Silvia Calpe | University of Amsterdam (original) (raw)

Papers by Silvia Calpe

Molecular cancer therapeutics, Jan 8, 2015

Bone Morphogenetic Proteins (BMPs) have important but distinct roles in tissue homeostasis and di... more Bone Morphogenetic Proteins (BMPs) have important but distinct roles in tissue homeostasis and disease, including carcinogenesis and tumor progression. A large number of BMP inhibitors are available to study BMP function; however, since most of these antagonists are promiscuous, evaluating specific effects of individual BMPs is not feasible. Because the oncogenic role of the different BMPs varies for each neoplasm, highly selective BMP inhibitors are required. Here we describe the generation of three types of llama-derived heavy chain variable domains (VHHs) which selectively bind to either BMP4, to BMP2 and 4, or to BMP2,4,5 and 6. These generated VHHs have high affinity to their targets and are able to inhibit BMP signalling. Epitope binning and docking modelling have shed light into the basis for their BMP-specificity. As opposed to the wide structural reach of natural inhibitors, these small molecules target the grooves and pockets of BMPs involved in receptor binding. In organo...

Gastroenterology, 2015

Intestinal organoids" are structures that mirror the intestinal crypt-villus units. Because they ... more Intestinal organoids" are structures that mirror the intestinal crypt-villus units. Because they recapitulate the complete intestinal stem cell differentiation hierarchy, they are emerging as powerful tools in which to study the functional relationship between the different intestinal cell types. As organoids are currently being used in human disease models, in future, they will represent compelling therapeutic tools.

Gut, 2015

The risk of developing adenocarcinoma in non-dysplastic Barrett&a... more The risk of developing adenocarcinoma in non-dysplastic Barrett's oesophagus is low and difficult to predict. Accurate tools for risk stratification are needed to increase the efficiency of surveillance. We aimed to develop a prediction model for progression using clinical variables and genetic markers. In a prospective cohort of patients with non-dysplastic Barrett's oesophagus, we evaluated six molecular markers: p16, p53, Her-2/neu, 20q, MYC and aneusomy by DNA fluorescence in situ hybridisation on brush cytology specimens. Primary study outcomes were the development of high-grade dysplasia or oesophageal adenocarcinoma. The most predictive clinical variables and markers were determined using Cox proportional-hazards models, receiver operating characteristic curves and a leave-one-out analysis. A total of 428 patients participated (345 men; median age 60 years) with a cumulative follow-up of 2019 patient-years (median 45 months per patient). Of these patients, 22 progressed; nine developed high-grade dysplasia and 13 oesophageal adenocarcinoma. The clinical variables, age and circumferential Barrett's length, and the markers, p16 loss, MYC gain and aneusomy, were significantly associated with progression on univariate analysis. We defined an 'Abnormal Marker Count' that counted abnormalities in p16, MYC and aneusomy, which significantly improved risk prediction beyond using just age and Barrett's length. In multivariate analysis, these three factors identified a high-risk group with an 8.7-fold (95% CI 2.6 to 29.8) increased HR when compared with the low-risk group, with an area under the curve of 0.76 (95% CI 0.66 to 0.86). A prediction model based on age, Barrett's length and the markers p16, MYC and aneusomy determines progression risk in non-dysplastic Barrett's oesophagus.

Annals of the New York Academy of Sciences, 2014

The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentari... more The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on signaling pathways that can be targeted with immunotherapy; the role of micro-RNAs in the immune response to esophageal cancer; and the association between obesity, the immune system, and esophageal adenocarcinoma.

Frontiers in Oncology, 2013

have contributed equally to this work.

X-linked lymphoproliferative (XLP) dis- ease is a primary immunodeficiency caused by a defect in ... more X-linked lymphoproliferative (XLP) dis- ease is a primary immunodeficiency caused by a defect in the SH2D1A gene. At least 3 major manifestations character- ize its clinical presentation: fatal infec- tious mononucleosis (FIM), lymphomas, and immunoglobulin deficiencies. Com- mon variable immunodeficiency (CVID) is a syndrome characterized by immuno- globulin deficiency leading to susceptibil- ity to infection. In some patients with CVID,

Genes, Chromosomes and Cancer, 2014

Barrett&a... more Barrett's esophagus (BE) goes through a sequence of low grade dysplasia (LGD) and high grade dysplasia (HGD) to esophageal adenocarcinoma (EAC). The current gold standard for BE outcome prediction, histopathological staging, can be unreliable. TP53 abnormalities may serve as prognostic biomarkers. TP53 protein accumulation detected by immunohistochemistry (IHC) indirectly assesses TP53 mutations. DNA fluorescent in situ hybridization (FISH) on brush cytology specimens directly evaluates gene locus loss. We evaluated if IHC and FISH are complementary tools to assess TP53 abnormalities and tested their prognostic value in a long-term prospective follow-up of a BE cohort. TP53 IHC on tissue sections and FISH on brush cytology specimens were evaluated for 116 BE patients with respect to the different histological stages. The TP53 abnormalities were further studied in a panel of cell lines representative of the Barrett's carcinogenic sequence. For 91patients, the predictive value of TP53 abnormalities with respect to progression to HGD/EAC was tested after long term follow-up. The frequency of IHC and FISH TP53 abnormalities increased significantly with increasing histological stage (P < 0.001, Chi(2) -test). Combining the techniques detected TP53 abnormalities in 100% of patients with LGD, HGD, and EAC. Multivariate analysis showed that IHC (hazard ratio: 17, 95% CI: 3.2-96, P = 0.001) and FISH (hazard ratio: 7.3, 95% CI: 1.3-41, P = 0.02) were both independent significant predictors of progression. Combining FISH and IHC in assessing TP53 abnormalities leads to an increased detection rate of TP53 aberrations and improved accuracy for predicting BE progression.

The Journal of Immunology, 2010

EAT-2A and EAT-2B are single SH2-domain proteins, which bind to phosphorylated tyrosines of SLAM ... more EAT-2A and EAT-2B are single SH2-domain proteins, which bind to phosphorylated tyrosines of SLAM family receptors in murine NK cells. Whilst EAT-2 is a positive regulator in human cells, a negative regulatory role was attributed to the adapter in NK cells derived from EAT-2A-deficient 129Sv mice. To evaluate whether the genetic background or the presence of a selection marker in the mutant mice could influence the regulatory mode of these adapters, we generated EAT-2A-, EAT-2B-and EAT-2A/B-deficient mice using C57BL/6 (B6) ES cells. We found that NK cells from EAT-2A-and EAT-2A/B-deficient mice were unable to kill tumor cells in a CD244 or CD84 dependent manner. Furthermore, EAT-2A/B positively regulate phosphorylation of Vav-1, which is known to be implicated in NK cell killing. Thus, like in humans, the EAT-2 adapters act as positive regulators of SLAM family receptor specific NK cell functions in B6 mice.

Journal of Experimental Medicine, 2011

Immunogenetics, 2006

Human EAT-2 (SH2D1B) and SLAM-associated protein (SAP) (SH2D1A) are single SH2-domain adapters, w... more Human EAT-2 (SH2D1B) and SLAM-associated protein (SAP) (SH2D1A) are single SH2-domain adapters, which bind to specific tyrosine residues in the cytoplasmic tail of six signaling lymphocytic activation molecule (SLAM) (SLAMF1)-related receptors. Here we report that, unlike in humans, the mouse and rat Eat2 genes are duplicated with an identical genomic organization. The coding regions of the mouse Eat2a and Eat2b genes share 91% identity at the nucleotide level and 84% at the protein level; similarly, segments of introns are highly conserved.

Immunity, 2011

To design successful vaccines for chronic diseases, an understanding of memory CD8 + T cell respo... more To design successful vaccines for chronic diseases, an understanding of memory CD8 + T cell responses to persistent antigen restimulation is critical. However, most studies comparing memory and naive cell responses have been performed only in rapidly cleared acute infections. Herein, by comparing the responses of memory and naive CD8 + T cells to acute and chronic lymphocytic choriomeningitis virus infection, we show that memory cells dominated over naive cells and were protective when present in sufficient numbers to quickly reduce infection. In contrast, when infection was not rapidly reduced, because of high antigen load or persistence, memory cells were quickly lost, unlike naive cells. This loss of memory cells was due to a block in sustaining cell proliferation, selective regulation by the inhibitory receptor 2B4, and increased reliance on CD4 + T cell help. Thus, emphasizing the importance of designing vaccines that elicit effective CD4 + T cell help and rapidly control infection.

Advances in immunology, 2008

The nine SLAM-family genes, SLAMF1-9, a subfamily of the immunoglobulin superfamily, encode diffe... more The nine SLAM-family genes, SLAMF1-9, a subfamily of the immunoglobulin superfamily, encode differentially expressed cell-surface receptors of hematopoietic cells. Engagement with their ligands, which are predominantly homotypic, leads to distinct signal transduction events, for instance those that occur in the T or NK cell immune synapse. Upon phosphorylation of one or more copies of a unique tyrosine-based signaling motif in their cytoplasmic tails, six of the SLAM receptors recruit the highly specific single SH2-domain adapters SLAM-associated protein (SAP), EAT-2A, and/or EAT-2B. These adapters in turn bind to the tyrosine kinase Fyn and/or other protein tyrosine kinases connecting the receptors to signal transduction networks. Individuals deficient in the SAP gene, SH2D1A, develop an immunodeficiency syndrome: X-linked lympho-proliferative disease. In addition to operating in the immune synapse, SLAM receptors initiate or partake in multiple effector functions of hematopoietic ...

Molecular cancer therapeutics, Jan 8, 2015

Bone Morphogenetic Proteins (BMPs) have important but distinct roles in tissue homeostasis and di... more Bone Morphogenetic Proteins (BMPs) have important but distinct roles in tissue homeostasis and disease, including carcinogenesis and tumor progression. A large number of BMP inhibitors are available to study BMP function; however, since most of these antagonists are promiscuous, evaluating specific effects of individual BMPs is not feasible. Because the oncogenic role of the different BMPs varies for each neoplasm, highly selective BMP inhibitors are required. Here we describe the generation of three types of llama-derived heavy chain variable domains (VHHs) which selectively bind to either BMP4, to BMP2 and 4, or to BMP2,4,5 and 6. These generated VHHs have high affinity to their targets and are able to inhibit BMP signalling. Epitope binning and docking modelling have shed light into the basis for their BMP-specificity. As opposed to the wide structural reach of natural inhibitors, these small molecules target the grooves and pockets of BMPs involved in receptor binding. In organo...

Gastroenterology, 2015

Intestinal organoids" are structures that mirror the intestinal crypt-villus units. Because they ... more Intestinal organoids" are structures that mirror the intestinal crypt-villus units. Because they recapitulate the complete intestinal stem cell differentiation hierarchy, they are emerging as powerful tools in which to study the functional relationship between the different intestinal cell types. As organoids are currently being used in human disease models, in future, they will represent compelling therapeutic tools.

Gut, 2015

The risk of developing adenocarcinoma in non-dysplastic Barrett&a... more The risk of developing adenocarcinoma in non-dysplastic Barrett's oesophagus is low and difficult to predict. Accurate tools for risk stratification are needed to increase the efficiency of surveillance. We aimed to develop a prediction model for progression using clinical variables and genetic markers. In a prospective cohort of patients with non-dysplastic Barrett's oesophagus, we evaluated six molecular markers: p16, p53, Her-2/neu, 20q, MYC and aneusomy by DNA fluorescence in situ hybridisation on brush cytology specimens. Primary study outcomes were the development of high-grade dysplasia or oesophageal adenocarcinoma. The most predictive clinical variables and markers were determined using Cox proportional-hazards models, receiver operating characteristic curves and a leave-one-out analysis. A total of 428 patients participated (345 men; median age 60 years) with a cumulative follow-up of 2019 patient-years (median 45 months per patient). Of these patients, 22 progressed; nine developed high-grade dysplasia and 13 oesophageal adenocarcinoma. The clinical variables, age and circumferential Barrett's length, and the markers, p16 loss, MYC gain and aneusomy, were significantly associated with progression on univariate analysis. We defined an 'Abnormal Marker Count' that counted abnormalities in p16, MYC and aneusomy, which significantly improved risk prediction beyond using just age and Barrett's length. In multivariate analysis, these three factors identified a high-risk group with an 8.7-fold (95% CI 2.6 to 29.8) increased HR when compared with the low-risk group, with an area under the curve of 0.76 (95% CI 0.66 to 0.86). A prediction model based on age, Barrett's length and the markers p16, MYC and aneusomy determines progression risk in non-dysplastic Barrett's oesophagus.

Annals of the New York Academy of Sciences, 2014

The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentari... more The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on signaling pathways that can be targeted with immunotherapy; the role of micro-RNAs in the immune response to esophageal cancer; and the association between obesity, the immune system, and esophageal adenocarcinoma.

Frontiers in Oncology, 2013

have contributed equally to this work.

X-linked lymphoproliferative (XLP) dis- ease is a primary immunodeficiency caused by a defect in ... more X-linked lymphoproliferative (XLP) dis- ease is a primary immunodeficiency caused by a defect in the SH2D1A gene. At least 3 major manifestations character- ize its clinical presentation: fatal infec- tious mononucleosis (FIM), lymphomas, and immunoglobulin deficiencies. Com- mon variable immunodeficiency (CVID) is a syndrome characterized by immuno- globulin deficiency leading to susceptibil- ity to infection. In some patients with CVID,

Genes, Chromosomes and Cancer, 2014

Barrett&a... more Barrett's esophagus (BE) goes through a sequence of low grade dysplasia (LGD) and high grade dysplasia (HGD) to esophageal adenocarcinoma (EAC). The current gold standard for BE outcome prediction, histopathological staging, can be unreliable. TP53 abnormalities may serve as prognostic biomarkers. TP53 protein accumulation detected by immunohistochemistry (IHC) indirectly assesses TP53 mutations. DNA fluorescent in situ hybridization (FISH) on brush cytology specimens directly evaluates gene locus loss. We evaluated if IHC and FISH are complementary tools to assess TP53 abnormalities and tested their prognostic value in a long-term prospective follow-up of a BE cohort. TP53 IHC on tissue sections and FISH on brush cytology specimens were evaluated for 116 BE patients with respect to the different histological stages. The TP53 abnormalities were further studied in a panel of cell lines representative of the Barrett's carcinogenic sequence. For 91patients, the predictive value of TP53 abnormalities with respect to progression to HGD/EAC was tested after long term follow-up. The frequency of IHC and FISH TP53 abnormalities increased significantly with increasing histological stage (P < 0.001, Chi(2) -test). Combining the techniques detected TP53 abnormalities in 100% of patients with LGD, HGD, and EAC. Multivariate analysis showed that IHC (hazard ratio: 17, 95% CI: 3.2-96, P = 0.001) and FISH (hazard ratio: 7.3, 95% CI: 1.3-41, P = 0.02) were both independent significant predictors of progression. Combining FISH and IHC in assessing TP53 abnormalities leads to an increased detection rate of TP53 aberrations and improved accuracy for predicting BE progression.

The Journal of Immunology, 2010

EAT-2A and EAT-2B are single SH2-domain proteins, which bind to phosphorylated tyrosines of SLAM ... more EAT-2A and EAT-2B are single SH2-domain proteins, which bind to phosphorylated tyrosines of SLAM family receptors in murine NK cells. Whilst EAT-2 is a positive regulator in human cells, a negative regulatory role was attributed to the adapter in NK cells derived from EAT-2A-deficient 129Sv mice. To evaluate whether the genetic background or the presence of a selection marker in the mutant mice could influence the regulatory mode of these adapters, we generated EAT-2A-, EAT-2B-and EAT-2A/B-deficient mice using C57BL/6 (B6) ES cells. We found that NK cells from EAT-2A-and EAT-2A/B-deficient mice were unable to kill tumor cells in a CD244 or CD84 dependent manner. Furthermore, EAT-2A/B positively regulate phosphorylation of Vav-1, which is known to be implicated in NK cell killing. Thus, like in humans, the EAT-2 adapters act as positive regulators of SLAM family receptor specific NK cell functions in B6 mice.

Journal of Experimental Medicine, 2011

Immunogenetics, 2006

Human EAT-2 (SH2D1B) and SLAM-associated protein (SAP) (SH2D1A) are single SH2-domain adapters, w... more Human EAT-2 (SH2D1B) and SLAM-associated protein (SAP) (SH2D1A) are single SH2-domain adapters, which bind to specific tyrosine residues in the cytoplasmic tail of six signaling lymphocytic activation molecule (SLAM) (SLAMF1)-related receptors. Here we report that, unlike in humans, the mouse and rat Eat2 genes are duplicated with an identical genomic organization. The coding regions of the mouse Eat2a and Eat2b genes share 91% identity at the nucleotide level and 84% at the protein level; similarly, segments of introns are highly conserved.

Immunity, 2011

To design successful vaccines for chronic diseases, an understanding of memory CD8 + T cell respo... more To design successful vaccines for chronic diseases, an understanding of memory CD8 + T cell responses to persistent antigen restimulation is critical. However, most studies comparing memory and naive cell responses have been performed only in rapidly cleared acute infections. Herein, by comparing the responses of memory and naive CD8 + T cells to acute and chronic lymphocytic choriomeningitis virus infection, we show that memory cells dominated over naive cells and were protective when present in sufficient numbers to quickly reduce infection. In contrast, when infection was not rapidly reduced, because of high antigen load or persistence, memory cells were quickly lost, unlike naive cells. This loss of memory cells was due to a block in sustaining cell proliferation, selective regulation by the inhibitory receptor 2B4, and increased reliance on CD4 + T cell help. Thus, emphasizing the importance of designing vaccines that elicit effective CD4 + T cell help and rapidly control infection.

Advances in immunology, 2008

The nine SLAM-family genes, SLAMF1-9, a subfamily of the immunoglobulin superfamily, encode diffe... more The nine SLAM-family genes, SLAMF1-9, a subfamily of the immunoglobulin superfamily, encode differentially expressed cell-surface receptors of hematopoietic cells. Engagement with their ligands, which are predominantly homotypic, leads to distinct signal transduction events, for instance those that occur in the T or NK cell immune synapse. Upon phosphorylation of one or more copies of a unique tyrosine-based signaling motif in their cytoplasmic tails, six of the SLAM receptors recruit the highly specific single SH2-domain adapters SLAM-associated protein (SAP), EAT-2A, and/or EAT-2B. These adapters in turn bind to the tyrosine kinase Fyn and/or other protein tyrosine kinases connecting the receptors to signal transduction networks. Individuals deficient in the SAP gene, SH2D1A, develop an immunodeficiency syndrome: X-linked lympho-proliferative disease. In addition to operating in the immune synapse, SLAM receptors initiate or partake in multiple effector functions of hematopoietic ...