Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 62
Filter
Add more filters

Country/Region as subject
Publication year range
1.
Immunity ; 56(11): 2650-2663.e6, 2023 Nov 14.
Article in English | MEDLINE | ID: mdl-37816353

ABSTRACT

The accurate selection of neoantigens that bind to class I human leukocyte antigen (HLA) and are recognized by autologous T cells is a crucial step in many cancer immunotherapy pipelines. We reprocessed whole-exome sequencing and RNA sequencing (RNA-seq) data from 120 cancer patients from two external large-scale neoantigen immunogenicity screening assays combined with an in-house dataset of 11 patients and identified 46,017 somatic single-nucleotide variant mutations and 1,781,445 neo-peptides, of which 212 mutations and 178 neo-peptides were immunogenic. Beyond features commonly used for neoantigen prioritization, factors such as the location of neo-peptides within protein HLA presentation hotspots, binding promiscuity, and the role of the mutated gene in oncogenicity were predictive for immunogenicity. The classifiers accurately predicted neoantigen immunogenicity across datasets and improved their ranking by up to 30%. Besides insights into machine learning methods for neoantigen ranking, we have provided homogenized datasets valuable for developing and benchmarking companion algorithms for neoantigen-based immunotherapies.


Subject(s)
Antigens, Neoplasm , Neoplasms , Humans , Antigens, Neoplasm/genetics , Neoplasms/genetics , Neoplasms/therapy , Histocompatibility Antigens Class I , Machine Learning , Peptides , Immunotherapy/methods
2.
Mol Cell Proteomics ; 20: 100080, 2021.
Article in English | MEDLINE | ID: mdl-33845167

ABSTRACT

Mass spectrometry (MS) is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across human leukocyte antigen (HLA) allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) is widely used, as it generates high-quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that impairs sensitivity and reproducibility. In contrast, in data-independent acquisition (DIA), the systematic fragmentation and acquisition of all fragment ions within given isolation m/z windows yield a comprehensive map for a given sample. However, many DIA approaches commonly require generating comprehensive DDA-based spectrum libraries, which can become impractical for studying noncanonical and personalized neoantigens. Because the amount of HLA peptides eluted from biological samples such as small tissue biopsies is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity-from sample-specific libraries to libraries combining 2 to 40 different immunopeptidomics samples. Analyzing DIA immunopeptidomics data against a complex multi-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. Furthermore, we demonstrated the implementation of DIA for sensitive personalized neoantigen discovery through the analysis of DIA data with predicted MS/MS spectra of clinically relevant HLA ligands. We conclude that a comprehensive multi-HLA library for DIA approach in combination with MS/MS prediction is highly advantageous for clinical immunopeptidomics, especially when low amounts of biological samples are available.


Subject(s)
Histocompatibility Antigens , Peptides , Proteomics/methods , Computer Simulation , Peptide Library , Tandem Mass Spectrometry
3.
Mol Cell Proteomics ; 20: 100032, 2021.
Article in English | MEDLINE | ID: mdl-33592498

ABSTRACT

CD4+ T cell responses are crucial for inducing and maintaining effective anticancer immunity, and the identification of human leukocyte antigen class II (HLA-II) cancer-specific epitopes is key to the development of potent cancer immunotherapies. In many tumor types, and especially in glioblastoma (GBM), HLA-II complexes are hardly ever naturally expressed. Hence, little is known about immunogenic HLA-II epitopes in GBM. With stable expression of the class II major histocompatibility complex transactivator (CIITA) coupled to a detailed and sensitive mass spectrometry-based immunopeptidomics analysis, we here uncovered a remarkable breadth of the HLA-ligandome in HROG02, HROG17, and RA GBM cell lines. The effect of CIITA expression on the induction of the HLA-II presentation machinery was striking in each of the three cell lines, and it was significantly higher compared with interferon gamma (IFNÉ£) treatment. In total, we identified 16,123 unique HLA-I peptides and 32,690 unique HLA-II peptides. In order to genuinely define the identified peptides as true HLA ligands, we carefully characterized their association with the different HLA allotypes. In addition, we identified 138 and 279 HLA-I and HLA-II ligands, respectively, most of which are novel in GBM, derived from known GBM-associated tumor antigens that have been used as source proteins for a variety of GBM vaccines. Our data further indicate that CIITA-expressing GBM cells acquired an antigen presenting cell-like phenotype as we found that they directly present external proteins as HLA-II ligands. Not only that CIITA-expressing GBM cells are attractive models for antigen discovery endeavors, but also such engineered cells have great therapeutic potential through massive presentation of a diverse antigenic repertoire.


Subject(s)
Antigens, Neoplasm/immunology , Brain Neoplasms/immunology , Glioblastoma/immunology , Histocompatibility Antigens Class II/immunology , Nuclear Proteins/immunology , Trans-Activators/immunology , Animals , Cattle , Cell Line, Tumor , Humans , Nuclear Proteins/genetics , Peptides/immunology , Trans-Activators/genetics
4.
Community Ment Health J ; 58(8): 1544-1553, 2022 11.
Article in English | MEDLINE | ID: mdl-35524906

ABSTRACT

Increasing social connection and access to care has been found to decrease the rate of suicide in U.S. veterans. The Veteran Outreach Into the Community to Expand Social Support (VOICES) is an intervention developed by Department Veteran Affairs (VA) staff to improve social connection and provide information about services by implementing community-based Veterans Socials. Seventy veterans at eight locations completed an anonymous cross-sectional survey. This evaluation examined three domains, acceptability (i.e., perceived value), demand (i.e., estimated or actual use), and expansion (i.e., sustainability and increase of Veterans Socials across time and locations). Findings indicated considerable levels of acceptability, demand for, and expansion of this intervention. Additionally, data suggested this intervention may increase social connection and utilization of VA services among attendees.


Subject(s)
Veterans , United States , Humans , United States Department of Veterans Affairs , Cross-Sectional Studies , Feasibility Studies , Social Support
5.
Psychiatr Q ; 92(3): 981-994, 2021 09.
Article in English | MEDLINE | ID: mdl-33409927

ABSTRACT

Severe Post-Traumatic Stress Disorder (PTSD) has been identified as a significant impediment to employment. However, little is known about correlates of employment recovery after a period of not working among veterans with severe PTSD treated in specialized intensive treatment programs. This study examines rates and correlates of transitioning from not being employed at admission to working four months after discharge using national Veterans Health Administration (VHA) program evaluation data on veterans engaged in specialized intensive PTSD treatment (N = 27,339). Results suggest that only 5.68% of the sample made the transition to employment while 10.6% lost employment, 8.9% worked both at admission and following discharge, and 74.9%, did not work either at admission or following discharge. Multinomial regression analysis found that compared to other groups, veterans who became employed were younger, less likely to receive service-connected disability payments, and experienced a significantly greater reduction in PTSD symptoms. Findings from this study highlight that this distinct population has very poor employment outcomes and deserves more attention, and that reducing PTSD symptoms can lead to improved employment outcomes. Efforts to integrate evidence-based vocational rehabilitation practice into residential PTSD treatment targeting PTSD symptoms is encouraged.


Subject(s)
Stress Disorders, Post-Traumatic , Veterans , Employment , Humans , Rehabilitation, Vocational , Stress Disorders, Post-Traumatic/therapy , United States , United States Department of Veterans Affairs
6.
Int J Mol Sci ; 21(21)2020 Nov 09.
Article in English | MEDLINE | ID: mdl-33182400

ABSTRACT

Androgen insensitivity syndrome (AIS), manifesting incomplete virilization in 46,XY individuals, is caused mostly by androgen receptor (AR) gene mutations. Therefore, a search for AR mutations is a routine approach in AIS diagnosis. However, some AIS patients lack AR mutations, which complicates the diagnosis. Here, we describe a patient suffering from partial androgen insensitivity syndrome (PAIS) and lacking AR mutations. The whole exome sequencing of the patient and his family members identified a heterozygous FKBP4 gene mutation, c.956T>C (p.Leu319Pro), inherited from the mother. The gene encodes FKBP prolyl isomerase 4, a positive regulator of the AR signaling pathway. This is the first report describing a FKBP4 gene mutation in association with a human disorder of sexual development (DSD). Importantly, the dysfunction of a homologous gene was previously reported in mice, resulting in a phenotype corresponding to PAIS. Moreover, the Leu319Pro amino acid substitution occurred in a highly conserved position of the FKBP4 region, responsible for interaction with other proteins that are crucial for the AR functional heterocomplex formation and therefore the substitution is predicted to cause the disease. We proposed the FKBP4 gene as a candidate AIS gene and suggest screening that gene for the molecular diagnosis of AIS patients lacking AR gene mutations.


Subject(s)
Androgen-Insensitivity Syndrome/genetics , Receptors, Androgen/genetics , Signal Transduction/genetics , Tacrolimus Binding Proteins/genetics , Amino Acid Sequence , Amino Acid Substitution/genetics , Child , Exome/genetics , Humans , Male , Mutation/genetics , Sexual Development/genetics
7.
J Clin Psychol ; 76(5): 896-904, 2020 05.
Article in English | MEDLINE | ID: mdl-31909827

ABSTRACT

Veterans face a range of challenges as they transition out of the military and into civilian life. For some, this period of transition is characterized by loss of identity, loss of daily structure, loss of community, and confusion about where they fit within society. If not attended to, problems associated with the military-to-civilian transition can lead to significant functional impairment. Yet, little is known about how psychotherapy can support this period of adjustment that every veteran will face. This article presents a case study of a veteran struggling to adjust to the civilian world following his service in the military. Critical areas of assessment, conceptualization, and intervention are explicated to help inform best practices for mental health providers working with veterans.


Subject(s)
Community Integration , Psychotherapy/methods , Veterans/psychology , Adult , Humans , Male , Mental Health , Military Personnel/psychology
8.
N Engl J Med ; 374(26): 2553-2562, 2016 Jun 30.
Article in English | MEDLINE | ID: mdl-27355534

ABSTRACT

BACKGROUND: Cortical-bone fragility is a common feature in osteoporosis that is linked to nonvertebral fractures. Regulation of cortical-bone homeostasis has proved elusive. The study of genetic disorders of the skeleton can yield insights that fuel experimental therapeutic approaches to the treatment of rare disorders and common skeletal ailments. METHODS: We evaluated four patients with Pyle's disease, a genetic disorder that is characterized by cortical-bone thinning, limb deformity, and fractures; two patients were examined by means of exome sequencing, and two were examined by means of Sanger sequencing. After a candidate gene was identified, we generated a knockout mouse model that manifested the phenotype and studied the mechanisms responsible for altered bone architecture. RESULTS: In all affected patients, we found biallelic truncating mutations in SFRP4, the gene encoding secreted frizzled-related protein 4, a soluble Wnt inhibitor. Mice deficient in Sfrp4, like persons with Pyle's disease, have increased amounts of trabecular bone and unusually thin cortical bone, as a result of differential regulation of Wnt and bone morphogenetic protein (BMP) signaling in these two bone compartments. Treatment of Sfrp4-deficient mice with a soluble Bmp2 receptor (RAP-661) or with antibodies to sclerostin corrected the cortical-bone defect. CONCLUSIONS: Our study showed that Pyle's disease was caused by a deficiency of sFRP4, that cortical-bone and trabecular-bone homeostasis were governed by different mechanisms, and that sFRP4-mediated cross-regulation between Wnt and BMP signaling was critical for achieving proper cortical-bone thickness and stability. (Funded by the Swiss National Foundation and the National Institutes of Health.).


Subject(s)
Bone Density/genetics , Bone Remodeling/genetics , Osteochondrodysplasias/genetics , Proto-Oncogene Proteins/deficiency , Proto-Oncogene Proteins/genetics , Adolescent , Animals , Biomarkers/blood , Bone Morphogenetic Proteins/metabolism , Bone Remodeling/physiology , Bone and Bones/pathology , Bone and Bones/physiology , Child, Preschool , Disease Models, Animal , Female , Gene Deletion , Homeostasis , Humans , Male , Mice , Mice, Knockout , Middle Aged , Osteochondrodysplasias/physiopathology , Sequence Analysis, DNA , Signal Transduction , Wnt Proteins/metabolism
9.
J Transl Med ; 17(1): 391, 2019 11 26.
Article in English | MEDLINE | ID: mdl-31771601

ABSTRACT

BACKGROUND: Most ovarian cancer patients are diagnosed at a late stage with 85% of them relapsing after surgery and standard chemotherapy; for this reason, new treatments are urgently needed. Ovarian cancer has become a candidate for immunotherapy by reason of their expression of shared tumor-associated antigens (TAAs) and private mutated neoantigens (NeoAgs) and the recognition of the tumor by the immune system. Additionally, the presence of intraepithelial tumor infiltrating lymphocytes (TILs) is associated with improved progression-free and overall survival of patients with ovarian cancer. The aim of active immunotherapy, including vaccination, is to generate a new anti-tumor response and amplify an existing immune response. Recently developed NeoAgs-based cancer vaccines have the advantage of being more tumor specific, reducing the potential for immunological tolerance, and inducing robust immunogenicity. METHODS: We propose a randomized phase I/II study in patients with advanced ovarian cancer to compare the immunogenicity and to assess safety and feasibility of two personalized DC vaccines. After standard of care surgery and chemotherapy, patients will receive either a novel vaccine consisting of autologous DCs pulsed with up to ten peptides (PEP-DC), selected using an agnostic, yet personalized, epitope discovery algorithm, or a sequential combination of a DC vaccine loaded with autologous oxidized tumor lysate (OC-DC) prior to an equivalent PEP-DC vaccine. All vaccines will be administered in combination with low-dose cyclophosphamide. This study is the first attempt to compare the two approaches and to use NeoAgs-based vaccines in ovarian cancer in the adjuvant setting. DISCUSSION: The proposed treatment takes advantage of the beneficial effects of pre-treatment with OC-DC prior to PEP-DC vaccination, prompting immune response induction against a wide range of patient-specific antigens, and amplification of pre-existing NeoAgs-specific T cell clones. Trial registration This trial is already approved by Swissmedic (Ref.: 2019TpP1004) and will be registered at http://www.clinicaltrials.gov before enrollment opens.


Subject(s)
Cancer Vaccines/immunology , Dendritic Cells/immunology , Neoplasms, Cystic, Mucinous, and Serous/pathology , Neoplasms, Cystic, Mucinous, and Serous/therapy , Ovarian Neoplasms/pathology , Ovarian Neoplasms/therapy , Peptides/immunology , Clinical Trials, Phase I as Topic , Clinical Trials, Phase II as Topic , Female , Humans , Neoplasm Grading , Neoplasm Staging , Transplantation, Autologous
10.
Proc Natl Acad Sci U S A ; 111(11): E1007-15, 2014 Mar 18.
Article in English | MEDLINE | ID: mdl-24594598

ABSTRACT

CD8αß plays crucial roles in the thymic selection, differentiation, and activation of some, but not all, CD8(+) T cells, whereas CD8αα does not. To investigate these roles, we produced mice that expressed transgene P14 T-cell receptor ß (TCRß) chain and CD8ß or did not (WT and KO mice, respectively). The primary CD8(+) T-cell response to acute lymphocytic choriomeningitis virus (LCMV) infection was predominantly D(b)/GP33 specific and CD8 independent in KO mice and was mostly CD8 dependent in WT mice. Cytotoxic T lymphocytes (CTL) from KO mice failed to mobilize intracellular Ca(2+) and to kill via perforin/granzyme. Their strong Fas/FasL-mediated cytotoxicity and IFN-γ response were signaled via a Ca(2+)-independent, PI3K-dependent pathway. This was also true for 15-20% of CD8-independent CTL found in WT mice. Conversely, the perforin/granzyme-mediated killing and IFN-γ response of CD8-dependent CTL were signaled via a Ca(2+), p56(lck), and nuclear factor of activated T cells-dependent pathway. Deep sequencing of millions of TCRα chain transcripts revealed that the TCR repertoires of preimmune CD8(+) T cells were highly diverse, but those of LCMV D(b)/GP33-specific CTL, especially from KO mice, were narrow. The immune repertoires exhibited biased use of Vα segments that encoded different complementary-determining region 1α (CDR1α) and CDR2α sequences. We suggest that TCR from WT CD8-independent T cells may engage MHC-peptide complexes in a manner unfavorable for efficient CD8 engagement and Ca(2+) signaling but permissive for Ca(2+)-independent, PI3K-dependent signaling. This duality of the CD8 compartment may provide organisms with broader protective immunity.


Subject(s)
CD8 Antigens/metabolism , Cell Differentiation/immunology , Immunity, Cellular/immunology , NFATC Transcription Factors/metabolism , Signal Transduction/immunology , T-Lymphocytes, Cytotoxic/metabolism , Animals , Base Sequence , Calcium/metabolism , Cell Line, Tumor , High-Throughput Nucleotide Sequencing , Mice , Mice, Knockout , Molecular Sequence Data , Phosphatidylinositol 3-Kinases/metabolism , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes, Cytotoxic/physiology
11.
BMC Genomics ; 17: 717, 2016 09 07.
Article in English | MEDLINE | ID: mdl-27604219

ABSTRACT

BACKGROUND: The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strains treated with the ß-blocker atenolol (ATE) and the ß-agonist isoproterenol (ISO). RESULTS: Differential expression analyses revealed a large set of genes responding to ISO (n = 1770 at FDR = 0.0001) and a comparatively small one responding to ATE (n = 23 at FDR = 0.0001). At a less stringent definition of differential expression, the transcriptional responses to these two antagonistic drugs are reciprocal for many genes, with an overall anti-correlation of r = -0.3. This trend is also observed at the level of most individual strains even though the power to detect differential expression is significantly reduced. The inversely expressed gene sets are enriched with genes annotated for heart-related functions. Modular analysis revealed gene sets that exhibit coherent transcription profiles across some strains and/or treatments. Correlations between these modules and a broad spectrum of cardiovascular traits are stronger than expected by chance. This provides evidence for the overall importance of transcriptional regulation for these organismal responses and explicits links between co-expressed genes and the traits they are associated with. Gene set enrichment analysis of differentially expressed groups of genes pointed to pathways related to heart development and functionality. CONCLUSIONS: Our study provides new insights into the transcriptional response of the heart to perturbations of the ß-adrenergic system, implicating several new genes that had not been associated to this system previously.


Subject(s)
Atenolol/pharmacology , Gene Expression Profiling/methods , Gene Regulatory Networks/drug effects , Heart/drug effects , Isoproterenol/pharmacology , Sequence Analysis, RNA/methods , Animals , Computational Biology/methods , Gene Expression Regulation/drug effects , Gene Ontology , Mice , Mice, Inbred Strains , Software
12.
EMBO J ; 31(7): 1666-78, 2012 Apr 04.
Article in English | MEDLINE | ID: mdl-22373576

ABSTRACT

Although the T-cell receptor αδ (TCRαδ) locus harbours large libraries of variable (TRAV) and junctional (TRAJ) gene segments, according to previous studies the TCRα chain repertoire is of limited diversity due to restrictions imposed by sequential coordinate TRAV-TRAJ recombinations. By sequencing tens of millions of TCRα chain transcripts from naive mouse CD8(+) T cells, we observed a hugely diverse repertoire, comprising nearly all possible TRAV-TRAJ combinations. Our findings are not compatible with sequential coordinate gene recombination, but rather with a model in which contraction and DNA looping in the TCRαδ locus provide equal access to TRAV and TRAJ gene segments, similarly to that demonstrated for IgH gene recombination. Generation of the observed highly diverse TCRα chain repertoire necessitates deletion of failed attempts by thymic-positive selection and is essential for the formation of highly diverse TCRαß repertoires, capable of providing good protective immunity.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor , Genes, T-Cell Receptor alpha , Recombination, Genetic/immunology , Animals , Base Sequence , Mice , Mice, Inbred C57BL , Molecular Sequence Data
13.
PLoS Comput Biol ; 11(3): e1004050, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25768678

ABSTRACT

Angiogenesis plays a key role in tumor growth and cancer progression. TIE-2-expressing monocytes (TEM) have been reported to critically account for tumor vascularization and growth in mouse tumor experimental models, but the molecular basis of their pro-angiogenic activity are largely unknown. Moreover, differences in the pro-angiogenic activity between blood circulating and tumor infiltrated TEM in human patients has not been established to date, hindering the identification of specific targets for therapeutic intervention. In this work, we investigated these differences and the phenotypic reversal of breast tumor pro-angiogenic TEM to a weak pro-angiogenic phenotype by combining Boolean modelling and experimental approaches. Firstly, we show that in breast cancer patients the pro-angiogenic activity of TEM increased drastically from blood to tumor, suggesting that the tumor microenvironment shapes the highly pro-angiogenic phenotype of TEM. Secondly, we predicted in silico all minimal perturbations transitioning the highly pro-angiogenic phenotype of tumor TEM to the weak pro-angiogenic phenotype of blood TEM and vice versa. In silico predicted perturbations were validated experimentally using patient TEM. In addition, gene expression profiling of TEM transitioned to a weak pro-angiogenic phenotype confirmed that TEM are plastic cells and can be reverted to immunological potent monocytes. Finally, the relapse-free survival analysis showed a statistically significant difference between patients with tumors with high and low expression values for genes encoding transitioning proteins detected in silico and validated on patient TEM. In conclusion, the inferred TEM regulatory network accurately captured experimental TEM behavior and highlighted crosstalk between specific angiogenic and inflammatory signaling pathways of outstanding importance to control their pro-angiogenic activity. Results showed the successful in vitro reversion of such an activity by perturbation of in silico predicted target genes in tumor derived TEM, and indicated that targeting tumor TEM plasticity may constitute a novel valid therapeutic strategy in breast cancer.


Subject(s)
Breast Neoplasms/physiopathology , Models, Biological , Monocytes/physiology , Neovascularization, Pathologic/physiopathology , Animals , Breast Neoplasms/metabolism , Breast Neoplasms/mortality , Cell Line , Computational Biology , Cytokines/metabolism , Cytokines/physiology , Female , Humans , Kaplan-Meier Estimate , Mice , Mice, Transgenic , Middle Aged , Monocytes/chemistry , Monocytes/classification , Neoplasms, Experimental , Phenotype , Signal Transduction/physiology
14.
Proc Natl Acad Sci U S A ; 110(3): E221-30, 2013 Jan 15.
Article in English | MEDLINE | ID: mdl-23267099

ABSTRACT

Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4; CD152) is of pivotal importance for self-tolerance, with deficiency or unfavorable polymorphisms leading to autoimmune disease. Tolerance to self-antigens is achieved through thymic deletion of highly autoreactive conventional T (Tconv) cells and generation of FoxP3(+) regulatory T (Treg) cells. The main costimulatory molecule, CD28, augments the negative selection of Tconv cells and promotes the generation of FoxP3(+) Treg cells. The role of its antagonistic homolog CTLA-4, however, remains a topic of debate. To address this topic, we investigated the thymic development of T cells in the presence and absence of CTLA-4 in a T-cell receptor (TCR) transgenic mouse model specific for the myelin basic protein peptide Ac1-9. We reveal that CTLA-4 is expressed in the corticomedullary region of the thymus. Its absence alters the response of CD4(+)CD8(-) thymocytes to self-antigen recognition, which affects the quantity of the Treg cells generated and broadens the repertoire of peripheral Tconv cells. T-cell repertoire alteration after deletion of CTLA-4 results from changes in TCR Vα and Jα segment selection as well as CDR3α composition in Tconv and Treg cells. CTLA-4, therefore, regulates the early development of self-reactive T cells in the thymus and plays a key role in central tolerance.


Subject(s)
CTLA-4 Antigen/immunology , Gene Rearrangement, T-Lymphocyte , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes/immunology , Amino Acid Sequence , Animals , Antigenic Variation , CTLA-4 Antigen/deficiency , CTLA-4 Antigen/genetics , Cell Differentiation , Complementarity Determining Regions , Cytokines/biosynthesis , Dendritic Cells/cytology , Dendritic Cells/immunology , Encephalomyelitis, Autoimmune, Experimental/genetics , Encephalomyelitis, Autoimmune, Experimental/immunology , Female , Male , Mice , Mice, Knockout , Mice, Transgenic , Molecular Sequence Data , Receptors, Antigen, T-Cell, alpha-beta/genetics , Self Tolerance , T-Lymphocytes/cytology , T-Lymphocytes, Regulatory/cytology , Thymus Gland/cytology , Thymus Gland/growth & development , Thymus Gland/immunology
15.
Genome Res ; 22(2): 246-58, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22156296

ABSTRACT

While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.


Subject(s)
Breast Neoplasms/genetics , Chromatin Assembly and Disassembly , DNA Methylation , Gene Silencing , Alleles , Breast Neoplasms/metabolism , Cell Line, Tumor , Chromatin/genetics , Chromatin/metabolism , Cluster Analysis , Epigenesis, Genetic , Female , Gene Expression Regulation, Neoplastic , Histones/metabolism , Humans , Models, Genetic , Repetitive Sequences, Nucleic Acid , Transcription, Genetic
16.
J Neurooncol ; 119(1): 59-70, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24797829

ABSTRACT

In the present study, we searched for genes highly expressed in placenta and that could contribute to the establishment and maintenance of a malignant phenotype in different types of tumours, and in astrocytomas in particular. We employed a strategy based on the integration of in silico data from previously generated massively parallel signature sequencing and public serial analysis of gene expression databases. Among 12 selected genes, CD99 exhibited the highest relative mRNA expression in GBM compared to non-neoplastic brain tissues. In a larger cohort of astrocytic tumours, we further demonstrated increased CD99 expression in all malignant grades, with GBMs showing the highest values. These findings were confirmed at the protein level by Western blotting and immunohistochemistry. Additionally, we demonstrated the CD99 localisation profile in astrocytic tumours. Interestingly, CD99 expression was confined to the cytoplasm or membrane in more malignant astrocytomas, in contrast to non-neoplastic brain tissue or non-infiltrative pilocytic astrocytoma, which showed no obvious staining in these structures. Comparison of three GBM cell lines revealed higher CD99 expression at the membrane and higher migratory capacity in the A172 and U87MG lines, but lower CD99 expression and no migratory ability in the T98 line. Knocking down CD99 expression by siRNA decreased significantly the migration of both cell lines. These integrated CD99 gene and protein expression results suggest that CD99 expression in astrocytomas of different malignant grades might contribute to the infiltrative ability and support the importance of CD99 as a potential target to reduce infiltrative astrocytoma capacity in migration and invasion.


Subject(s)
Antigens, CD/metabolism , Astrocytoma/metabolism , Brain Neoplasms/metabolism , Brain/metabolism , Cell Adhesion Molecules/metabolism , Cell Movement/genetics , Placenta/metabolism , Up-Regulation , 12E7 Antigen , Antigens, CD/genetics , Astrocytoma/genetics , Astrocytoma/pathology , Brain/pathology , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Adhesion Molecules/genetics , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic , Humans , Neoplasm Grading , Pregnancy
17.
Nat Commun ; 15(1): 2357, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38490980

ABSTRACT

Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5' cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs. We increase the analytical stringency of our workflow by retaining peptides identified independently by two mass spectrometry search engines and/or by applying a group-specific FDR for canonical-derived and circRNA-derived peptides. A subset of circRNA-derived peptides specifically encoded by the region spanning the back-splice junction (BSJ) are validated with targeted MS, and with direct Sanger sequencing of the respective source transcripts. Our workflow identifies 54 unique BSJ-spanning circRNA-derived peptides in the immunopeptidome of melanoma and lung cancer samples. Our approach enlarges the catalog of source proteins that can be explored for immunotherapy.


Subject(s)
Peptides , RNA, Circular , Humans , RNA, Circular/metabolism , RNA, Messenger , Histocompatibility Antigens Class I
18.
Psychol Serv ; 20(4): 918-928, 2023 Nov.
Article in English | MEDLINE | ID: mdl-35849363

ABSTRACT

The concept of recovery has become an increasingly common framework for organizing mental health care, thus many psychologists find themselves working in settings that espouse a recovery orientation to service delivery. However, the concepts of recovery and recovery-oriented services are complex and have many definitions and psychologists struggle to know whether or not the psychotherapy they provide is aligned with recovery-oriented care. This article provides practical recommendations on how to integrate recovery into the common processes of psychotherapy that cut across all theoretical orientations or particular treatment approaches. Specifically, this article details the process of building a therapeutic bond, conceptualizing a client's problems and goals, implementing a treatment plan, and discharge planning, all from a recovery-oriented perspective. A case demonstration and analysis is presented to illustrate the recovery-oriented psychotherapy process described in this article. (PsycInfo Database Record (c) 2023 APA, all rights reserved).


Subject(s)
Mental Disorders , Humans , Mental Disorders/therapy , Mental Disorders/psychology , Psychotherapy
19.
J Career Dev ; 50(4): 947-964, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37463233

ABSTRACT

Veterans living with mental health conditions have ambitious career goals and want support to find employment that meets their interests and preferences. Despite calls from researchers to "invest" and "commit" to career development research and practice for individuals living with psychiatric conditions, we still do not have empirically tested models for facilitating career development among individuals with mental health conditions, especially veterans. This qualitative study investigates the career development needs and recommended intervention strategies of veterans living with mental health conditions. Vocational counselors from the Veterans Health Administration (VHA) and veterans receiving vocational rehabilitation services (N = 13) participated in semi-structured focus groups. Findings illuminate the tasks, barriers, interventions, implementation strategies, and transitional work context that hinder and support career development of veterans with mental health conditions. Findings offer theoretical and applied guidance to researchers and counselors regarding career development of veterans living with mental health conditions.

20.
Psychol Serv ; 2023 Nov 13.
Article in English | MEDLINE | ID: mdl-37956056

ABSTRACT

The high incidence of untreated mental health concerns among veterans can harm other areas of life, including employment. Loss of employment can lead to other adverse outcomes, such as financial instability, functional decline, and increased risk for suicide. Current Veterans Health Administration (VHA) vocational services are limited in that they primarily serve veterans who are unemployed and already enrolled in VHA. There is a need to prevent job loss among veterans who are struggling with mental health and vocational concerns and are not accessing VHA services, thus decreasing the risk of suicide and more costly interventions. Consistent with the existing national VHA initiatives on increasing access to health care and preventing suicide, a novel work-based intervention, Supported Employment: Engage and Keep (SEEK), was created. Building on the supported employment framework, SEEK assertively outreaches to already employed veterans by collaborating with workplaces that employ veterans. SEEK providers build rapport with employers and veterans and become a trusted VHA resource. SEEK engages veterans, facilitates enrollment in needed health care, and provides needed job maintenance support. This article outlines the SEEK model and provides a case demonstration and analysis of the course of SEEK care provided to a veteran at risk of losing their job. Clinical recommendations for implementing SEEK and future directions for evaluating this model are discussed. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

SELECTION OF CITATIONS
SEARCH DETAIL