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1.
Med Image Anal ; 93: 103063, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38194735

ABSTRACT

The frequency of basal cell carcinoma (BCC) cases is putting an increasing strain on dermatopathologists. BCC is the most common type of skin cancer, and its incidence is increasing rapidly worldwide. AI can play a significant role in reducing the time and effort required for BCC diagnostics and thus improve the overall efficiency of the process. To train such an AI system in a fully-supervised fashion however, would require a large amount of pixel-level annotation by already strained dermatopathologists. Therefore, in this study, our primary objective was to develop a weakly-supervised for the identification of basal cell carcinoma (BCC) and the stratification of BCC into low-risk and high-risk categories within histopathology whole-slide images (WSI). We compared Clustering-constrained Attention Multiple instance learning (CLAM) with StreamingCLAM and hypothesized that the latter would be the superior approach. A total of 5147 images were used to train and validate the models, which were subsequently tested on an internal set of 949 images and an external set of 183 images. The labels for training were automatically extracted from free-text pathology reports using a rule-based approach. All data has been made available through the COBRA dataset. The results showed that both the CLAM and StreamingCLAM models achieved high performance for the detection of BCC, with an area under the ROC curve (AUC) of 0.994 and 0.997, respectively, on the internal test set and 0.983 and 0.993 on the external dataset. Furthermore, the models performed well on risk stratification, with AUC values of 0.912 and 0.931, respectively, on the internal set, and 0.851 and 0.883 on the external set. In every single metric the StreamingCLAM model outperformed the CLAM model or is on par. The performance of both models was comparable to that of two pathologists who scored 240 BCC positive slides. Additionally, in the public test set, StreamingCLAM demonstrated a comparable AUC of 0.958, markedly superior to CLAM's 0.803. This difference was statistically significant and emphasized the strength and better adaptability of the StreamingCLAM approach.


Subject(s)
Carcinoma, Basal Cell , Skin Neoplasms , Humans , Carcinoma, Basal Cell/diagnostic imaging , Area Under Curve , Skin Neoplasms/diagnostic imaging , Supervised Machine Learning
2.
Front Oncol ; 13: 1107171, 2023.
Article in English | MEDLINE | ID: mdl-36845702

ABSTRACT

Clonality assessment using the unique rearrangements of immunoglobulin (IG) and T-cell receptor (TR) genes in lymphocytes is a widely applied supplementary test for the diagnosis of B-cell and T-cell lymphoma. To enable a more sensitive detection and a more precise comparison of clones compared with conventional clonality analysis based on fragment analysis, the EuroClonality NGS Working Group developed and validated a next-generation sequencing (NGS)-based clonality assay for detection of the IG heavy and kappa light chain and TR gene rearrangements for formalin-fixed and paraffin-embedded tissues. We outline the features and advantages of NGS-based clonality detection and discuss potential applications for NGS-based clonality testing in pathology, including site specific lymphoproliferations, immunodeficiency and autoimmune disease and primary and relapsed lymphomas. Also, we briefly discuss the role of T-cell repertoire of reactive lymphocytic infiltrations in solid tumors and B-lymphoma.

3.
Hum Reprod ; 37(10): 2275-2290, 2022 09 30.
Article in English | MEDLINE | ID: mdl-35944167

ABSTRACT

STUDY QUESTION: What is the accuracy and agreement of embryologists when assessing the implantation probability of blastocysts using time-lapse imaging (TLI), and can it be improved with a data-driven algorithm? SUMMARY ANSWER: The overall interobserver agreement of a large panel of embryologists was moderate and prediction accuracy was modest, while the purpose-built artificial intelligence model generally resulted in higher performance metrics. WHAT IS KNOWN ALREADY: Previous studies have demonstrated significant interobserver variability amongst embryologists when assessing embryo quality. However, data concerning embryologists' ability to predict implantation probability using TLI is still lacking. Emerging technologies based on data-driven tools have shown great promise for improving embryo selection and predicting clinical outcomes. STUDY DESIGN, SIZE, DURATION: TLI video files of 136 embryos with known implantation data were retrospectively collected from two clinical sites between 2018 and 2019 for the performance assessment of 36 embryologists and comparison with a deep neural network (DNN). PARTICIPANTS/MATERIALS, SETTING, METHODS: We recruited 39 embryologists from 13 different countries. All participants were blinded to clinical outcomes. A total of 136 TLI videos of embryos that reached the blastocyst stage were used for this experiment. Each embryo's likelihood of successfully implanting was assessed by 36 embryologists, providing implantation probability grades (IPGs) from 1 to 5, where 1 indicates a very low likelihood of implantation and 5 indicates a very high likelihood. Subsequently, three embryologists with over 5 years of experience provided Gardner scores. All 136 blastocysts were categorized into three quality groups based on their Gardner scores. Embryologist predictions were then converted into predictions of implantation (IPG ≥ 3) and no implantation (IPG ≤ 2). Embryologists' performance and agreement were assessed using Fleiss kappa coefficient. A 10-fold cross-validation DNN was developed to provide IPGs for TLI video files. The model's performance was compared to that of the embryologists. MAIN RESULTS AND THE ROLE OF CHANCE: Logistic regression was employed for the following confounding variables: country of residence, academic level, embryo scoring system, log years of experience and experience using TLI. None were found to have a statistically significant impact on embryologist performance at α = 0.05. The average implantation prediction accuracy for the embryologists was 51.9% for all embryos (N = 136). The average accuracy of the embryologists when assessing top quality and poor quality embryos (according to the Gardner score categorizations) was 57.5% and 57.4%, respectively, and 44.6% for fair quality embryos. Overall interobserver agreement was moderate (κ = 0.56, N = 136). The best agreement was achieved in the poor + top quality group (κ = 0.65, N = 77), while the agreement in the fair quality group was lower (κ = 0.25, N = 59). The DNN showed an overall accuracy rate of 62.5%, with accuracies of 62.2%, 61% and 65.6% for the poor, fair and top quality groups, respectively. The AUC for the DNN was higher than that of the embryologists overall (0.70 DNN vs 0.61 embryologists) as well as in all of the Gardner groups (DNN vs embryologists-Poor: 0.69 vs 0.62; Fair: 0.67 vs 0.53; Top: 0.77 vs 0.54). LIMITATIONS, REASONS FOR CAUTION: Blastocyst assessment was performed using video files acquired from time-lapse incubators, where each video contained data from a single focal plane. Clinical data regarding the underlying cause of infertility and endometrial thickness before the transfer was not available, yet may explain implantation failure and lower accuracy of IPGs. Implantation was defined as the presence of a gestational sac, whereas the detection of fetal heartbeat is a more robust marker of embryo viability. The raw data were anonymized to the extent that it was not possible to quantify the number of unique patients and cycles included in the study, potentially masking the effect of bias from a limited patient pool. Furthermore, the lack of demographic data makes it difficult to draw conclusions on how representative the dataset was of the wider population. Finally, embryologists were required to assess the implantation potential, not embryo quality. Although this is not the traditional approach to embryo evaluation, morphology/morphokinetics as a means of assessing embryo quality is believed to be strongly correlated with viability and, for some methods, implantation potential. WIDER IMPLICATIONS OF THE FINDINGS: Embryo selection is a key element in IVF success and continues to be a challenge. Improving the predictive ability could assist in optimizing implantation success rates and other clinical outcomes and could minimize the financial and emotional burden on the patient. This study demonstrates moderate agreement rates between embryologists, likely due to the subjective nature of embryo assessment. In particular, we found that average embryologist accuracy and agreement were significantly lower for fair quality embryos when compared with that for top and poor quality embryos. Using data-driven algorithms as an assistive tool may help IVF professionals increase success rates and promote much needed standardization in the IVF clinic. Our results indicate a need for further research regarding technological advancement in this field. STUDY FUNDING/COMPETING INTEREST(S): Embryonics Ltd is an Israel-based company. Funding for the study was partially provided by the Israeli Innovation Authority, grant #74556. TRIAL REGISTRATION NUMBER: N/A.


Subject(s)
Artificial Intelligence , Embryo Implantation , Blastocyst , Embryo Culture Techniques/methods , Female , Fertilization in Vitro , Humans , Probability , Retrospective Studies
4.
J Immunother Cancer ; 10(5)2022 05.
Article in English | MEDLINE | ID: mdl-35550553

ABSTRACT

BACKGROUND: Immune checkpoint inhibitors (ICI) can lead to long-term responses in patients with metastatic melanoma. Still many patients with melanoma are intrinsically resistant or acquire secondary resistance. Previous studies have used primary or metastatic tumor tissue for biomarker assessment. Especially in melanoma, metastatic lesions are often present at different anatomical sites such as skin, lymph nodes, and visceral organs. The anatomical site may directly affect the tumor microenvironment (TME). To evaluate the impact of tumor evolution on the TME and on ICI treatment outcome, we directly compared paired primary and metastatic melanoma lesions for tumor mutational burden (TMB), HLA-ABC status, and tumor infiltrating lymphocytes (TILs) of patients that received ipilimumab. METHODS: TMB was analyzed by sequencing primary and metastatic melanoma lesions using the TruSight Oncology 500 assay. Tumor tissues were subjected to multiplex immunohistochemistry to assess HLA-ABC status and for the detection of TIL subsets (B cells, cytotoxic T cells, helper T cells, and regulatory T cells), by using a machine-learning algorithm. RESULTS: While we observed a very good agreement between TMB of matched primary and metastatic melanoma lesions (intraclass coefficient=0.921), such association was absent for HLA-ABC status, TIL density, and subsets thereof. Interestingly, analyses of different metastatic melanoma lesions within a single patient revealed that TIL density and composition agreed remarkably well, rejecting the hypothesis that the TME of different anatomical sites affects TIL infiltration. Similarly, the HLA-ABC status between different metastatic lesions within patients was also comparable. Furthermore, high TMB, of either primary or metastatic melanoma tissue, directly correlated with response to ipilimumab, whereas lymphocyte density or composition did not. Loss of HLA-ABC in the metastatic lesion correlated to a shorter progression-free survival on ipilimumab. CONCLUSIONS: We confirm the link between TMB and HLA-ABC status and the response to ipilimumab-based immunotherapy in melanoma, but no correlation was found for TIL density, neither in primary nor metastatic lesions. Our finding that TMB between paired primary and metastatic melanoma lesions is highly stable, demonstrates its independency of the time point and location of acquisition. TIL and HLA-ABC status in metastatic lesions of different anatomical sites are highly similar within an individual patient.


Subject(s)
Melanoma , Biomarkers, Tumor/metabolism , Humans , Ipilimumab/therapeutic use , Lymphocytes, Tumor-Infiltrating , Melanoma/drug therapy , Melanoma/genetics , Tumor Microenvironment
5.
Ann Diagn Pathol ; 58: 151915, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35276548

ABSTRACT

BACKGROUND: Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are rare cutaneous neoplasms forming a spectrum. Case reports with recurrences and metastasis have been published despite the current view that AFX is benign. The aim of this study was to identify clinical and histopathological features that predict tumor recurrence. METHODS: A retrospective review of AFX and PDS cases was performed. Clinical characteristics were obtained from patient records. RESULTS: A total of 29 AFX and 23 PDS cases were identified. Review led to re-classification of 12 cases (18%). In 14/50 (26.9%) cases a recurrence occurred. Recurrences were significantly more likely to occur when the tumor showed any infiltration in the subcutaneous fat (100% vs 43.2%, p = 0.000) or when the tumor diameter exceeded 2 cm (46.2% vs 16.2%, p = 0.030). CONCLUSIONS: This study shows that histopathological distinction between AFX and PDS remains difficult with reclassification in 12 out of 52 (18%) cases upon review. All AFX cases solely confined to the dermis behaved benign. We therefore advocate to classify all cases with any form of subcutaneous extension as PDS, and only lesions without as AFX. This contrasts with the current general opinion in which superficial subcutaneous invasion is still accepted in AFX.


Subject(s)
Bone Neoplasms , Breast Neoplasms , Histiocytoma, Malignant Fibrous , Sarcoma , Skin Neoplasms , Biomarkers, Tumor , Breast Neoplasms/complications , Diagnosis, Differential , Female , Humans , Recurrence , Sarcoma/diagnosis , Sarcoma/pathology , Skin Neoplasms/pathology , Subcutaneous Fat/pathology , Subcutaneous Tissue/pathology
6.
J Perinat Med ; 49(9): 1071-1083, 2021 Nov 25.
Article in English | MEDLINE | ID: mdl-34114389

ABSTRACT

OBJECTIVES: Preeclampsia is a dangerous pregnancy complication. The source of preeclampsia is unknown, though the placenta is believed to have a central role in its pathogenesis. An association between maternal infection and preeclampsia has been demonstrated, yet the involvement of the placental microbiome in the etiology of preeclampsia has not been determined. In this study, we examined whether preeclampsia is associated with an imbalanced microorganism composition in the placenta. METHODS: To this end, we developed a novel method for the identification of bacteria/viruses based on sequencing of small non-coding RNA, which increases the microorganism-to-host ratio, this being a major challenge in microbiome methods. We validated the method on various infected tissues and demonstrated its efficiency in detecting microorganisms in samples with extremely low bacterial/viral biomass. We then applied the method to placenta specimens from preeclamptic and healthy pregnancies. Since the placenta is a remarkably large and heterogeneous organ, we explored the bacterial and viral RNA at each of 15 distinct locations. RESULTS: Bacterial RNA was detected at all locations and was consistent with previous studies of the placental microbiome, though without significant differences between the preeclampsia and control groups. Nevertheless, the bacterial RNA composition differed significantly between various areas of the placenta. Viral RNA was detected in extremely low quantities, below the threshold of significance, thus viral abundance could not be determined. CONCLUSIONS: Our results suggest that the bacterial and viral abundance in the placenta may have only limited involvement in the pathogenesis of preeclampsia. The evidence of a heterogenic bacterial RNA composition in the various placental locations warrants further investigation to capture the true nature of the placental microbiome.


Subject(s)
Microbiota/genetics , Placenta/microbiology , Pre-Eclampsia , RNA, Bacterial , RNA, Viral , Sequence Analysis, RNA , Adult , Bacteria/classification , Bacteria/isolation & purification , Correlation of Data , Female , Humans , Outcome Assessment, Health Care , Placenta/pathology , Pre-Eclampsia/blood , Pre-Eclampsia/diagnosis , Pre-Eclampsia/microbiology , Pregnancy , RNA, Bacterial/analysis , RNA, Bacterial/isolation & purification , RNA, Untranslated/analysis , RNA, Untranslated/isolation & purification , RNA, Viral/analysis , RNA, Viral/isolation & purification , Reproducibility of Results , Sequence Analysis, RNA/methods , Sequence Analysis, RNA/statistics & numerical data , Specimen Handling/methods
7.
Cancers (Basel) ; 13(7)2021 Mar 31.
Article in English | MEDLINE | ID: mdl-33807446

ABSTRACT

Merkel cell carcinoma (MCC) is a rare neuroendocrine tumor of the skin mainly seen in the elderly. Its incidence is rising due to ageing of the population, increased sun exposure, and the use of immunosuppressive medication. Additionally, with the availability of specific immunohistochemical markers, MCC is easier to recognize. Typically, these tumors are rapidly progressive and behave aggressively, emphasizing the need for early detection and prompt diagnostic work-up and start of treatment. In this review, the tumor biology and immunology, current diagnostic and treatment modalities, as well as new and combined therapies for MCC, are discussed. MCC is a very immunogenic tumor which offers good prospects for immunotherapy. Given its rarity, the aggressiveness, and the frail patient population it concerns, MCC should be managed in close collaboration with an experienced multidisciplinary team.

8.
Proc Natl Acad Sci U S A ; 115(17): 4459-4464, 2018 04 24.
Article in English | MEDLINE | ID: mdl-29626130

ABSTRACT

The evolution of development has been studied through the lens of gene regulation by examining either closely related species or extremely distant animals of different phyla. In nematodes, detailed cell- and stage-specific expression analyses are focused on the model Caenorhabditis elegans, in part leading to the view that the developmental expression of gene cascades in this species is archetypic for the phylum. Here, we compared two species of an intermediate evolutionary distance: the nematodes C. elegans (clade V) and Acrobeloides nanus (clade IV). To examine A. nanus molecularly, we sequenced its genome and identified the expression profiles of all genes throughout embryogenesis. In comparison with C. elegans, A. nanus exhibits a much slower embryonic development and has a capacity for regulative compensation of missing early cells. We detected conserved stages between these species at the transcriptome level, as well as a prominent middevelopmental transition, at which point the two species converge in terms of their gene expression. Interestingly, we found that genes originating at the dawn of the Ecdysozoa supergroup show the least expression divergence between these two species. This led us to detect a correlation between the time of expression of a gene and its phylogenetic age: evolutionarily ancient and young genes are enriched for expression in early and late embryogenesis, respectively, whereas Ecdysozoa-specific genes are enriched for expression during the middevelopmental transition. Our results characterize the developmental constraints operating on each individual embryo in terms of developmental stages and genetic evolutionary history.


Subject(s)
Evolution, Molecular , Gene Expression Regulation, Developmental/physiology , Phylogeny , Rhabditida/embryology , Transcriptome/physiology , Animals , Rhabditida/classification , Rhabditida/genetics
9.
J Perinat Med ; 44(8): 887-892, 2016 Oct 01.
Article in English | MEDLINE | ID: mdl-26677882

ABSTRACT

OBJECTIVE: To compare indications for delivery and neonatal morbidities between twins and singletons born between 34 and 35 weeks of gestation. STUDY DESIGN: A prospective observational study was performed in which all infants born between January and August 2008, at Sheba Medical Center at 34 0/7-35 6/7 weeks of gestational age were included. Indications for delivery, infants' morbidities and medical interventions were documented. Twins and singletons were compared for antenatal maternal characteristics, risks of short-term neonatal complications and interventions. RESULTS: One hundred and seventy-three mothers and 229 neonates (114 twins and 115 singletons) were included. Background maternal characteristics as well as the use of antenatal steroids and MgSO4 were similar between the groups. Only 44% of all deliveries were spontaneous, while the rest were indicated deliveries. Twins were born lighter and 31.9% of them were SGA. Nevertheless, singletons were significantly more likely to receive medical interventions such as prolonged oxygen use (>1 day) and phototherapy. All late preterm infants (n=5) needing surfactant administration were singletons. Overall, the risk of needing any medical intervention was significantly higher for singletons compared with twins (OR 1.8, 95% CI 1.02-3.2). CONCLUSIONS: A significant proportion of late preterm births is iatrogenic. Twins and singletons are dissimilar with regards to risks of short-term complications. Despite being born smaller and more SGA, twins are at lower risk of requiring medical intervention in the immediate neonatal period compared with singletons.


Subject(s)
Infant, Premature , Pregnancy, Multiple , Premature Birth , Twins , Adult , Female , Gestational Age , Humans , Infant , Infant Mortality , Infant, Newborn , Israel/epidemiology , Male , Pregnancy , Pregnancy Outcome , Pregnancy, Multiple/statistics & numerical data , Premature Birth/epidemiology , Prospective Studies , Twins/statistics & numerical data
11.
J Matern Fetal Neonatal Med ; 28(8): 876-82, 2015 May.
Article in English | MEDLINE | ID: mdl-24962498

ABSTRACT

OBJECTIVE: To ascertain the most common early morbidities in a cohort of infants born at 34-35 weeks gestation and to identify the risk factors associated with these morbidities. METHODS: Retrospective analysis of data collected prospectively for all 235 infants born at 34-35 weeks of gestation during an eight-month period at a single tertiary medical center. Study group infants (SG) were compared with 470 term infants (TI), matched both for gender and for mode of delivery. RESULTS: Jaundice requiring phototherapy (32%), respiratory disease (19.1%) and cyanotic episodes (15.7%) were the most frequent early morbidities, followed by hypoglycemia, temperature instability and feeding intolerance. The risk of having a complication was 13.3-times higher in the SG compared with the TI group (95% CI 8.9-19.6, p < 0.001). Modifiable interventions associated with these morbidities were antenatal steroids, MgSO4 and mode of delivery. Non-modifiable factors were maternal age, parity, twins and gender. CONCLUSIONS: Jaundice requiring phototherapy, respiratory disease and cyanotic episodes are the most frequent early morbidities among infants born at 34-35 weeks. Medically modifiable factors were found to be associated with the above morbidities. Whether specific recommendations for the care of these infants will affect early morbidities needs to be studied in controlled prospective studies.


Subject(s)
Infant, Premature, Diseases/etiology , Adult , Female , Humans , Infant, Newborn , Infant, Premature , Infant, Premature, Diseases/epidemiology , Israel/epidemiology , Logistic Models , Male , Multivariate Analysis , Pregnancy , Pregnancy Complications/epidemiology , Prevalence , Retrospective Studies , Risk Factors
12.
Acute Med ; 11(3): 138-42, 2012.
Article in English | MEDLINE | ID: mdl-22993743

ABSTRACT

Venous thromboembolic disease (VTE) is a common presentation in acute medicine and ensuring fast, accurate diagnosis and appropriate management is important. Getting it right not only reduces mortality but can also reduce the long-term complications associated with the disease such as post-thrombotic syndrome (PTS) and chronic thromboembolic pulmonary hypertension.


Subject(s)
Anticoagulants/administration & dosage , Practice Guidelines as Topic , Thrombolytic Therapy/methods , Thrombophilia/diagnosis , Venous Thromboembolism/drug therapy , Anticoagulants/adverse effects , Blood Coagulation Tests/methods , Disease Management , Female , Follow-Up Studies , Guideline Adherence , Humans , Male , Phlebography/methods , Pulmonary Embolism/diagnostic imaging , Pulmonary Embolism/drug therapy , Risk Assessment , Role , Thrombolytic Therapy/adverse effects , Treatment Outcome , United Kingdom , Venous Thromboembolism/diagnostic imaging , Venous Thrombosis/diagnostic imaging , Venous Thrombosis/drug therapy
13.
Biol Blood Marrow Transplant ; 18(2): 210-9, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22015995

ABSTRACT

After HLA class I-mismatched stem cell transplantation, allo-HLA-directed CD8 T cell responses can be activated without the help of CD4 T cells if memory CD8 T cells cross-reactive against the allo-HLA class I are present or if naïve CD8 T cells are administered during inflammatory conditions. However, in the absence of inflammatory conditions, cooperation between CD4 and CD8 T cells likely is required for an effective primary CD8 T cell response directed against allo-HLA class I. In this study we investigated whether a coordinated response of CD8 and CD4 T cells could be demonstrated in an HLA class I-directed immune response in a patient who developed severe graft-versus-host disease (GVHD) after the administration HLA-A2-mismatched donor lymphocyte infusion in the absence of inflammatory conditions. A previously administered donor lymphocyte infusion from the same donor did not lead to an immune response, excluding the presence of a substantial pool of CD8 T cells cross-reactive against HLA-A2 within the memory T cell compartment of the donor. Analysis of isolated donor CD8 and CD4 T cell clones activated during the GVHD revealed a polyclonal CD8 T cell response directed against the mismatched HLA-A2 and a polyclonal CD4 T cell response recognizing HLA-A2-derived peptides presented in HLA class II. In addition, leukemic blasts present at the time of the emergence of GVHD expressed HLA-A2 and HLA class II and could activate both the CD4 and CD8 alloreactive T cells. Our results demonstrate that the GVHD was mediated by a cooperative CD4 and CD8 response directed against the mismatched HLA-A2 and suggest that leukemic blasts possibly activated this CD8 and CD4 T cell response.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Graft vs Host Disease/immunology , HLA-A2 Antigen/immunology , Lymphocyte Activation , Stem Cell Transplantation , Acute Disease , CD4-Positive T-Lymphocytes/pathology , CD8-Positive T-Lymphocytes/pathology , Graft vs Host Disease/pathology , Histocompatibility Antigens Class II/immunology , Histocompatibility Testing , Humans , Immunologic Memory , Leukemia, Myeloid, Acute/immunology , Leukemia, Myeloid, Acute/therapy , Male , Middle Aged
14.
Blood ; 118(26): 6733-42, 2011 Dec 22.
Article in English | MEDLINE | ID: mdl-21972290

ABSTRACT

T-cell alloreactivity directed against non-self-HLA molecules has been assumed to be less peptide specific than conventional T-cell reactivity. A large variation in degree of peptide specificity has previously been reported, including single peptide specificity, polyspecificity, and peptide degeneracy. Peptide polyspecificity was illustrated using synthetic peptide-loaded target cells, but in the absence of confirmation against endogenously processed peptides this may represent low-avidity T-cell reactivity. Peptide degeneracy was concluded based on recognition of Ag-processing defective cells. In addition, because most investigated alloreactive T cells were in vitro activated and expanded, the previously determined specificities may have not been representative for alloreactivity in vivo. To study the biologically relevant peptide specificity and avidity of alloreactivity, we investigated the degree of peptide specificity of 50 different allo-HLA-reactive T-cell clones which were activated and expanded in vivo during GVHD. All but one of the alloreactive T-cell clones, including those reactive against Ag-processing defective T2 cells, recognized a single peptide allo-HLA complex, unique for each clone. Down-regulation of the expression of the recognized Ags using silencing shRNAs confirmed single peptide specificity. Based on these results, we conclude that biologically relevant alloreactivity selected during in vivo immune response is peptide specific.


Subject(s)
Graft vs Host Disease/immunology , HLA Antigens/immunology , Peptides/immunology , T-Lymphocytes/immunology , Amino Acid Sequence , Amino Acid Substitution , Cell Line, Transformed , Cells, Cultured , Chromatography, High Pressure Liquid , Gene Expression , Graft vs Host Disease/etiology , HLA Antigens/genetics , HLA-A2 Antigen/genetics , HLA-A2 Antigen/immunology , Hematopoietic Stem Cell Transplantation/adverse effects , Humans , Isoantigens/immunology , K562 Cells , Lymphocyte Activation/immunology , Mass Spectrometry , Peptides/genetics , Peptides/isolation & purification , RNA Interference , Reverse Transcriptase Polymerase Chain Reaction , T-Lymphocytes/metabolism
15.
Clin Cancer Res ; 17(17): 5615-25, 2011 Sep 01.
Article in English | MEDLINE | ID: mdl-21771875

ABSTRACT

PURPOSE: In human leukocyte antigen (HLA)-matched stem cell transplantation (SCT), it has been shown that beneficial immune response mediating graft-versus-tumor (GVT) responses can be separated from graft-versus-host disease (GVHD) immune responses. In this study, we investigated whether it would be possible to dissect the beneficial immune response of allo-HLA-reactive T cells with potent antitumor reactivity from GVHD-inducing T cells present in the detrimental immune response after HLA-mismatched SCT. EXPERIMENTAL DESIGN: The presence of specific tumor-reactive T cells in the allo-HLA repertoire was analyzed at the time of severe GVHD after HLA-mismatched SCT, using tetramers composed of different tumor-associated antigens (TAA). RESULTS: High-avidity allo-HLA-restricted T cells specific for the TAA preferentially expressed antigen on melanomas (PRAME) were identified that exerted highly single-peptide-specific reactivity. The T cells recognized multiple different tumor cell lines and leukemic cells, whereas no reactivity against a large panel of nonmalignant cells was observed. These T cells, however, also exerted low reactivity against mature dendritic cells (DC) and kidney epithelial cells, which was shown to be because of low PRAME expression. CONCLUSIONS: On the basis of potential beneficial specificity and high reactivity, the T-cell receptors of these PRAME-specific T cells may be effective tools for adoptive T-cell therapy. Clinical studies have to determine the significance of the reactivity observed against mature DCs and kidney epithelial cells.


Subject(s)
Antigens, Neoplasm/immunology , Genes, T-Cell Receptor , Graft vs Tumor Effect , Neoplasms/therapy , T-Lymphocytes, Cytotoxic/immunology , Dendritic Cells/immunology , Gene Transfer Techniques , Graft vs Host Disease , Histocompatibility Antigens Class I/immunology , Histocompatibility Antigens Class II/immunology , Humans , Immunotherapy, Adoptive , Kidney/immunology , RNA Interference , RNA, Small Interfering , Stem Cell Transplantation
16.
Proc Natl Acad Sci U S A ; 107(24): 10972-7, 2010 Jun 15.
Article in English | MEDLINE | ID: mdl-20534461

ABSTRACT

Adoptive transfer of T cell receptor (TCR)-transduced T cells may be an attractive strategy to target both hematological malignancies and solid tumors. By introducing a TCR, large numbers of T cells with defined antigen (Ag) specificity can be obtained. However, by introduction of a TCR, mixed TCR dimers can be formed. Besides the decrease in TCR expression of the introduced and endogenous TCR, these mixed TCR dimers could harbor potentially harmful specificities. In this study, we demonstrate that introduction of TCRs resulted in formation of neoreactive mixed TCR dimers, composed of the introduced TCR chains pairing with either the endogenous TCR alpha or beta chain. Neoreactivities observed were HLA class I or class II restricted. Most neoreactive mixed TCR dimers were allo-HLA reactive; however, neoreactive mixed TCR dimers with autoreactive activity were also observed. We demonstrate that inclusion of an extra disulfide bond between the constant domains of the introduced TCR markedly reduced neoreactivity, whereas enhanced effectiveness of the introduced TCR was observed. In conclusion, TCR transfer results in the formation of neoreactive mixed TCR dimers with the potential to generate off-target effects, underlining the importance of searching for techniques to facilitate preferential pairing.


Subject(s)
Receptors, Antigen, T-Cell/chemistry , Receptors, Antigen, T-Cell/metabolism , Adoptive Transfer , Cell Line , Cysteine/chemistry , Dimerization , HLA Antigens/metabolism , Humans , In Vitro Techniques , Protein Multimerization , Receptors, Antigen, T-Cell/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , T-Lymphocytes/immunology , Transduction, Genetic
17.
Blood ; 115(15): 3146-57, 2010 Apr 15.
Article in English | MEDLINE | ID: mdl-20160165

ABSTRACT

Graft-versus-host disease and graft rejection are major complications of allogeneic HLA-mismatched stem cell transplantation or organ transplantation that are caused by alloreactive T cells. Because a range of acute viral infections have been linked to initiating these complications, we hypothesized that the cross-reactive potential of virus-specific memory T cells to allogeneic (allo) HLA molecules may be able to mediate these complications. To analyze the allo-HLA reactivity, T cells specific for Epstein-Barr virus, cytomegalovirus, varicella zoster virus, and influenza virus were tested against a panel of HLA-typed target cells, and target cells transduced with single HLA molecules. Eighty percent of T-cell lines and 45% of virus-specific T-cell clones were shown to cross-react against allo-HLA molecules. The cross-reactivity of the CD8 and CD4 T-cell clones was directed primarily against HLA class I and II, respectively. However, a restricted number of CD8 T cells exhibited cross-reactivity to HLA class II. T-cell receptor (TCR) gene transfer confirmed that allo-HLA reactivity and virus specificity were mediated via the same TCR. These results demonstrate that a substantial proportion of virus-specific T cells exert allo-HLA reactivity, which may have important clinical implications in transplantation settings as well as adoptive transfer of third-party virus-specific T cells.


Subject(s)
HLA Antigens/immunology , Immunologic Memory/immunology , T-Lymphocytes/immunology , T-Lymphocytes/virology , Viruses/immunology , Cell Line , Clone Cells , Cytotoxicity, Immunologic , Herpesvirus 4, Human/immunology , Humans , Lymphocyte Subsets/immunology , Lymphocyte Subsets/virology , Receptors, Antigen, T-Cell/immunology , Species Specificity , Transplantation, Homologous
19.
J Biol Chem ; 278(33): 30828-34, 2003 Aug 15.
Article in English | MEDLINE | ID: mdl-12799378

ABSTRACT

T cell factor (Tcf) proteins bind beta-catenin and are downstream effectors of Wnt/beta-catenin signals. A recently demonstrated interaction between beta-catenin and the androgen receptor (AR) ligand binding domain has suggested that AR may be a Tcf-independent Wnt/beta-catenin effector. This study demonstrates that there is a direct interaction between the AR DNA binding domain (DBD) and Tcf4. Tcf4 bound specifically to a glutathione S-transferase-ARDBD fusion protein and could be coimmunoprecipitated with beta-catenin and transfected AR or endogenous AR in prostate cancer cells. Transfected Tcf4 repressed the transcriptional activity of full-length AR and a VP16-ARDBD fusion protein, and this repression was only partially reversed by transfected beta-catenin. AR activation by cyproterone acetate, a partial agonist that did not support beta-catenin binding to the AR, was also repressed by Tcf4, further indicating that repression was not due to beta-catenin sequestration. Tcf4 could recruit beta-catenin to the AR DBD in vitro and to the cyproterone acetate-liganded AR in vivo. Chromatin immunoprecipitation experiments in LNCaP prostate cancer cells showed that endogenous AR was bound to a Tcf4-responsive element in the c-myc promoter. These findings indicate that AR and Tcf4 can interact directly and that this interaction may occur on the promoters or enhancers of particular genes. The direct AR-Tcf4 interaction, in conjunction AR- and Tcf4-beta-catenin binding, provides a mechanism for cooperative and selective gene regulation by AR and the Wnt/beta-catenin-Tcf pathway that may contribute to normal and neoplastic prostate growth.


Subject(s)
Cytoskeletal Proteins/metabolism , Prostatic Neoplasms , Receptors, Androgen/metabolism , Trans-Activators/metabolism , Transcription Factors/metabolism , Zebrafish Proteins , Androgen Antagonists/metabolism , Androgen Antagonists/pharmacology , Cyproterone Acetate/metabolism , Cyproterone Acetate/pharmacology , Humans , Ligands , Male , Protein Binding/physiology , Proto-Oncogene Proteins/metabolism , Receptors, Androgen/genetics , Signal Transduction/physiology , TCF Transcription Factors , Transcription Factor 7-Like 2 Protein , Transcription Factors/genetics , Transcriptional Activation/physiology , Transfection , Tumor Cells, Cultured , Wnt Proteins , beta Catenin
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