Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues.

The development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium vs. microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy. Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of cell populations differed. Cells with low mRNA content such as T cells were underrepresented in the droplet-based system, at least partly due to lower RNA capture rates. In contrast, microwell-based scRNA-seq recovered less cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation. Overall, our study provides important information for selection of the appropriate scRNA-seq platform and for the interpretation of published results.

Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer.

Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.

Comprehensive characterization of the prostate tumor microenvironment identifies CXCR4/CXCL12 crosstalk as a novel antiangiogenic therapeutic target in prostate cancer.

BACKGROUND: Crosstalk between neoplastic and stromal cells fosters prostate cancer (PCa) progression and dissemination. Insight in cell-to-cell communication networks provides new therapeutic avenues to mold processes that contribute to PCa tumor microenvironment (TME) alterations. Here we performed a detailed characterization of PCa tumor endothelial cells (TEC) to delineate intercellular crosstalk between TEC and the PCa TME. METHODS: TEC isolated from 67 fresh radical prostatectomy (RP) specimens underwent multi-omic ex vivo characterization as well as orthogonal validation of both TEC functions and key markers by immunohistochemistry (IHC) and immunofluorescence (IF). To identify cell-cell interaction targets in TEC, we performed single-cell RNA sequencing (scRNA-seq) in four PCa patients who underwent a RP to catalogue cellular TME composition. Targets were cross-validated using IHC, publicly available datasets, cell culture expriments as well as a PCa xenograft mouse model. RESULTS: Compared to adjacent normal endothelial cells (NEC) bulk RNA-seq analysis revealed upregulation of genes associated with tumor vasculature, collagen modification and extracellular matrix remodeling in TEC. PTGIR, PLAC9, CXCL12 and VDR were identified as TEC markers and confirmed by IF and IHC in an independent patient cohort. By scRNA-seq we identified 27 cell (sub)types, including endothelial cells (EC) with arterial, venous and immature signatures, as well as angiogenic tip EC. A focused molecular analysis revealed that arterial TEC displayed highest CXCL12 mRNA expression levels when compared to all other TME cell (sub)populations and showed a negative prognostic role. Receptor-ligand interaction analysis predicted interactions between arterial TEC derived CXCL12 and its cognate receptor CXCR4 on angiogenic tip EC. CXCL12 was in vitro and in vivo validated as actionable TEC target by highlighting the vessel number- and density- reducing activity of the CXCR4-inhibitor AMD3100 in murine PCa as well as by inhibition of TEC proliferation and migration in vitro. CONCLUSIONS: Overall, our comprehensive analysis identified novel PCa TEC targets and highlights CXCR4/CXCL12 interaction as a potential novel target to interfere with tumor angiogenesis in PCa.

Antioxidant, antibacterial and antifungal potential study of Salvia macrosiphon Boiss. stem extracts.

The aim of present research work was to evaluate the Salvia macrosiphon Boiss. of Lamiaceae (mint family), using biochemical and biological assays. Plant's phytochemicals extraction was performed in methanol, butanol and water by mechanical shaking process. TPC and TFC were determined by Folin-Ciocalteu and aluminum chloride colorimetric procedures, respectively. The highest TPC (99.61±3.45 mg GAE/g) and TFC (234.72±7.12mg CE/g) were obtained in butanol and methanol, respectively. Regarding the antioxidant potential methanol extract showed the highest DPPH° scavenging potential (78.0±2.0%) and reducing activity (0.923±0.020 absorbance). The antibacterial activity of butanol extract against P. aeruginosa were found highest (ZOI = 23±2.00 mm). Antifungal study of methanol extract showed the ZOI (11 ±0.67mm) against F. brachygibbosum. The results revealed that the methanol stem extract of S. macrosiphon bear significant medicinal value and could be used for formulating phytomedicines and food preservers.

C5aR inhibition of nonimmune cells suppresses inflammation and maintains epithelial integrity in SARS-CoV-2-infected primary human airway epithelia.

BACKGROUND: Excessive inflammation triggered by a hitherto undescribed mechanism is a hallmark of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and is associated with enhanced pathogenicity and mortality. OBJECTIVE: Complement hyperactivation promotes lung injury and was observed in patients suffering from Middle East respiratory syndrome-related coronavirus, SARS-CoV-1, and SARS-CoV-2 infections. Therefore, we investigated the very first interactions of primary human airway epithelial cells on exposure to SARS-CoV-2 in terms of complement component 3 (C3)-mediated effects. METHODS: For this, we used highly differentiated primary human 3-dimensional tissue models infected with SARS-CoV-2 patient isolates. On infection, viral load, viral infectivity, intracellular complement activation, inflammatory mechanisms, and tissue destruction were analyzed by real-time RT-PCR, high content screening, plaque assays, luminex analyses, and transepithelial electrical resistance measurements. RESULTS: Here, we show that primary normal human bronchial and small airway epithelial cells respond to SARS-CoV-2 infection by an inflated local C3 mobilization. SARS-CoV-2 infection resulted in exaggerated intracellular complement activation and destruction of the epithelial integrity in monolayer cultures of primary human airway cells and highly differentiated, pseudostratified, mucus-producing, ciliated respiratory tissue models. SARS-CoV-2-infected 3-dimensional cultures secreted significantly higher levels of C3a and the proinflammatory cytokines IL-6, monocyte chemoattractant protein 1, IL-1α, and RANTES. CONCLUSIONS: Crucially, we illustrate here for the first time that targeting the anaphylotoxin receptors C3a receptor and C5a receptor in nonimmune respiratory cells can prevent intrinsic lung inflammation and tissue damage. This opens up the exciting possibility in the treatment of COVID-19.

Phytochemical Analysis, Antioxidant and Antimicrobial Screening of Seriphidium Oliverianum Plant Extracts.

The aim of this study was to investigate the phytochemicals using reverse-phase high pressure liquid chromatography (RP-HPLC), antioxidant, antifungal and antibacterial activities of Seriphidium oliverianum stem extracts. The extraction was carried out by conventional shaking process (CSP) and ultrasonic assisted process (UAP). The highest total phenolic contents (97.85 ± 0.735 mg gallic acid equivalent (GAE)/g sample) and flavonoid contents (188.15 ± 0.53 mg catechin equivalent (CE)/g sample) were found in methanol extract obtained by CSP. Antioxidant activity was investigated using DPPH° scavenging assay and reducing power assay. Methanol extract using UAP showed the highest DPPH° scavenging activity (79.95% ± 1.80%) followed by methanol and butanol extracts obtained through CSP. Moreover, methanol extracts using CSP showed highest reducing activity (1.032 ± 0.0205 absorbance). In-vitro antimicrobial activity was studied using most common infection causing fungal and bacterial strains. Anti-fungal activity of methanol extract using CSP showed the highest zone of inhibition (10.5 mm) against F. avenaceum fungal strain, while aqueous extracts obtained through showed the highest antibacterial activity (22 ± 1.32 mm zone of inhibition) against S. aureus. The results showed that the methanol stem extract of S. oliverianum is a valued candidate for further screening and could be processed for in-vivo infection induced animal trials.

Synthesis, characterization, biological evaluation and QSAR of some Schiff base esters: promising new antitumor, antioxidant and anti-inflammatory agents.

We report the synthesis, characterization, biological evaluation and quantitative structure-activity relationship of some Schiff base esters as promising new antitumor, antioxidant and anti-inflammatory agents. The Schiff base esters were synthesized by two synthetic routes using variably substituted hydroxy benzaldehydes with para amino phenol in appreciable yields. All the newly synthesized esters have been characterized by (1)H-NMR,(.13)C-NMR, FT-IR techniques and elemental analysis. The synthesized esters were examined for antioxidant, antitumor and anti-inflammatory potentials through different bioassays and quantitative structure-activity relationship was studied. Bioassays showed encouraging results and indicated that some of these title compounds may have potential for further pharmacological investigations.