Abstract
Cure rates of classical Hodgkin Lymphoma (cHL) in children and young adult patients currently exceed 90%. Nonetheless, survivors are confronted with chronic therapy-related health conditions ...such as infertility, cardiovascular disease, and high rates of novel second cancers. This calls for development of new targeted and less toxic treatments. cHL is characterized by a low frequency (~0.1-5%) of malignant Hodgkin Reed-Sternberg (HRS) cells, while most of the tissue is composed of nonmalignant immune cells. It is thought that the HRS cells depend on interactions with the tumor microenvironment (TME) for their survival. Indeed, a vast number of interactions between different immune and HRS cells have been reported; however, most of these reports are based on immunohistochemistry or in vitro studies. Here, we systematically characterized the in vivo interactions by applying single-cell RNA sequencing (scRNAseq) to nine primary pediatric and adolescent cHL biopsies and three noncancerous control biopsies of reactive lymph nodes. With scRNAseq, we first sorted live cells to get an unbiased overview of the TME. Then we used a previously published flow cytometry antibody panel to enrich for HRS cells, allowing us to directly assess interactions on a per-tumor basis. Tumor cell identity was confirmed by marker expression as identified by pathology, single-cell copy-number status and the ratio of immunoglobulin kappa/lambda expression. Immune cell identity was determined by canonical marker expression. Using the scRNAseq data, we found that the TME expression profiles in cHL and control biopsies mostly overlap but harbor some differences. First, we identified genes that are consistently overexpressed in HRS cells. These included transcription factors, neural markers, multiple interleukins and other signaling molecules. Second, the extensively described immunosuppressive interactions between HRS, T and NK cells (expressing CTLA-4, TIM-3, and LAG-3) were the strongest and most common interactions that we could identify in HL but not in noncancerous reactive lymph nodes. Third, while the inflammation in the reactive lymph nodes was driven by IFN-g signaling, this pathway was inactive in HL tumors. Other interactions like recruitment of CXCR3+ and CCR4+ T cells, CD47 signaling and interleukin signaling were less pronounced in cHL compared to the controls or were less consistent between tumors. These findings were validated in bulk RNA sequencing of 45 HL tumors. A model arises in which the presence of HRS cells induces inflammation that in most ways resembles lymph node infections. This inflammation and HRS survival are controled by patient-specific interactions between HRS cells and the TME, and by T cell exhaustion, which is universal and the most essential interaction in cHL.
Citation Format: Jurrian K. de Kanter, Thanasis Margaritis, Auke Beishuizen, Marijn Scheijde-Vermeulen, Liset Westera, Arianne M. Brandsma, Ruben van Boxtel, Friederike Meyer-Wentrup. Single-cell RNA sequencing reveals that childhood classical Hodgkin Lymphoma resembles normal inflammation except for T cell exhaustion abstract. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A37.
Cistus creticus subsp. creticus is a plant of intrinsic scientific interest due to the distinctive pharmaceutical properties of its resin. Labdane-type diterpenes, the main constituents of the resin, ...exhibit considerable antibacterial and cytotoxic activities. In this study chemical analysis of isolated trichomes from different developmental stages revealed that young leaves of 1-2 cm length displayed the highest content of labdane-type diterpenes (80 mg/g fresh weight) whereas trichomes from older leaves (2-3 or 3-4 cm) exhibited gradual decreased concentrations. A cDNA library was constructed enriched in transcripts from trichomes isolated from young leaves, which are characterized by high levels of labdane-type diterpenes. Functional annotation of 2,022 expressed sequence tags (ESTs) from the trichome cDNA library based on homology to A. thaliana genes suggested that 8% of the putative identified sequences were secondary metabolism-related and involved primarily in flavonoid and terpenoid biosynthesis. A significant proportion of the ESTs (38%) displayed no significant similarity to any other DNA deposited in databases, indicating a yet unknown function. Custom DNA microarrays constructed with 1,248 individual clones from the cDNA library facilitated transcriptome comparisons between trichomes and trichome-free tissues. In addition, gene expression studies in various Cistus tissues and organs for one of the genes highlighted as the most differentially expressed by the microarray experiments revealed a putative sesquiterpene synthase with a trichome-specific expression pattern. Full length cDNA isolation and heterologous expression in E. coli followed by biochemical analysis, led to the characterization of the produced protein as germacrene B synthase.
DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing ...some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene‐ And Slide‐Specific Correction, GASSCO) is presented, whereby sequence‐specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence‐based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.
Recent research trends focus on how multiscale biomedical information can be modeled and transformed into knowledge, in order to lead to a less interfering but also more individualized diagnosis and ...therapy. In order to assess the clinical importance of models of human pathology (e.g. cancer), it is necessary to validate them with prior and post treatment clinical data which in turn requires the determination of the tumor size and shape with high resolution, accuracy and precision, as well as structural and physiological information. This paper discusses some of the most important image analysis challenges in order to define an optimal method for extracting more accurate and precise anatomical and functional information related to the underlying pathology, which can be used for initializing and validating models of pathophysiology as well as simulations/predictions of the response to therapeutical regimes.
DNA microarrays have demonstrated an excellent potential in correlating specific gene expression profiles to specific conditions. However, they are affected by inherent noise. This paper presents a ...two-stage approach for noise removal that processes the additive and the multiplicative noise component. The proposed approach first decomposes the signal by a multiresolution transform and then accounts for both the multiscale correlation of the subband decompositions and their heavy-tailed statistics. Real microarray images have been processed by the proposed method and its improved performance is shown through quantitative measures and qualitative visual evaluation.
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