Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell-intrinsic Stemness or Mesenchymality Characteristics

Epithelial-to-mesenchymal transition (EMT) in cancer cells confers migratory abilities, a crucial aspect in the metastasis of tumors that frequently leads to death. In multiple studies, authors proposed gene expression signatures for EMT, stemness, or mesenchymality of tumors based on bulk tumor expression profiling. However, recent studies suggested that noncancerous cells from the microenvironment or macroenvironment heavily influence such signature profiles. Here, we strengthen these findings by investigating 11 published and frequently referenced gene expression signatures that were proposed to describe EMT-related (EMT, mesenchymal, or stemness) characteristics in various cancer types. By analyses of bulk, single-cell, and pseudobulk expression data, we show that the cell type composition of a tumor sample frequently dominates scores of these EMT-related signatures. A comprehensive, integrated analysis of bulk RNA sequencing (RNA-seq) and single-cell RNA-seq data shows that stromal cells, most often fibroblasts, are the main drivers of EMT-related signature scores. We call attention to the risk of false conclusions about tumor properties when interpreting EMT-related signatures, especially in a clinical setting: high patient scores of EMT-related signatures or calls of "stemness subtypes" often result from low cancer cell content in tumor biopsies rather than cancer cell-specific stemness or mesenchymal/EMT characteristics.

SIGNIFICANCE

Cancer self-renewal and migratory abilities are often characterized via gene module expression profiles, also called EMT or stemness gene expression signatures. Using published clinical tumor samples, cancer cell lines, and single cancer cells, we highlight the dominating influence of noncancer cells in low cancer cell content biopsies on their scores. We caution on their application for low cancer cell content clinical cancer samples with the intent to assign such characteristics or subtypes.

Identification of a Notch transcriptomic signature for breast cancer

BACKGROUND

Dysregulated Notch signalling contributes to breast cancer development and progression, but validated tools to measure the level of Notch signalling in breast cancer subtypes and in response to systemic therapy are largely lacking. A transcriptomic signature of Notch signalling would be warranted, for example to monitor the effects of future Notch-targeting therapies and to learn whether altered Notch signalling is an off-target effect of current breast cancer therapies. In this report, we have established such a classifier.

METHODS

To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated or reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by γ-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort and sought to validate in independent datasets.

RESULTS

An optimal 20-gene transcriptomic signature was selected. We validated the signature on two independent patient datasets (METABRIC and Oslo2), and it showed an improved coherence score and tumour specificity compared with previously published signatures. Furthermore, the signature score was particularly high for basal-like breast cancer, indicating an enhanced level of Notch signalling in this subtype. The signature score was increased after neoadjuvant treatment in the PROMIX and BEAUTY patient cohorts, and a lower signature score generally correlated with better clinical outcome.

CONCLUSIONS

The 20-gene transcriptional signature will be a valuable tool to evaluate the response of future Notch-targeting therapies for breast cancer, to learn about potential effects on Notch signalling from conventional breast cancer therapies and to better stratify patients for therapy considerations.

Abstract 6776: Spatial transcriptomics of response to tepotinib treatment in a patient with NSCLC

Background: While cancer therapies are becoming increasingly more targeted, our understanding of the genomic changes occurring during these treatments is lacking. Moreover, the tumoral heterogeneity and its spatial distribution remain important obstacles in predicting tumor evolution and treatment responses. In recent years, genomic spatial profiling techniques have shed light on this complexity by detecting gene expression changes in heterogenous tumor regions and their microenvironment over the course of treatment.

Methods: Tepotinib is a highly selective and potent MET class Ib inhibitor, approved for the treatment of patients with NSCLC with MET exon 14 skipping alterations. To detect genomic changes during neoadjuvant treatment with tepotinib, a GeoMx® digital spatial profiler (DSP; Nanostring Technologies) analysis was conducted in paired baseline and on-treatment patient samples. GeoMx® DSP was performed by selecting regions of interest with nuclear, TTF-1, CD3 and CD33 morphology markers followed by next-generation sequencing (NGS) using the Cancer Transcriptome Atlas RNA panel (>1,800 cancer-related genes).

Results: Following a poor response to chemotherapy, neoadjuvant tepotinib treatment was initiated in a 54-year-old female, never-smoker with NSCLC harboring a MET exon 14 alteration. Owing to a good response to tepotinib, surgical resection of the tumor was decided by the tumor board given the downgrading (from IIIB to IA1) and resulting in a major pathological response. This resection allowed spatial transcriptomics to be compared to a baseline biopsy from the same patient. MET signaling inhibition by tepotinib treatment increased immune cell infiltration in the tumor microenvironment compared to the baseline sample. This enhanced tumoral immune cell density was shown by the fluorescent morphology markers and confirmed through spatial deconvolution of the NGS results. It was further characterized by the significantly altered gene expression levels between the two samples. Gene ontology (GO) assessment of the differentially expressed genes revealed GO terms associated with tumorigenesis in the basal sample, such as cell mobility and motility, vascular epithelial growth factor production and cell communication. In turn, the tepotinib-treated tissue mainly exhibited tumor-clearing characteristics, including antigen processing and presentation through major histocompatibility complex classes I & II, T cell-mediated toxicity, and granulocyte and leukocyte activation.

Conclusion: This is the first spatial genomic characterization of the effect of tepotinib on the tumor and its microenvironment in a patient with NSCLC over time. Results from this case report highlight the impact of MET inhibition by tepotinib on the tumor immune microenvironment, likely enabling the recruitment of antigen-presenting cells for tumor clearance, while reducing the expression of tumor-promoting genes.

Citation Format: Manon A. Simard, Felix Geist, Carlos Cabrera, Santiago Viteri, Joachim Albers, Michael Zuehlsdorf, Niki Karachaliou. Spatial transcriptomics of response to tepotinib treatment in a patient with NSCLC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6776.

Abstract 3351: Identification of a NOTCH transcriptomic signature for basal-like breast cancer

Breast cancer is a heterogeneous disease, where different subtypes differ in terms of biology, treatment options and prognosis. It is an emerging view that dysregulation of major signaling pathways, including Notch signaling, contributes to breast cancer development and progression, but precisely how and in which subtypes Notch signaling is hyperactivated still largely remains to be determined. To gain further insights into dysregulation of Notch in cancer, we set out to identify and evaluate a novel Notch transcriptomic signature focusing initially on breast cancer. We first established Notch-regulated transcriptomes from six breast cancer cell of the basal subtype in response to activation of Notch (by culturing on immobilized Notch ligand) or blockade of Notch (by γ-secretase inhibitors) for 8 and 72 hours. Our data reveal that a core set of Notch-responsive genes can be identified from both time-points and we are validating the transcriptomic signature on a broader set of additional 19 breast cancer cell lines from various breast cancer subtypes. The Notch transcriptomic signature showed robust coherence scores in breast cancer patient data, and robust correlation with basal-like transcriptomes was demonstrated. Analysis of single cell transcriptomic data from breast cancer patients demonstrated that the Notch signature showed additionally good correlation with immune cells in the tumor stroma, notably tumor associated macrophages, indicating that Notch signaling is upregulated in specific cell types of the tumor stroma. Collectively, the data provide a robust transcriptional signature to read out activation of the Notch signaling pathway in basal-like breast cancer and the signature will be important to better stratify patients and to evaluate and predict outcome of future Notch-based therapies for breast cancer.

Citation Format: Eike-Benjamin Braune, Felix Geist, Dirk Wienke, Anita Seshire, Urban Lendahl. Identification of a NOTCH transcriptomic signature for basal-like breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3351.

The Dimethylbismuth Cation: Entry Into Dative Bi-Bi Bonding and Unconventional Methyl Exchange

The isolation of simple, fundamentally important, and highly reactive organometallic compounds remains among the most challenging tasks in synthetic chemistry. The detailed characterization of such compounds is key to the discovery of novel bonding scenarios and reactivity. The dimethylbismuth cation, [BiMe2 (SbF6 )] (1), has been isolated and characterized. Its reaction with BiMe3 gives access to an unprecedented dative bond, a Bi→Bi donor-acceptor interaction. The exchange of methyl groups (arguably the simplest hydrocarbon moiety) between different metal atoms is among the most principal types of reactions in organometallic chemistry. The reaction of 1 with BiMe3 enables an SE 2(back)-type methyl exchange, which is, for the first time, investigated in detail for isolable, (pseudo-)homoleptic main-group compounds.

RosettaSX: Reliable gene expression signature scoring of cancer models and patients

Gene expression signatures have proven their potential to characterize important cancer phenomena like oncogenic signaling pathway activities, cellular origins of tumors, or immune cell infiltration into tumor tissues. Large collections of expression signatures provide the basis for their application to data sets, but the applicability of each signature in a new experimental context must be reassessed. We apply a methodology that utilizes the previously developed concept of coherent expression of genes in signatures to identify translatable signatures before scoring their activity in single tumors. We present a web interface (www.rosettasx.com) that applies our methodology to expression data from the Cancer Cell Line Encyclopaedia and The Cancer Genome Atlas. Configurable heat maps visualize per-cancer signature scores for 293 hand-curated literature-derived gene sets representing a wide range of cancer-relevant transcriptional modules and phenomena. The platform allows users to complement heatmaps of signature scores with molecular information on SNVs, CNVs, gene expression, gene dependency, and protein abundance or to analyze own signatures. Clustered heatmaps and further plots to drill-down results support users in studying oncological processes in cancer subtypes, thereby providing a rich resource to explore how mechanisms of cancer interact with each other as demonstrated by exemplary analyses of 2 cancer types.

Aminotroponiminates: Impact of the NO2 Functional Group on Coordination, Isomerisation, and Backbone Substitution

Aminotroponiminate (ATI) ligands are a versatile class of redox-active and potentially cooperative ligands with a rich coordination chemistry that have consequently found a wide range of applications in synthesis and catalysis. While backbone substitution of these ligands has been investigated in some detail, the impact of electron-withdrawing groups on the coordination chemistry and reactivity of ATIs has been little investigated. We report here Li, Na, and K salts of an ATI ligand with a nitro-substituent in the backbone. It is demonstrated that the NO₂ group actively contributes to the coordination chemistry of these complexes, effectively competing with the N,N-binding pocket as a coordination site. This results in an unprecedented E/Z isomerisation of an ATI imino group and culminates in the isolation of the first "naked" (i. e., without directional bonding to a metal atom) ATI anion. Reactions of sodium ATIs with silver(I) and tritylium salts gave the first N,N-coordinated silver ATI complexes and unprecedented backbone substitution reactions. Analytical techniques applied in this work include multinuclear (VT-)NMR spectroscopy, single-crystal X-ray diffraction analysis, and DFT calculations.

Abstract 3714: Efficient derivation and expansion of tumor cell lines from primary and xenotransplanted pancreatic, ovarian and renal tumors

Cancer cell lines are widely used as in vitro models to study tumor biology and for efficacy testing of novel anti-cancer therapeutics. In the past, most of this work has been done using established cell lines that have been cultured for decades. Extensive in vitro propagation has been shown to lead to the acquisition of multiple genetic and epigenetic alterations in cell lines, leading to decreased heterogeneity and the lack of tumor initiating as well as multi-lineage differentiation capacity. Consequently, established cell lines only insufficiently resemble the characteristics of tumors and thus have limited applicability as in vitro models for example. To overcome this hurdles, cell lines can be derived from primary cancer biopsies. However, this process is very inefficient for most tumor entities. In addition, most of the media used include largely undefined serum, such as FBS, which has been shown to drive primary tumor cell cultures to a more differentiated state when used over multiple passages. We have developed advanced, serum-free media for derivation and expansion of tumor cell lines from pancreatic, ovarian or renal tumors. Our media have been optimized concerning formulation, stability, and usability and allow for efficient generation of primary cell lines from both, patient and xenotransplanted tumors. Primary cell lines derived with our media retained their tumorigenic potential and could therefore be xenotransplanted and propagated in immunodeficient mice. Notably, the resulting tumors closely resembled the initial patient tumor as shown on the histomorphological as well as functional level. Moreover, the primary cell lines closely resembled essential characteristics of the parental tumor in vitro, including expression of subtype-specific markers, cellular heterogeneity, as well as genetic and epigenetic signatures. Taken together, we have developed serum-free medium for efficient derivation and expansion of tumor cell lines from primary and xenotransplanted pancreatic, ovarian and renal tumors, allowing for the establishment of easily accessible in vitro as well as corresponding xenografting vivo models. This facilitates the translation of in vitro findings directly into in vivo settings, allowing for more reliable pre-clinical modelling.

Citation Format: Olaf Hardt, David Agorku, Anne Langhammer, Franziska Zickgraf, Felix Geist, Elisa M. Noll, Christian Eisen, Andreas Bosio, Martin R. Sprick, Andreas Trumpp. Efficient derivation and expansion of tumor cell lines from primary and xenotransplanted pancreatic, ovarian and renal tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3714.

ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier

Podocytes, highly specialized epithelial cells, build the outer part of the kidney filtration barrier and withstand high mechanical forces through a complex network of cellular protrusions. Here, we show that Arp2/3-dependent actin polymerization controls actomyosin contractility and focal adhesion maturation of podocyte protrusions and thereby regulates formation, maintenance, and capacity to adapt to mechanical requirements of the filtration barrier. We find that N-WASP-Arp2/3 define the development of complex arborized podocyte protrusions in vitro and in vivo. Loss of dendritic actin networks results in a pronounced activation of the actomyosin cytoskeleton and the generation of over-maturated but less efficient adhesion, leading to detachment of podocytes. Our data provide a model to explain podocyte protrusion morphology and their mechanical stability based on a tripartite relationship between actin polymerization, contractility, and adhesion.

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ARP3-dependent actin assembly is required for podocyte process formation

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Arp2/3 thereby links process formation, podocyte adhesion and mechano-adaptation

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Arp2/3 function is regulated by a reciprocal interplay with actomyosin

Abstract 1063: A clear cell renal cancer metastasis model identifies novel mediators of tumor aggressiveness and predictors of patient survival

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma with a 5-year survival rate of only 10.5%, and chemotherapy and radiotherapy regimen have shown limited efficacy. On the molecular level, significant inter- and intra-tumor heterogeneity hamper identification of drug targets, biomarkers and unraveling of disease mechanisms.

We developed a novel patient-derived model system of ccRCC that recapitulates the heterogeneity of the originating cancer enabling us to study ccRCC on a functional level. In five rounds and in three biological replicates of an in vivo selection, we transplanted the metastases of orthotopically transplanted tumor cells into the renal capsules of NOD scid gamma (NSG) mice. The tumor was enriched for cells with higher growth and metastatic potential compared to the initial heterogeneous population. Comparative gene-expression analysis revealed candidate genes associated with enhanced malignant growth and metastasis. Absolute shrinkage and selection operator (LASSO) regression identified a gene signature that can robustly predict patient survival. The prognostic power of our signature was additionally verified in independent patient cohorts suggesting that this approach leverages efficient stratification of patients into distinctive risk groups.

One of the hallmark genes in this signature is known to alter cellular signaling properties. Therefore, we hypothesized that this gene contributes to tumor growth and metastasis and thus to aggressiveness of ccRCC. In fact, in knockdown and overexpression xenografts experiments we could confirm an essential role for tumor aggressiveness in vivo suggesting that the gene and associated downstream signaling pathways are attractive targets for treatment of clear cell renal cancer.

Citation Format: Felix Geist, Teresa Dolt, Thomas Höfner, Corinna Klein, Vanessa Vogel, Albrecht Stenzinger, Tim Holland-Letz, Ornella Kossi, Wilko Weichert, Peter Schirmacher, Sascha Pahernik, Markus Hohenfellner, Andreas Trumpp, Martin Sprick. A clear cell renal cancer metastasis model identifies novel mediators of tumor aggressiveness and predictors of patient survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1063.

Endoscopic sedation and monitoring practice in Germany: re-evaluation from the first nationwide survey 3 years after the implementation of an evidence and consent based national guideline

BACKGROUND AND STUDY AIMS

The use of sedation (e. g., of short-acting propofol) for gastrointestinal endoscopy has shown an upward trend in the USA and Europe over the last decade. To improve patient's safety different nationwide guidelines have been developed. This survey aimed at providing nationwide re-evaluated data 3 years after the implementation of consent- and evidence-based national guideline on sedation for gastrointestinal endoscopy.

METHODS

A 24-item survey regarding current practices of endoscopy, sedation and monitoring in gastrointestinal endoscopy was sent to 4 405 members of the German Society of Digestive and Metabolic Diseases (DGVS).

RESULTS

A total of 741/4405 (17 %) questionnaires were returned. Compared to 2007 we documented a further increase of the use of sedation during the performance of esophagogastro-duodenoscopies (EGDs) (82 vs. 74 % in 2007) and colonoscopies (91 vs. 87 % in 2007), accompanied with an increased rate of using propofol as a sedative agent in 97 vs. 74 % of the cases in 2007. In contrast the use of midazolam substantially decreased to 69 % versus 82 % in 2007. Most commonly used sedation regimens are still propofol ± benzodiazepines (43 vs. 38 % in 2007), while a combination of midazolam ± opioid decreased to 15 % versus 35 % in 2007. Unchanged to data from 2007, patients were routinely monitored by pulse oximetry (99 %). Routine use of an automated blood pressure monitoring increased to 40 % (versus 29 % in 2007) and the use of electrocardiography monitoring nearly doubled to 24 vs. 13 % in 2007. Supplemental oxygen is nowadays routinely administered in 64 % compared to 34 % of the cases in 2007. Regarding the administration of sedation we observed a profound increase of nurse-administered propofol sedation (NAPS; 73 % in 2011, 39 % in 2007) with a decrease of endoscopist-directed propofol sedation (29 % in 2011 vs. 59 % in 2007). However, monitored anaesthesia care was still only rarely used in Germany (2 %).

CONCLUSION

After the implementation of the first national sedation guideline the use of propofol has become the most popular sedation regime in Germany, mainly administered as NAPS by trained nurses as a standard procedure. Automated blood pressure measurements and ECG recording were more often implemented in the monitoring practice and also the routine use of supplemental oxygen has been clearly improved.

Vps34 deficiency reveals the importance of endocytosis for podocyte homeostasis

The molecular mechanisms that maintain podocytes and consequently, the integrity of the glomerular filtration barrier are incompletely understood. Here, we show that the class III phosphoinositide 3-kinase vacuolar protein sorting 34 (Vps34) plays a central role in modulating endocytic pathways, maintaining podocyte homeostasis. In mice, podocyte-specific conditional knockout of Vps34 led to early proteinuria, glomerular scarring, and death within 3-9 weeks of age. Vps34-deficient podocytes exhibited substantial vacuolization and foot process effacement. Although the formation of autophagosomes and autophagic flux were impaired, comparisons between podocyte-specific Vps34-deficient mice, autophagy-deficient mice, and doubly deficient mice suggested that defective autophagy was not primarily responsible for the severe phenotype caused by the loss of Vps34. In fact, Rab5-positive endosomal compartments, endocytosis, and fluid-phase uptake were severely disrupted in Vps34-deficient podocytes. Vps34 deficiency in nephrocytes, the podocyte-like cells of Drosophila melanogaster, resulted in a block between Rab5- and Rab7-positive endosomal compartments. In summary, these data identify Vps34 as a major regulator of endolysosomal pathways in podocytes and underline the fundamental roles of endocytosis and fluid-phase uptake for the maintenance of the glomerular filtration barrier.