Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dendritic Cell Vaccination in Patients With Lynch Syndrome or Colorectal Cancer With MSI

ABSTRACT: Objectives: In this Radboud University Nijmegen Medical Centre (RUNMC) initiated study our first objective is to investigate toxicity (safety and feasibility) of vaccination with frameshift-derived neoantigen-loaded DC of CRC patients with an MSI-positive CRC and persons who are known to be carrier of a germline MMR-gene mutation with no signs of disease yet. The secondary objectives of the study are: * to demonstrate that peptide-loaded DC can induce or enhance an immune response to tumor-associated antigen CEA and specific frameshift-derived neoantigens in the study population. * to study the pathological and clinical responses, e.g. disease-free survival, determined according to the standard protocol. Study design: This study is a phase I/II open-label study. Study population: Two groups of adults will be vaccinated: Group I) CRC patients, who are known to carry a germline MMR-gene mutation and patients with an MSI-positive CRC and yet unknown or negative MMR-gene mutation status. Group II) persons who are known to be carrier of a germline MMR-gene mutation with no signs of disease yet. All participants need to be HLA-A2.1 positive.

DISEASE(S): In This Study Our Primary Objective Is To Induce Or Enhance An Immune Response To Tumor Antigens In Lynch Syndrome Mutation Carriers (with And Without Colorectal Adenomas Or Carcinomas) And Patients With Sporadic Colorectal Cancer (crc) Showing Microsatellite Instability (msi-high), The Hallmark Of Mmr Dysfunction, And Test The Hypothesis That Dc Vaccination Might Be Effective As Prophylactic Treatment In Hereditary Non-polyposis Colorectal Cancer (hnpcc) Or Lynch Syndrome Mutation Carriers.,Colorectal Cancer,Colorectal Neoplasms,Colorectal Neoplasms, Hereditary Nonpolyposis

PROVIDER: 2147264 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals [FFPE]

Project description:Background: In ~50% of Lynch syndrome (LS)-suspected patients (also called Lynch-like syndrome, LLS), the causal mechanism for cancer predisposition remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive genetic and epigenetic analysis. Methods: One hundred and fifteen LLS patients harboring MMR deficient tumors and no pathogenic germline MMR gene mutations were included in this study. Mutational analysis of 26 colorectal cancer associated genes was performed by using a customized multigene panel and massively parallel sequencing. Pathogenicity of MMR variants was assessed by mRNA analysis and multifactorial likelihood calculations. Genome-wide methylome analysis was perfomed by using the Infinium HumanMethylation450K BeadChip. Results: The multigene panel analysis revealed the presence of two MMR gene truncating mutations not found in previous analysis. Of a total of 15 MMR variants of unknown significance identified, five - present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes (MSH3, MUTYH, POLD1, APC, EPCAM, BUB1, FAN1, EXO1 or PSM1) were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation in an individual diagnosed with CRC at age 42, but no additional differentially methylated regions were identified in LLS compared to LS patients or healthy individuals. Conclusions: In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allows the identification of deleterious MMR mutations as well as new LLS candidate genes. Moreover, constitutional epimutations in non-LS-associated genes are not responsible for the MMR-deficient phenotype observed in LLS patients.

2019-03-09 | GSE128067 | GEO

Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals [Blood]

2019-03-09 | GSE128064 | GEO

NPM1 mutation-modulated microRNAâmRNA regulation in acute myeloid leukemia [mRNA]

Project description:Mutation in the nucleophosmin (NPM1) gene is frequent in acute myeloid leukemia (AML). This mutation has remarkable prognostic significance and correlates with distinct biological features. Our data from the sample-paired microRNA (miRNA) and mRNA microarrays of de novo AML patients strongly indicated that miRNAâmRNA regulation (MMR) may be dynamic and can be modulated by NPM1 mutation. We identified 493 NPM1 mutation-modulated MMR pairs by a systematic framework, in which MMR was attenuated specifically in patients carrying NPM1 mutations. The involved miRNAs/mRNAs were associated with cancer and hematological diseases, as well as known functions of NPM1 mutation including cell death and cellular response to therapeutics. The NPM1 mutation modulation could be validated with three approaches, including two independent cohort datasets, a high-throughput dataset derived from cell line-based experiments, and two in vitro models. Our study provides novel biological insights into the role of NPM1 mutation as a modulator of MMR, based on which novel prognostic markers are derived in AML. Cryopreserved bone marrow cells were obtained from 109 de novo AML patients. Each sample was analyzed with Illumina HumanHT-12 V4.0 expression beadchip.

2017-05-03 | E-GEOD-68466 | biostudies-arrayexpress

NPM1 mutation-modulated microRNAâmRNA regulation in acute myeloid leukemia [miRNA]

2017-05-03 | E-GEOD-68467 | biostudies-arrayexpress

NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia [miRNA]

Project description:Mutation in the nucleophosmin (NPM1) gene is frequent in acute myeloid leukemia (AML). This mutation has remarkable prognostic significance and correlates with distinct biological features. Our data from the sample-paired microRNA (miRNA) and mRNA microarrays of de novo AML patients strongly indicated that miRNA−mRNA regulation (MMR) may be dynamic and can be modulated by NPM1 mutation. We identified 493 NPM1 mutation-modulated MMR pairs by a systematic framework, in which MMR was attenuated specifically in patients carrying NPM1 mutations. The involved miRNAs/mRNAs were associated with cancer and hematological diseases, as well as known functions of NPM1 mutation including cell death and cellular response to therapeutics. The NPM1 mutation modulation could be validated with three approaches, including two independent cohort datasets, a high-throughput dataset derived from cell line-based experiments, and two in vitro models. Our study provides novel biological insights into the role of NPM1 mutation as a modulator of MMR, based on which novel prognostic markers are derived in AML.

2017-05-03 | GSE68467 | GEO

NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia [mRNA]

Project description:Mutation in the nucleophosmin (NPM1) gene is frequent in acute myeloid leukemia (AML). This mutation has remarkable prognostic significance and correlates with distinct biological features. Our data from the sample-paired microRNA (miRNA) and mRNA microarrays of de novo AML patients strongly indicated that miRNA−mRNA regulation (MMR) may be dynamic and can be modulated by NPM1 mutation. We identified 493 NPM1 mutation-modulated MMR pairs by a systematic framework, in which MMR was attenuated specifically in patients carrying NPM1 mutations. The involved miRNAs/mRNAs were associated with cancer and hematological diseases, as well as known functions of NPM1 mutation including cell death and cellular response to therapeutics. The NPM1 mutation modulation could be validated with three approaches, including two independent cohort datasets, a high-throughput dataset derived from cell line-based experiments, and two in vitro models. Our study provides novel biological insights into the role of NPM1 mutation as a modulator of MMR, based on which novel prognostic markers are derived in AML.

2017-05-03 | GSE68466 | GEO

Mismatch-repair signature mutations activate gene enhancers across human colorectal cancer epigenomes

Project description:We show that mismatch-repair (MMR) signature mutations can activate colorectal cancer (CRC)-specific enhancers, through analysis of enhancer DNA associated with the active enhancer histone mark H3K27ac. We demonstrate that MMR mutations activate enhancers using a xenograft metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection.

2019-02-07 | GSE126188 | GEO

Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens

Project description:High correlation was observed between T cell responses to SARS-CoV-2 and MMR and Tdap vaccine proteins in infected and uninfected individuals; the overlapping T cell population contained an effector memory T cell subset previously implicated in protective anti-viral immunity and their activation required APC-derived IL-15, known to sensitize T cells to activation. We were able to detect cross-reactive TCR repertoire in antigen experienced T cells recognizing SARS-CoV-2, MMR and Tdap epitopes using clonotyping and scRNA-seq. Indices of disease severity were reduced in MMR or Tdap vaccinated individuals by 32-38% and 20-23% respectively, among 73.582 COVID-19 positive patients.

2021-08-02 | GSE181046 | GEO

Clinical validation study of RAKSET-B, a multiple detection kit for BRAF and RAS gene mutations in colorectal cancer

Project description:Primary outcome(s): BRAF gene mutation* - Overall concordance rate, positive concordance rate, and negative concordance rate of BRAF gene mutations between standard genetic testing such as sanger sequencing and RASKET-B kit RAS gene mutation** - Overall concordance rate, positive concordance rate, and negative concordance rate of RAS gene mutations between MEBGEN RASKET KIT (an established in vitro diagnostic (IVD) kit for detecting RAS mutations) and RASKET-B kit *BRAF gene mutation codon 600 (p.V600E) **RAS gene mutation codon 12, 13, 59, 61, 117, 146

| 2637999 | ecrin-mdr-crc

Germline NPM1 mutations lead to altered rRNA 2’-O-methylation and cause dyskeratosis congenita (microarray)

Project description:We identify nucleophosmin (NPM1) as an essential regulator of 2’-O-methylation on rRNA by directly binding C/D box small nucleolar RNAs (snoRNAs), thereby modulating translation. We demonstrate the importance of 2’-O-Me regulated translation for cellular growth, differentiation and hematopoietic stem cells (HSC) maintenance, and show that Npm1-inactivation in adult HSCs results in bone marrow failure (BMF). We identify NPM1 germline mutations in DC patients presenting with BMF; and demonstrate that they are deficient in snoRNA binding. CRISPR knock-in mice harboring the DC germline NPM1 mutation recapitulate both hematological and non-hematological features of DC. Thus, our findings provide a direct demonstration of the role of 2’-O-Me in the pathogenesis of human disease

2019-08-13 | GSE135725 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data