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Article ; Online: Clinically-relevant Germline Variants in Children with Non-Medullary Thyroid Cancer.

van der Tuin, Karin / Ruano, Dina / Knijnenburg, Jeroen / van der Luijt, Rob B / Morreau, Hans / Links, Thera P / Hes, Frederik J

The Journal of clinical endocrinology and metabolism

2024

Abstract: Context: The underlying genetic cause of non-medullary thyroid cancer (NMTC) in children is often unknown, hampering both predictive testing of family members and preventive clinical management.: Objective: Our objectives were to investigated the ... ...

Abstract	Context: The underlying genetic cause of non-medullary thyroid cancer (NMTC) in children is often unknown, hampering both predictive testing of family members and preventive clinical management. Objective: Our objectives were to investigated the potential heritability in the largest childhood NMTC cohort that has been genotyped to date. Design: Nationwide retrospective cohort study. Setting: Tertiary referral centers. Patients: In total, 97 patients diagnosed with pediatric NMTC between 1970-2020 were included in this study. Intervention: Germline whole genome sequencing (WGS). Main outcome: The main outcome measures were mutation detection yield in 1) clinically-relevant tumor predisposition genes, and 2) genes previously associated with NMTC. Results: In total, 13 of 97 patients (13%) carried a germline (likely) pathogenic (P/LP) variant in a well-known tumor predisposition gene: APC (n=1), BRCA2 (n=2), CHEK2 (n=4), DICER1 (n=4), HOXB13 (n=1), , and MITF (n=1). In addition, one patient was diagnosed with Pendred syndrome (SLC26A4) and nine variants of high interest were found in other NMTC candidate susceptibility genes. Conclusion: The reported prevalence (13%) of germline variants in well-known tumor predisposing genes and the added value of a revised personal-/family history and histology led us to recommend genetic counseling for all childhood NMTC patients.The detected tumor predisposition syndromes are associated with a risk for second cancers which necessitates additional surveillance of the index patients and pre-symptomatic genetic testing of at risk family members.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	3029-6
ISSN	1945-7197 ; 0021-972X
ISSN (online)	1945-7197
ISSN	0021-972X
DOI	10.1210/clinem/dgae107
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Article ; Online: Enrichment of colibactin-associated mutational signatures in unexplained colorectal polyposis patients.

Terlouw, Diantha / Boot, Arnoud / Ducarmon, Quinten R / Nooij, Sam / Suerink, Manon / van Leerdam, Monique E / van Egmond, Demi / Tops, Carli M / Zwittink, Romy D / Ruano, Dina / Langers, Alexandra M J / Nielsen, Maartje / van Wezel, Tom / Morreau, Hans

BMC cancer

2024 Volume 24, Issue 1, Page(s) 104

Abstract: Background: Colibactin, a genotoxin produced by polyketide synthase harboring (pks: Methods: In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation ...

Abstract	Background: Colibactin, a genotoxin produced by polyketide synthase harboring (pks Methods: In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation Sequencing (NGS) was performed for 379 patients. Additionally, for a subset of 29 patients, metagenomics was performed on feces and mutational signature analyses using Whole-Genome Sequencing (WGS) on Formalin-Fixed Paraffin Embedded (FFPE) colorectal tissue blocks. Results: NGS showed somatic APC variants fitting SBS88 or ID18 in at least one colorectal adenoma or carcinoma in 29% of patients. Fecal metagenomic analyses revealed enriched presence of pks genes in patients with somatic variants fitting colibactin-associated signatures compared to patients without variants fitting colibactin-associated signatures. Also, mutational signature analyses showed enrichment of SBS88 and ID18 in patients with variants fitting these signatures in NGS compared to patients without. Conclusions: These findings further support colibactins ability to mutagenize colorectal mucosa and contribute to the development of colorectal adenomas and carcinomas explaining a relevant part of patients with unexplained polyposis.
MeSH term(s)	Humans ; Mutation ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/microbiology ; Peptides/genetics ; Polyketides ; Escherichia coli/genetics ; Adenoma/genetics ; Carcinoma
Chemical Substances	colibactin ; Peptides ; Polyketides
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-024-11849-y
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Article ; Online: A clinically applicable molecular classification of oncocytic cell thyroid nodules.

de Koster, Elizabeth J / Corver, Willem E / de Geus-Oei, Lioe-Fee / Oyen, Wim J G / Ruano, Dina / Schepers, Abbey / Snel, Marieke / van Wezel, Tom / Vriens, Dennis / Morreau, Hans

Endocrine-related cancer

2023 Volume 30, Issue 9

Abstract: Whole chromosome instability with near-whole genome haploidization (GH) and subsequent endoreduplication is considered a main genomic driver in the tumorigenesis of oncocytic cell thyroid neoplasms (OCN). These copy number alterations (CNA) occur less ... ...

Abstract	Whole chromosome instability with near-whole genome haploidization (GH) and subsequent endoreduplication is considered a main genomic driver in the tumorigenesis of oncocytic cell thyroid neoplasms (OCN). These copy number alterations (CNA) occur less frequently in oncocytic thyroid adenoma (OA) than in oncocytic carcinoma (OCA), suggesting a continuous process. The current study described the CNA patterns in a cohort of 30 benign and malignant OCN, observed using a next-generation sequencing (NGS) panel that assesses genome-wide loss of heterozygosity (LOH) and chromosomal imbalances using 1500 single-nucleotide polymorphisms (SNPs) across all autosomes and the X chromosome in DNA derived from cytological and histological samples. Observed CNA patterns were verified using multiparameter DNA flow cytometry with or without whole-genome SNP array analysis and lesser-allele intensity-ratio (LAIR) analysis. On CNA-LOH analysis using the NGS panel, GH-type CNA were observed in 4 of 11 (36%) OA and in 14 of 16 OCA (88%). Endoreduplication was suspected in 8 of 16 (50%) OCA, all with more extensive GH-type CNA (P < 0.001). Reciprocal chromosomal imbalance type CNA, characterized by (imbalanced) chromosomal copy number gains and associated with benign disease, were observed in 6 of 11 (55%) OA and one equivocal case of OCA. CNA patterns were different between the histopathological subgroups (P < 0.001). By applying the structured interpretation and considerations provided by the current study, CNA-LOH analysis using an NGS panel that is feasible for daily practice may be of great added value to the widespread application of molecular diagnostics in the diagnosis and risk stratification of OCN.
MeSH term(s)	Humans ; Thyroid Nodule/genetics ; DNA Copy Number Variations ; Loss of Heterozygosity ; Thyroid Neoplasms/genetics ; Thyroid Neoplasms/pathology ; Genome
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1218450-0
ISSN	1479-6821 ; 1351-0088
ISSN (online)	1479-6821
ISSN	1351-0088
DOI	10.1530/ERC-23-0047
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Article ; Online: CD103 and CD39 coexpression identifies neoantigen-specific cytotoxic T cells in colorectal cancers with low mutation burden.

van den Bulk, Jitske / van der Ploeg, Manon / Ijsselsteijn, Marieke E / Ruano, Dina / van der Breggen, Ruud / Duhen, Rebekka / Peeters, Koen C M J / Fariña-Sarasqueta, Arantza / Verdegaal, Els M E / van der Burg, Sjoerd H / Duhen, Thomas / de Miranda, Noel F C C

Journal for immunotherapy of cancer

2023 Volume 11, Issue 2

Abstract: Background: Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8: Experimental design: Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to ... ...

Abstract	Background: Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8 Experimental design: Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to determine the presence of putative neoantigens. In parallel, tumor-infiltrating lymphocytes (TILs) were cultured from the tumor fragments and, in parallel, CD8 Results: Neoantigen-directed reactivity was only encountered in bulk TIL populations and CD103 Conclusion: Coexpression of CD103 and CD39 is characteristic of neoantigen-specific CD8
MeSH term(s)	Humans ; CD8-Positive T-Lymphocytes ; T-Lymphocytes, Cytotoxic ; T-Lymphocyte Subsets/pathology ; Mutation ; Colorectal Neoplasms
Language	English
Publishing date	2023-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2022-005887
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Article ; Online: Tumor-Infiltrating T Cells Can Be Expanded Successfully from Primary Uveal Melanoma after Separation from Their Tumor Environment.

Gezgin, Gülçin / Visser, Marten / Ruano, Dina / Santegoets, Saskia J / de Miranda, Noel F C C / van der Velden, Pieter A / Luyten, Gregorius P M / van der Burg, Sjoerd H / Verdegaal, Els M / Jager, Martine J

Ophthalmology science

2022 Volume 2, Issue 2, Page(s) 100132

Abstract: Purpose: To evaluate whether expanded tumor-infiltrating lymphocytes (TILs) can be obtained from primary uveal melanoma (UM) for potential use as adjuvant treatment in patients at risk of developing metastatic disease.: Design: Experimental research ... ...

Abstract	Purpose: To evaluate whether expanded tumor-infiltrating lymphocytes (TILs) can be obtained from primary uveal melanoma (UM) for potential use as adjuvant treatment in patients at risk of developing metastatic disease. Design: Experimental research study. Participants: Freshly obtained primary UM from 30 patients. Methods: Three different methods were used to expand TILs: (1) direct culture from small fragments of fresh tumor tissue, (2) single-cell tissue preparation by enzymatic digestion and subsequent enrichment of mononuclear cells, and (3) selection of CD3 Main outcome measures: The feasibility of expanding TILs from primary UM, testing their reactivity to autologous UM cells, and evaluating the impact of an immunomodulatory environment. Results: Direct culture of tumor parts led to successful TIL culture in 4 of 22 tumors (18%), enrichment of mononuclear cells gave rise to TILs in 5 of 12 tumors (42%), while preselection of CD3 Conclusions: The need to separate TILs from their tumor microenvironment for their successful expansion and the presence of UM-reactive T cells among TILs suggests that these UM-reactive T cells are strongly suppressed in vivo and that UM is immunogenic. These findings indicate that adoptive TIL therapy could be an option as an adjuvant treatment in primary UM patients at high risk of developing metastatic disease.
Language	English
Publishing date	2022-03-01
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-9145
ISSN (online)	2666-9145
DOI	10.1016/j.xops.2022.100132
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Article: A Paradoxical Role for Regulatory T Cells in the Tumor Microenvironment of Pancreatic Cancer.

Brouwer, Thomas / Ijsselsteijn, Marieke / Oosting, Jan / Ruano, Dina / van der Ploeg, Manon / Dijk, Frederike / Bonsing, Bert / Fariña, Arantza / Morreau, Hans / Vahrmeijer, Alexander / Miranda, Noel de

Cancers

2022 Volume 14, Issue 16

Abstract: Pancreatic ductal adenocarcinoma (PDAC) is considered to be a poorly immunogenic cancer type that combines a low mutation burden with a strong immunosuppressive tumor microenvironment. Regulatory T cells (Tregs) are major drivers of immune suppression ... ...

Abstract	Pancreatic ductal adenocarcinoma (PDAC) is considered to be a poorly immunogenic cancer type that combines a low mutation burden with a strong immunosuppressive tumor microenvironment. Regulatory T cells (Tregs) are major drivers of immune suppression but their prognostic role, particularly in gastrointestinal malignancies, remains controversial. Lymphocytic infiltration in 122 PDAC samples was assessed by multispectral immunofluorescence with anti-Keratin, -CD3, -CD8, -FOXP3 and -CD163 antibodies. Differential infiltration by Tregs was analyzed in the context of transcriptomic profiles that were available for 65 tumors. High infiltration of CD3
Language	English
Publishing date	2022-08-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14163862
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Article: Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis

Boot, Arnoud / Oosting, Jan / Doorn, Saskia / Ouahoud, Sarah / Ventayol Garcia, Marina / Ruano, Dina / Morreau, Hans / van Wezel, Tom

International Journal of Genomics. 2019 Apr. 10, v. 2019

2019

Abstract: Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or ... ...

Abstract	Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes. The results of this initial analysis were extended and validated in a set of 89 paired normal mucosa and CRC samples. We found that 14% of genes showed ASE in one or more cell lines and identified allelic switching of the potential cell survival genes DLX5, GRB10, and SVOPL on chromosome 7, whereby the most abundantly expressed allele in the normal tissue is the lowest expressed allele in the tumor and vice versa. We established that this allelic switch does not result from loss of imprinting. The allelic switching of SVOPL may be a result of transcriptional downregulation, while the exact mechanisms resulting in the allelic switching of DLX5 and GRB10 remain to be elucidated. In conclusion, our results show that profound changes take place in allelic transcriptional regulation during the tumorigenesis of CRC.
Keywords	alleles ; carcinogenesis ; cell lines ; cell viability ; chromosomes ; colorectal neoplasms ; complementary DNA ; gene expression regulation ; homozygosity ; humans ; mucosa ; transcription (genetics)
Language	English
Dates of publication	2019-0410
Publishing place	Hindawi
Document type	Article
ZDB-ID	2711883-6
ISSN	2314-4378 ; 2314-436X
ISSN (online)	2314-4378
ISSN	2314-436X
DOI	10.1155/2019/1287671
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA.

Hos, Brett J / Tondini, Elena / Camps, Marcel G M / Rademaker, Wesley / van den Bulk, Jitske / Ruano, Dina / Janssen, George M C / de Ru, Arnoud H / van den Elsen, Peter J / de Miranda, Noel F C C / van Veelen, Peter A / Ossendorp, Ferry

Cell reports

2022 Volume 41, Issue 8, Page(s) 111680

Language	English
Publishing date	2022-11-23
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111680
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Article ; Online: Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA.

Cell reports

2022 Volume 41, Issue 2, Page(s) 111485

Abstract: We report an approach to identify tumor-specific ... ...

Abstract	We report an approach to identify tumor-specific CD4
MeSH term(s)	Animals ; Cancer Vaccines ; Epitopes, T-Lymphocyte ; HLA Antigens ; Histocompatibility Antigens Class II ; Humans ; Mice ; Neoplasms ; Nuclear Proteins/genetics ; Peptides ; Trans-Activators/genetics ; Vaccines, Subunit
Chemical Substances	Cancer Vaccines ; Epitopes, T-Lymphocyte ; HLA Antigens ; Histocompatibility Antigens Class II ; MHC class II transactivator protein ; Nuclear Proteins ; Peptides ; Trans-Activators ; Vaccines, Subunit
Language	English
Publishing date	2022-10-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111485
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Article ; Online: Targeted DNA sequencing to identify genetic aberrations in glioblastoma that underlie venous thromboembolism; a cohort study.

Kapteijn, Maaike Y / Kaptein, Fleur H J / Stals, Milou A M / Klaase, Eva E / García-Ortiz, Inés / van Eijk, Ronald / Ruano, Dina / van Duinen, Sjoerd G / Cannegieter, Suzanne C / Taphoorn, Martin J B / Dirven, Linda / Koekkoek, Johan A F / Klok, Frederikus A / Versteeg, Henri H / Buijs, Jeroen T

Thrombosis research

2022 Volume 221, Page(s) 10–18

Abstract: Background and objectives: Patients with glioblastoma have a high risk of developing venous thromboembolism (VTE). However, the role of underlying genetic risk factors remains largely unknown. Therefore, the aim of this study was to discover whether ... ...

Abstract	Background and objectives: Patients with glioblastoma have a high risk of developing venous thromboembolism (VTE). However, the role of underlying genetic risk factors remains largely unknown. Therefore, the aim of this study was to discover whether genetic aberrations in glioblastoma associate with VTE risk. Methods: In this cohort study, all consecutive patients diagnosed with glioblastoma in two Dutch hospitals between February 2017 and August 2020 were included. Targeted DNA next-generation sequencing of all glioblastomas was performed for diagnostic purposes and included mutational status of the genes ATRX, BRAF, CIC, FUBP1, H3F3A, IDH1, IDH2, PIK3CA, PTEN and TP53 and amplification/gain or deletion of BRAF, CDKN2A, EGFR, NOTCH1 and PTEN. The primary outcome was VTE within three months before glioblastoma diagnosis until two years after. Cumulative incidences were determined using competing risk analysis adjusting for mortality. Univariable Cox regression analysis was performed to determine hazard ratios. Results: From 324 patients with glioblastoma, 25 were diagnosed with VTE. Patients with a CDKN2A deletion had a 12-month adjusted cumulative incidence of VTE of 12.5 % (95%CI: 7.3-19.3) compared with 5.4 % (95%CI: 2.6-9.6) in patients with CDKN2A wildtype (p = 0.020), corresponding to a HR of 2.53 (95%CI: 1.12-5.73, p = 0.026). No significant associations were found between any of the other investigated genes and VTE. Conclusion: This study suggests a potential role for CDKN2A deletion in glioblastoma-related VTE. Therefore, once independently validated, CDKN2A mutational status may be a promising predictor to identify glioblastoma patients at high risk for VTE, who may benefit from thromboprophylaxis.
Language	English
Publishing date	2022-11-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	121852-9
ISSN	1879-2472 ; 0049-3848
ISSN (online)	1879-2472
ISSN	0049-3848
DOI	10.1016/j.thromres.2022.11.013
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