Predicting microenvironment in CXCR4- and FAP-positive solid tumors - a pan-cancer machine learning workflow for theranostic target structures

Simple Summary Imaging based on positron emission tomography (PET) is a crucial part of up-to-date cancer care. For this purpose, PET employs and marks target structures at the cellular surface. Recently, C-X-C Motif Chemokine Receptor 4 (CXCR4) and Fibroblast Activation Protein Alpha (FAP) emerged as clinically relevant PET targets. However, it is unclear whether high levels of CXCR4 and FAP represent distinct cancer states—especially in solid tumors. Therefore, we established a machine learning model based on 9242 samples from 29 different cancer entities. Our analysis revealed that—in most solid tumors—high levels of CXCR4 were associated with immune cells infiltrating these tumors. Instead, FAP-positive tumors were characterized by high amounts of tumor vessels. Our machine learning approach potentially can identify the Achilles’ heel of tumors in a non-invasive manner—by performing PET without having to obtain tumor tissue beforehand. Abstract (1) Background: C-X-C Motif Chemokine Receptor 4 (CXCR4) and Fibroblast Activation Protein Alpha (FAP) are promising theranostic targets. However, it is unclear whether CXCR4 and FAP positivity mark distinct microenvironments, especially in solid tumors. (2) Methods: Using Random Forest (RF) analysis, we searched for entity-independent mRNA and microRNA signatures related to CXCR4 and FAP overexpression in our pan-cancer cohort from The Cancer Genome Atlas (TCGA) database—representing n = 9242 specimens from 29 tumor entities. CXCR4- and FAP-positive samples were assessed via StringDB cluster analysis, EnrichR, Metascape, and Gene Set Enrichment Analysis (GSEA). Findings were validated via correlation analyses in n = 1541 tumor samples. TIMER2.0 analyzed the association of CXCR4 / FAP expression and infiltration levels of immune-related cells. (3) Results: We identified entity-independent CXCR4 and FAP gene signatures representative for the majority of solid cancers. While CXCR4 positivity marked an immune-related microenvironment, FAP overexpression highlighted an angiogenesis-associated niche. TIMER2.0 analysis confirmed characteristic infiltration levels of CD8+ cells for CXCR4-positive tumors and endothelial cells for FAP-positive tumors. (4) Conclusions: CXCR4- and FAP-directed PET imaging could provide a non-invasive decision aid for entity-agnostic treatment of microenvironment in solid malignancies. Moreover, this machine learning workflow can easily be transferred towards other theranostic targets

On-target restoration of a split T cell-engaging antibody for precision immunotherapy

T cell-engaging immunotherapies are changing the landscape of current cancer care. However, suitable target antigens are scarce, restricting these strategies to very few tumor types. Here, we report on a T cell-engaging antibody derivative that comes in two complementary halves and addresses antigen combinations instead of single molecules. Each half, now coined hemibody, contains an antigen-specific single-chain variable fragment (scFv) fused to either the variable light (V-L) or variable heavy (V-H) chain domain of an anti-CD3 antibody. When the two hemibodies simultaneously bind their respective antigens on a single cell, they align and reconstitute the original CD3-binding site to engage T cells. Employing preclinical models for aggressive leukemia and breast cancer, we show that by the combinatorial nature of this approach, T lymphocytes exclusively eliminate dual antigen-positive cells while sparing single positive bystanders. This allows for precision targeting of cancers not amenable to current immunotherapies

TNFAIP3 (A20) is a tumor suppressor gene in Hodgkin lymphoma and primary mediastinal B cell lymphoma

Proliferation and survival of Hodgkin and Reed/Sternberg (HRS) cells, the malignant cells of classical Hodgkin lymphoma (cHL), are dependent on constitutive activation of nuclear factor κB (NF-κB). NF-κB activation through various stimuli is negatively regulated by the zinc finger protein A20. To determine whether A20 contributes to the pathogenesis of cHL, we sequenced TNFAIP3, encoding A20, in HL cell lines and laser-microdissected HRS cells from cHL biopsies. We detected somatic mutations in 16 out of 36 cHLs (44%), including missense mutations in 2 out of 16 Epstein-Barr virus–positive (EBV+) cHLs and a missense mutation, nonsense mutations, and frameshift-causing insertions or deletions in 14 out of 20 EBV− cHLs. In most mutated cases, both TNFAIP3 alleles were inactivated, including frequent chromosomal deletions of TNFAIP3. Reconstitution of wild-type TNFAIP3 in A20-deficient cHL cell lines revealed a significant decrease in transcripts of selected NF-κB target genes and caused cytotoxicity. Extending the mutation analysis to primary mediastinal B cell lymphoma (PMBL), another lymphoma with constitutive NF-κB activity, revealed destructive mutations in 5 out of 14 PMBLs (36%). This report identifies TNFAIP3 (A20), a key regulator of NF-κB activity, as a novel tumor suppressor gene in cHL and PMBL. The significantly higher frequency of TNFAIP3 mutations in EBV− than EBV+ cHL suggests complementing functions of TNFAIP3 inactivation and EBV infection in cHL pathogenesis

Identification of Disparities in Personalized Cancer Care—A Joint Approach of the German WERA Consortium

(1) Background: molecular tumor boards (MTBs) are crucial instruments for discussing and allocating targeted therapies to suitable cancer patients based on genetic findings. Currently, limited evidence is available regarding the regional impact and the outreach component of MTBs; (2) Methods: we analyzed MTB patient data from four neighboring Bavarian tertiary care oncology centers in Würzburg, Erlangen, Regensburg, and Augsburg, together constituting the WERA Alliance. Absolute patient numbers and regional distribution across the WERA-wide catchment area were weighted with local population densities; (3) Results: the highest MTB patient numbers were found close to the four cancer centers. However, peaks in absolute patient numbers were also detected in more distant and rural areas. Moreover, weighting absolute numbers with local population density allowed for identifying so-called white spots—regions within our catchment that were relatively underrepresented in WERA MTBs; (4) Conclusions: investigating patient data from four neighboring cancer centers, we comprehensively assessed the regional impact of our MTBs. The results confirmed the success of existing collaborative structures with our regional partners. Additionally, our results help identifying potential white spots in providing precision oncology and help establishing a joint WERA-wide outreach strategy

Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells

Transcriptional signatures are an indispensible source of correlative information on disease-related molecular alterations on a genome-wide level. Numerous candidate genes involved in disease and in factors of predictive, as well as of prognostic, value have been deduced from such molecular portraits, e.g. in cancer. However, mechanistic insights into the regulatory principles governing global transcriptional changes are lagging behind extensive compilations of deregulated genes. To identify regulators of transcriptome alterations, we used an integrated approach combining transcriptional profiling of colorectal cancer cell lines treated with inhibitors targeting the receptor tyrosine kinase (RTK)/RAS/mitogen-activated protein kinase pathway, computational prediction of regulatory elements in promoters of co-regulated genes, chromatin-based and functional cellular assays. We identified commonly co-regulated, proliferation-associated target genes that respond to the MAPK pathway. We recognized E2F and NFY transcription factor binding sites as prevalent motifs in those pathway-responsive genes and confirmed the predicted regulatory role of Y-box binding protein 1 (YBX1) by reporter gene, gel shift, and chromatin immunoprecipitation assays. We also validated the MAPK-dependent gene signature in colorectal cancers and provided evidence for the association of YBX1 with poor prognosis in colorectal cancer patients. This suggests that MEK/ERK-dependent, YBX1-regulated target genes are involved in executing malignant properties

Die Bedeutung von Apoptoseresistenzmechanismen für die Pathogenese und Therapie maligner Lymphome

Apoptoseresistenzmechanismen spielen bei der Pathogenese maligner Lymphome eine zentrale Rolle. So konnte bei Hodgkin/Reed-Sternbergzellen eine Deregulation des Transkriptionsfaktors NF-_B beobachtet werden, die zu verstärkter Apotoseresistenz führt und so zum malignen Wachstum dieser Zellen wahrscheinlich entscheidend beiträgt. Es konnte gezeigt werden, dass die selektive Blockade von NF-_B sowohl zu erhöhter Apoptosesensitivität als auch zur Inhibition der Zellzyklusprogression in kultivierten Hodgkinzellen führt. Der genaue molekulare Mechanismus der NF-_B-Deregulation in Hodgkinzellen ist jedoch noch unklar. Apoptoseresistenzmechanismen sind nicht nur bei der Pathogenese maligner Lymphome, sondern auch bei der Entstehung von Therapieresistenz von Bedeutung. So konnte gezeigt werden, dass die Überexpression proapoptotischer Gene der bcl-2 Familie in resistenten malignen Zellen sowohl die Empfindlichkeit gegenüber Zytostatika als auch gegenüber Antikörperbehandlung wiederherstellen kann. Neben der bcl-2 Familie spielt wahrscheinlich auch das Apo-I/Fas-System eine wichtige Rolle bei der Entstehung von Zytostatikaresistenz und immunologischer Resistenz. Somit stellt neben der Überexpression des P-Glykoproteins (MDR1), das als transmembranes "Pumpenprotein" Zytostatika aus der Tumorzelle heraustransportieren kann, die Deregulation Apoptose-steuernder Gene einen weiteren wichtigen Therapie-Resistenzmechanismus dar. Eine Möglichkeit, intrazelluläre Resistenzmechanismen zu umgehen, stellt die indirekte Induktion von Zelltod mit Hilfe bispezifische Antikörper dar. Durch diese Moleküle kann eine T-Zell-vermittelte Zellyse von Lymphomzellen erreicht werden.Resistance towards apoptosis plays an important role in the pathogenesis of malignant lymphomas. It could be demonstrated that deregulation of the transcription factor NF-kB is a common molecular defect of Hodgkin/Reed-Sternberg cells that leads to enhanced resistance towards apoptosis and therefore probabaly contributes to the malignant growth of these cells. It couldbe shown that blocking of NF-kB leads to increased sensitivity towards apoptosis and decreased cell cycle progression. The precise molecular mechanism that leads deregulation of NF-kB is still unknown. Besides its role in the pathogenesis of malignant lymphoma resistance towards apoptosis plays an important role in the development of drug resistance. It could be shown that overexpression of pro-apoptotic members of the bcl-2 family in resistant tumor cells can restore sensitivity towards both cytotoxic drugs as well as antibody treatment. In addition to the bcl-2 family the Apo-I/Fas system is also involved in the development of drug resistance. Thus, besides overexpression of p-glycoprotein (MDR-1) that might pump cytotoxic drugs out of a malignant cell deregulation of apoptosis regulating genes is another important mechanisms of drug resistance development. One possibility to overcome drug resistance is the induction of cell death via bispecific antibodies. These molecules can induce T cell mediated lysis of lymohoma cells

Efficient Transient Transfection of Human Multiple Myeloma Cells by Electroporation - An Appraisal

Cell lines represent the everyday workhorses for in vitro research on multiple myeloma (MM) and are regularly employed in all aspects of molecular and pharmacological investigations. Although loss-of-function studies using RNA interference in MM cell lines depend on successful knockdown, no well-established and widely applied protocol for efficient transient transfection has so far emerged. Here, we provide an appraisal of electroporation as a means to introduce either short-hairpin RNA expression vectors or synthesised siRNAs into MM cells. We found that electroporation using siRNAs was much more efficient than previously anticipated on the basis of transfection efficiencies deduced from EGFP-expression off protein expression vectors. Such knowledge can even confidently be exploited in "hard-to-transfect" MM cell lines to generate large numbers of transient knockdown phenotype MM cells. In addition, special attention was given to developing a protocol that provides easy implementation, good reproducibility and manageable experimental costs

Electroporation of INA-6 cells stably expressing enhanced green fluorescent protein with an siRNA oligonucleotide against EGFP.

<p>INA-6-EGFP cells were electroporated with a solution containing a stealth siRNA targeting EGFP as well as an expression plasmid for CD4Δ. One day post-electroporation one half of the cell culture was purified according to the column procedure (red curves, also see Fig. 1b)–e)), whereas the other half only underwent debris removal with OptiPrep (blue curves, also see Fig. 1f)). Purified cells were further cultured and FACS-analysed for EGFP expression at the times indicated. Only the live cell fraction (as demarcated in the forward/sideward scatter) was analysed and plotted against similarly treated INA-6-EGFP cells (green curves) transfected with a non-EGFP targeting siRNA. Knockdown efficiency was essentially identical in strength and over time between both purification approaches. One representative experiment from a total of three is shown.</p

Electroporation and knockdown efficiencies in “easy-to-transfect” vs. “hard-to-transfect” MM cell lines.

<p>Left-hand panel: MM cell lines were electroporated with an expression vector for EGFP (pEGFP-N3; 10 µg/ml) and stealth siRNAs against either ERK2 (stERK2; 3 µM) or against no specific target (control; 3 µM). The FACS-measurements represent the cell cultures at day 1 post-electroporation after debris removal with OptiPrep. Right-hand panel: Knockdown of ERK2 and intrinsic levels of phospho-ERK2 (cells from the cultures represented on the left were harvested at day 3 post-electroporation for Western blotting). Good knockdown of ERK2 and lowered levels of phospho-ERK2 were found for all four MM cell lines tested. Shown is a representative experiment of two complete sets (Western blotting included). Anti-ERK1/2 antibody: Santa Cruz Biotechnology.</p