Breast Neoplasms/pathology , DNA Mutational Analysis , Female , Humans , Middle Aged , Neoplasm Proteins/genetics , Precision Medicine
12.
Blood ; 124(17): 2647-56, 2014 Oct 23.
Article in English | MEDLINE | ID: mdl-25217698

ABSTRACT

The mechanisms controlling the development of dendritic cells (DCs) remain incompletely understood. Using an Mysm1 knockout (Mysm1(-/-)) mouse model, we identified the histone H2A deubiquitinase Mysm1, as a critical regulator in DC differentiation. Mysm1(-/-) mice showed a global reduction of DCs in lymphoid organs, whereas development of granulocytes and macrophages were not severely affected. Hematopoietic progenitors and DC precursors were significantly decreased in Mysm1(-/-) mice and defective in Fms-like tyrosine kinase-3(Flt3) ligand-induced, but not in granulocyte macrophage-colony-stimulating factor (GM-CSF)-induced DC differentiation in vitro. Molecular studies demonstrated that the developmental defect of DCs from common myeloid progenitor (CMP) in Mysm1(-/-) mice is associated with decreased Flt3 expression and that Mysm1 derepresses transcription of the Flt3 gene by directing histone modifications at the Flt3 promoter region. Two molecular mechanisms were found to be responsible for the selective role of Mysm1 in lineage determination of DCs from CMPs: the selective expression of Mysm1 in a subset of CMPs and the different requirement of Mysm1 for PU.1 recruitment to the Flt3 locus vs GM-CSF-α and macrophage-colony-stimulating factor receptor loci. In conclusion, this study reveals an essential role of Mysm1 in epigenetic regulation of Flt3 transcription and DC development, and it provides a novel mechanism for lineage determination from CMP.


Subject(s)
Cell Differentiation/genetics , Dendritic Cells/metabolism , Endopeptidases/genetics , Epigenesis, Genetic , Myeloid Progenitor Cells/metabolism , Animals , Cell Differentiation/drug effects , Cells, Cultured , Endopeptidases/metabolism , Flow Cytometry , Gene Expression , Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology , HEK293 Cells , Histones/metabolism , Humans , Mice, Knockout , Promoter Regions, Genetic/genetics , Protein Binding , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Receptor, Macrophage Colony-Stimulating Factor/genetics , Receptor, Macrophage Colony-Stimulating Factor/metabolism , Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Trans-Activators/genetics , Trans-Activators/metabolism , Ubiquitin-Specific Proteases , fms-Like Tyrosine Kinase 3/genetics , fms-Like Tyrosine Kinase 3/metabolism
13.
Sci Rep ; 4: 5907, 2014 Aug 01.
Article in English | MEDLINE | ID: mdl-25080996

ABSTRACT

Identifying gene mutations in individual tumors is critical to improve the efficacy of cancer therapy by matching targeted drugs to specific mutations. Gastrointestinal stromal tumors (GIST) are stromal or mesenchymal subepithelial neoplasms affecting the gastrointestinal tract and frequently contain activating gene mutations in either KIT or platelet-derived growth factor A (PDGFRA). Although GIST is highly responsive to several selective tyrosine kinase inhibitors, combined use of inhibitors targeting other mutations is needed to further prolong survival in patients with GIST. In this study, we aim to screen and identify genetic mutations in GIST for targeted therapy using the new Ion Torrent next-generation sequencing platform. Utilizing the Ion Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes using DNA extracted from formalin-fixed and paraffin-embedded (FFPE) samples of 121 human gastrointestinal stromal tumors, set up stringent parameters for reliable variant calling by filtering out potential raw base calling errors, and identified frequent mutations in the KIT gene. This study demonstrates the utility of using Ion Torrent sequencing to efficiently identify human cancer mutations. This may provide a molecular basis for clinically developing new drugs targeting these gene mutations for GIST therapy.


Subject(s)
Gastrointestinal Neoplasms/genetics , Gastrointestinal Stromal Tumors/genetics , Proto-Oncogene Proteins c-kit/genetics , Antigens, CD34/metabolism , DNA Mutational Analysis , Female , Gastrointestinal Neoplasms/metabolism , Gastrointestinal Neoplasms/mortality , Gastrointestinal Stromal Tumors/metabolism , Gastrointestinal Stromal Tumors/mortality , Gene Frequency , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Kaplan-Meier Estimate , Male , Mutation, Missense , Polymorphism, Single Nucleotide
14.
PLoS One ; 9(7): e100442, 2014.
Article in English | MEDLINE | ID: mdl-25025766

ABSTRACT

Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7%) in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.


Subject(s)
Adenocarcinoma/genetics , Mutation , Stomach Neoplasms/genetics , Adult , Aged , Aged, 80 and over , DNA Mutational Analysis/methods , Exons , Female , Genetic Loci , High-Throughput Nucleotide Sequencing/methods , Humans , Male , Middle Aged , Mutation Rate , Mutation, Missense , Neoplasm Grading , Neoplasm Staging , Stomach Neoplasms/pathology , Tumor Suppressor Protein p53/genetics
15.
PLoS One ; 9(6): e99306, 2014.
Article in English | MEDLINE | ID: mdl-24918944

ABSTRACT

Breast cancer is the most common malignancy and the leading cause of cancer deaths in women worldwide. While specific genetic mutations have been linked to 5-10% of breast cancer cases, other environmental and epigenetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive breast cancer molecular profile is needed to develop more effective target therapies. Until recently, identifying genetic cancer mutations via personalized DNA sequencing was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 105 human breast cancer samples. The sequencing analysis revealed missense mutations in PIK3CA, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.


Subject(s)
Breast Neoplasms/genetics , Genes, p53 , Mutation, Missense , Phosphatidylinositol 3-Kinases/genetics , Sequence Analysis, DNA/methods , Class I Phosphatidylinositol 3-Kinases , Exons , Female , Humans
16.
PLoS One ; 9(4): e95228, 2014.
Article in English | MEDLINE | ID: mdl-24760004

ABSTRACT

Lung cancer is the most common malignancy and the leading cause of cancer deaths worldwide. While smoking is by far the leading cause of lung cancer, other environmental and genetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive lung cancer molecular profile is essential for developing more effective, tailored therapies. Until recently, personalized DNA sequencing to identify genetic mutations in cancer was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 76 human lung cancer samples. The sequencing analysis revealed missense mutations in KRAS, EGFR, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.


Subject(s)
ErbB Receptors/genetics , Lung Neoplasms/genetics , Proto-Oncogene Proteins/genetics , Sequence Analysis, DNA/methods , Tumor Suppressor Protein p53/genetics , ras Proteins/genetics , Adult , Aged , Aged, 80 and over , Carcinoma, Non-Small-Cell Lung/genetics , DNA Mutational Analysis/methods , Female , Humans , Male , Middle Aged , Mutation , Proto-Oncogene Proteins p21(ras)
17.
Blood ; 122(16): 2812-22, 2013 Oct 17.
Article in English | MEDLINE | ID: mdl-24014243

ABSTRACT

Epigenetic histone modifications play critical roles in the control of self-renewal and differentiation of hematopoietic stem cells (HSCs). Mysm1 is a recently identified histone H2A deubiquitinase with essential and intrinsic roles for maintaining functional HSCs. In this study, in addition to confirming this function of Mysm1, by using Mysm1-deficient (Mysm1(-/-)) mice, we provide more evidence for how Mysm1 controls HSC homeostasis. Mysm1 deletion drives HSCs from quiescence into rapid cycling and increases their apoptotic rate, resulting in an exhaustion of the stem cell pool, which leads to an impaired self-renewal and lineage reconstituting abilities in the Mysm1-deficient mice. Our study identified Gfi1 as one of the candidate genes responsible for the HSC defect in Mysm1-deficient mice. Mechanistic studies revealed that Mysm1 modulates histone modifications and directs the recruitment of key transcriptional factors such as Gata2 and Runx1 to the Gfi1 locus in HSCs. We found that Mysm1 directly associates with the Gfi1 enhancer element and promotes its transcription through Gata2 and Runx1 transactivation. Thus, our study not only elaborates on the initial reports of Mysm1 association with HSC homeostasis but also delineates a possible epigenetic mechanism through which Mysm1 carries out this function in the HSCs.


Subject(s)
Endopeptidases/physiology , Epigenesis, Genetic , Hematopoietic Stem Cells/cytology , Animals , Apoptosis , Cell Cycle , Cell Differentiation , Cell Proliferation , Cell Survival , Core Binding Factor Alpha 2 Subunit/metabolism , DNA-Binding Proteins/metabolism , Endopeptidases/genetics , GATA2 Transcription Factor/metabolism , Gene Deletion , Histones/metabolism , Homeostasis , Mice , Mice, Transgenic , Trans-Activators , Transcription Factors/metabolism , Ubiquitin-Specific Proteases
18.
Proc Natl Acad Sci U S A ; 110(41): E3927-36, 2013 Oct 08.
Article in English | MEDLINE | ID: mdl-24062447

ABSTRACT

Histone modifications play critical roles in regulating immunity; however, little is known about the epigenetic control of natural killer (NK) cell development. Here, we found that NK cell development is severely impaired in mice deficient in the histone H2A deubiquitinase MYSM1. We demonstrated that MYSM1 is required for NK cell maturation but not for NK lineage specification and commitment. We also found that MYSM1 intrinsically controls this NK cell maturation. Mechanistic studies revealed that the expression of transcription factor, inhibitor of DNA-binding protein (ID2), a critical factor for NK cell development, is impaired in Mysm1(-/-) NK cells. MYSM1 interacts with nuclear factor IL-3 (NFIL3, also known as E4BP4), a critical factor for mouse NK cell development, and the recruitment of nuclear factor Il-3 to the ID2 locus is dependent on MYSM1. Further, we observed that MYSM1 is involved in maintaining an active chromatin at the ID2 locus to promote NK cell development. Hence this study demonstrates the critical epigenetic regulation of NK cell development by the histone H2A deubiquitinase MYSM1 through the transcriptional control of transcription factors important for NK cell development.


Subject(s)
Adaptive Immunity/immunology , Endopeptidases/immunology , Epigenesis, Genetic/immunology , Killer Cells, Natural/immunology , Animals , Chromatin Immunoprecipitation , Endopeptidases/genetics , Endopeptidases/metabolism , Flow Cytometry , HEK293 Cells , Humans , Immunoblotting , Inhibitor of Differentiation Protein 2/metabolism , Interleukin-3/metabolism , Killer Cells, Natural/cytology , Mice , Mice, Knockout , Real-Time Polymerase Chain Reaction , Trans-Activators , Transduction, Genetic , Ubiquitin-Specific Proteases
19.
PLoS One ; 7(11): e48614, 2012.
Article in English | MEDLINE | ID: mdl-23144910

ABSTRACT

Persistent infections caused by pathogens such as hepatitis C virus are major human diseases with limited or suboptimal prophylactic and therapeutic options. Given the critical role of dendritic cell (DC) in inducing immune responses, DC vaccination is an attractive means to prevent and control the occurrence and persistence of the infections. However, DCs are built-in with inherent negative regulation mechanisms which attenuate their immune stimulatory activity and lead to their ineffectiveness in clinical application. In this study, we developed a super DC stimulant that consists of a modified, secretory Toll-like Receptor (TLR)-5 ligand and an inhibitor of the negative regulator, suppressor of cytokine sinaling-1 (SOCS1). We found that expressing the super stimulant in DCs is drastically more potent and persistent than using the commonly used DC stimuli to enhance the level and duration of inflammatory cytokine production by both murine and human DCs. Moreover, the DCs expressing the super stimulant are more potent to provoke both cellular and humoral immune responses against hepatitis C virus (HCV) antigen in vivo. Thus, the strategy capable of triggering and sustaining proinflammatory status of DCs may be used to boost efficiency of DC vaccine in preventing and combating the persistent infection of HCV or other chronic viruses.


Subject(s)
Dendritic Cells/immunology , Flagellin/immunology , Hepacivirus/immunology , Hepatitis C/immunology , Immunity , Toll-Like Receptors/agonists , Viral Hepatitis Vaccines/immunology , Acetylation , Animals , Cytokines/metabolism , Epigenesis, Genetic , Hepatitis C/prevention & control , Histones/metabolism , Humans , Immunity, Cellular/immunology , Immunity, Humoral/immunology , Immunization , Inflammation Mediators/metabolism , Mice , Monocytes/cytology , RNA, Small Interfering/metabolism , Suppressor of Cytokine Signaling 1 Protein , Suppressor of Cytokine Signaling Proteins/metabolism , Treatment Outcome
20.
PLoS One ; 7(11): e48930, 2012.
Article in English | MEDLINE | ID: mdl-23145026

ABSTRACT

Emerging evidence indicates that CD4(+) T cells possess cytotoxic potential for tumor eradication and perforin/granzyme-mediated cytotoxicity functions as one of the important mechanisms for CD4(+) T cell-triggered cell killing. However, the critical issue is how the cytotoxic CD4(+) T cells are developed. During the course of our work that aims at promoting immunostimulation of APCs by inhibition of negative regulators, we found that A20-silenced Mф drastically induced granzyme B expression in CD4(+) T cells. As a consequence, the granzyme-highly expressing CD4(+) T cells exhibited a strong cytotoxic activity that restricted tumor development. We found that A20-silenced Mф activated cytotoxic CD4(+) T cells by MHC class-II restricted mechanism and the activation was largely dependent on enhanced production of IFN-γ.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , DNA-Binding Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Macrophages/immunology , T-Lymphocytes, Cytotoxic/immunology , Ubiquitin-Protein Ligases/metabolism , Animals , CD4-Positive T-Lymphocytes/metabolism , Cell Line, Tumor , Cysteine Endopeptidases , Cytotoxicity, Immunologic/genetics , Cytotoxicity, Immunologic/immunology , DNA-Binding Proteins/immunology , Genes, MHC Class II/genetics , Genes, MHC Class II/immunology , Granzymes/immunology , Granzymes/metabolism , Interferon-gamma/immunology , Interferon-gamma/metabolism , Intracellular Signaling Peptides and Proteins/immunology , Macrophages/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , T-Lymphocytes, Cytotoxic/metabolism , Tumor Necrosis Factor alpha-Induced Protein 3 , Ubiquitin-Protein Ligases/immunology
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