Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 157
Filter
Add more filters

Country/Region as subject
Publication year range
1.
EMBO J ; 40(22): e108234, 2021 11 15.
Article in English | MEDLINE | ID: mdl-34586646

ABSTRACT

DNA methylation is a fundamental epigenetic modification, important across biological processes. The maintenance methyltransferase DNMT1 is essential for lineage differentiation during development, but its functions in tissue homeostasis are incompletely understood. We show that epidermis-specific DNMT1 deletion severely disrupts epidermal structure and homeostasis, initiating a massive innate immune response and infiltration of immune cells. Mechanistically, DNA hypomethylation in keratinocytes triggered transposon derepression, mitotic defects, and formation of micronuclei. DNA release into the cytosol of DNMT1-deficient keratinocytes activated signaling through cGAS and STING, thus triggering inflammation. Our findings show that disruption of a key epigenetic mark directly impacts immune and tissue homeostasis, and potentially impacts our understanding of autoinflammatory diseases and cancer immunotherapy.


Subject(s)
DNA Methylation , Dermatitis/genetics , Epidermis/physiopathology , Nucleotidyltransferases/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Animals , Chromosome Aberrations , Cytosol/physiology , DNA (Cytosine-5-)-Methyltransferase 1/genetics , Dermatitis/immunology , Dermatitis/pathology , Humans , Immunity, Innate/genetics , Interferon-Induced Helicase, IFIH1/metabolism , Keratinocytes/immunology , Keratinocytes/metabolism , Keratinocytes/pathology , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice, Transgenic , Nucleotidyltransferases/genetics
2.
Carcinogenesis ; 45(4): 210-219, 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38019590

ABSTRACT

Esophageal adenocarcinoma (EAC) is a leading cause of cancer-related mortality. Sitravatinib is a novel multi-gene tyrosine kinase inhibitor (TKI) that targets tumor-associated macrophage (TAM) receptors, VEGF, PDGF and c-Kit. Currently, sitravatinib is actively being studied in clinical trials across solid tumors and other TKIs have shown efficacy in combination with immune checkpoint inhibitors (ICI) in cancer models. In this study, we investigated the anti-tumor activity of sitravatinib alone and in combination with PD-1 blockade in an EAC rat model. Treatment response was evaluated by mortality, pre- and post-treatment MRI, gene expression, immunofluorescence and immunohistochemistry. Our results demonstrated adequate safety and significant tumor shrinkage in animals treated with sitravatinib, and more profoundly, sitravatinib and PD-1 inhibitor, AUNP-12 (P < 0.01). Suppression of TAM receptors resulted in increased gene expression of pro-inflammatory cytokines and decreased expression of anti-inflammatory cytokines, enhanced infiltration of CD8+ T cells, and M2 to M1 macrophage phenotype repolarization in the tumor microenvironment of treated animals (P < 0.01). Moreover, endpoint immunohistochemistry staining corroborated the anti-tumor activity by downregulation of Ki67 and upregulation of Caspase-3 in the treated animals. Additionally, pretreatment gene expression of TAM receptors and PD-L1 were significantly higher in major responders compared with the non-responders, in animals that received sitravatinib and AUNP-12 (P < 0.02), confirming that TAM suppression enhances the efficacy of PD-1 blockade. In conclusion, this study proposes a promising immunomodulatory strategy using a multi-gene TKI to overcome developed resistance to an ICI in EAC, establishing rationale for future clinical development.


Subject(s)
Adenocarcinoma , Anilides , Esophageal Neoplasms , Programmed Cell Death 1 Receptor , Pyridines , Rats , Animals , T-Lymphocytes, Cytotoxic , Cytokines/metabolism , Adenocarcinoma/drug therapy , Adenocarcinoma/metabolism , Macrophages/metabolism , Tumor Microenvironment , Cell Line, Tumor
3.
J Transl Med ; 22(1): 402, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38689325

ABSTRACT

Peritoneal carcinomatosis (PC) is a complex manifestation of abdominal cancers, with a poor prognosis and limited treatment options. Recent work identifying high concentrations of the cytokine interleukin-6 (IL-6) and its soluble receptor (sIL-6-Rα) in the peritoneal cavity of patients with PC has highlighted this pathway as an emerging potential therapeutic target. This review article provides a comprehensive overview of the current understanding of the potential role of IL-6 in the development and progression of PC. We discuss mechansims by which the IL-6 pathway may contribute to peritoneal tumor dissemination, mesothelial adhesion and invasion, stromal invasion and proliferation, and immune response modulation. Finally, we review the prospects for targeting the IL-6 pathway in the treatment of PC, focusing on common sites of origin, including ovarian, gastric, pancreatic, colorectal and appendiceal cancer, and mesothelioma.


Subject(s)
Interleukin-6 , Peritoneal Neoplasms , Humans , Peritoneal Neoplasms/drug therapy , Peritoneal Neoplasms/secondary , Interleukin-6/metabolism , Interleukin-6/antagonists & inhibitors , Animals , Molecular Targeted Therapy , Signal Transduction
4.
Ann Surg Oncol ; 31(3): 2069-2077, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37996643

ABSTRACT

BACKGROUND OR PURPOSE: Carcinomatosis, a distinct pattern of metastatic cancer in the peritoneal cavity, poses challenges for treatment and has limited therapeutic options. Understanding the immune environment of peritoneal surface malignancies is crucial for developing effective immunotherapeutic approaches. This study characterizes soluble immune mediators in the peritoneal fluid of patients with and without carcinomatosis to identify targets for novel treatment strategies. PATIENTS AND METHODS: Serum and peritoneal fluid samples were collected from surgical patients, and a multianalyte analysis was performed using the Luminex platform. Patient characteristics, tumor sites, and sample collection details were recorded. Soluble immune mediator levels were measured and compared between peritoneal fluid and serum samples and among clinical subgroups. Statistical analysis was conducted to assess differences in analyte concentrations and correlations between samples. RESULTS: There were 39 patients included in the study, with varying surgical indications. Significant differences were observed in soluble immune mediator levels between peritoneal fluid and serum, with peritoneal fluid exhibiting lower concentrations. Carcinomatosis was associated with elevated levels of proinflammatory mediators, including IL-6 and IL-8, while adaptive immune response markers were low in peritoneal fluid. CONCLUSIONS: The peritoneal immune microenvironment in carcinomatosis favors innate immunity, presenting a challenging environment for effective antitumor response. High levels of proinflammatory mediators suggest potential targets for intervention, such as the IL-6 axis, FGF2, IL-8, and CCL2; these could be explored as potential mitigators of malignant ascites and enhance anti-tumor immune responses. These findings provide valuable insights for developing immunotherapy strategies and improving outcomes in patients with peritoneal carcinomatosis.


Subject(s)
Carcinoma , Peritoneal Neoplasms , Humans , Peritoneal Neoplasms/secondary , Interleukin-8 , Interleukin-6 , Ascitic Fluid , Carcinoma/pathology , Immunotherapy , Tumor Microenvironment
5.
Ann Surg Oncol ; 31(7): 4726-4734, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38622456

ABSTRACT

BACKGROUND: For patients with peritoneal carcinomatosis, extent of disease and completeness of cytoreductive surgery (CRS) are major prognostic factors for long-term survival. Assessment of these factors could be improved using imaging agents. Pegsitacianine is a pH-sensitive polymeric micelle conjugated to the fluorophore indocyanine green. The micelle disassembles in acidic microenvironments, such as tumors, resulting in localized fluorescence unmasking. We assessed the utility of pegsitacianine in detecting residual disease following CRS. PATIENTS AND METHODS: NCT04950166 was a phase II, non-randomized, open-label, multicenter US study. Patients eligible for CRS were administered an intravenous dose of pegsitacianine at 1 mg/kg 24-72 h before surgery. Following CRS, the peritoneal cavity was reexamined under near-infrared (NIR) illumination to evaluate for fluorescent tissue. Fluorescent tissue identified was excised and evaluated by histopathology. The primary outcome was the rate of clinically significant events (CSE), defined as detection of histologically confirmed residual disease excised with pegsitacianine or a revision in the assessment of completeness of CRS. Secondary outcomes included acceptable safety and pegsitacianine performance. RESULTS: A total of 53 patients were screened, 50 enrolled, and 40 were evaluable for CSE across six primary tumor types. Residual disease was detected with pegsitacianine in 20 of 40 (50%) patients. Pegsitacianine showed high sensitivity and was well tolerated with no serious adverse events (SAEs). Transient treatment-related, non-anaphylactic infusion reactions occurred in 28% of patients. CONCLUSIONS: Pegsitacianine was well tolerated and facilitated the recognition of occult residual disease following CRS. The high rate of residual disease detected suggests that the use of pegsitacianine augmented surgeon assessment and performance during CRS.


Subject(s)
Cytoreduction Surgical Procedures , Indocyanine Green , Neoplasm, Residual , Peritoneal Neoplasms , Humans , Peritoneal Neoplasms/secondary , Peritoneal Neoplasms/diagnostic imaging , Female , Middle Aged , Male , Indocyanine Green/administration & dosage , Aged , Hydrogen-Ion Concentration , Prognosis , Adult , Follow-Up Studies , Fluorescent Dyes/administration & dosage
6.
Chemistry ; 30(35): e202401296, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38641990

ABSTRACT

To fill the need for environmentally sensitive fluorescent unnatural amino acids able to operate in the red region of the spectrum, we have designed and synthesized Alared, a red solvatochromic and fluorogenic amino acid derived from the Nile Red chromophore. The new unnatural amino acid can be easily integrated into bioactive peptides using classical solid-phase peptide synthesis. The fluorescence quantum yield and the emission maximum of Alared-labeled peptides vary in a broad range depending on the peptide's environment, making Alared a powerful reporter of biomolecular interactions. Due to its red-shifted absorption and emission spectra, Alared-labeled peptides could be followed in living cells with minimal interference from cellular autofluorescence. Using ratiometric fluorescence microscopy, we were able to track the fate of the Alared-labeled peptide agonists of the apelin G protein-coupled receptor upon receptor activation and internalization. Due to its color-shifting environmentally sensitive emission, Alared allowed for distinguishing the fractions of peptides that are specifically bound to the receptor or unspecifically bound to different cellular membranes.


Subject(s)
Amino Acids , Fluorescent Dyes , Microscopy, Fluorescence , Peptides , Fluorescent Dyes/chemistry , Peptides/chemistry , Amino Acids/chemistry , Humans , Microscopy, Fluorescence/methods , Oxazines/chemistry , Solid-Phase Synthesis Techniques , Spectrometry, Fluorescence
7.
Oncology (Williston Park) ; 38(5): 191-193, 2024 05 13.
Article in English | MEDLINE | ID: mdl-38776516

ABSTRACT

Well-differentiated papillary mesothelioma (WDPM) is a rare mesothelial tumor of uncertain malignant potential. We present a unique case of a woman with synchronous WDPM and well-differentiated endometrioid adenocarcinoma (EA) arising from extraovarian endometriosis. A 56-year-old postmenopausal woman presented with a several-month history of right lower quadrant abdominal pain. She had a history of supracervical hysterectomy and bilateral salpingo-oophorectomy secondary to endometriosis. Imaging reported a mass in the right lower quadrant originating from the distal ileum. At laparotomy, the patient underwent a right colectomy with resection of the terminal ileum and excision of a solitary peritoneal nodule. Pathology was consistent with a diagnosis of well-differentiated EA (arising from extraovarian endometriosis) and WDPM. Further treatment consisted of complete surgical staging/debulking and adjuvant chemotherapy directed toward metastatic well-differentiated EA. Surgeons should be familiar with WDPM as a potential finding in women of reproductive age undergoing abdominal surgery for any indication.


Subject(s)
Carcinoma, Endometrioid , Endometriosis , Humans , Female , Middle Aged , Endometriosis/complications , Endometriosis/pathology , Endometriosis/surgery , Carcinoma, Endometrioid/pathology , Carcinoma, Endometrioid/surgery , Mesothelioma/pathology , Mesothelioma/surgery , Neoplasms, Multiple Primary/pathology , Neoplasms, Multiple Primary/surgery , Endometrial Neoplasms/pathology , Endometrial Neoplasms/surgery
8.
HPB (Oxford) ; 26(5): 703-710, 2024 May.
Article in English | MEDLINE | ID: mdl-38443235

ABSTRACT

BACKGROUND: This study assessed the long-term quality of life (QOL) and priorities of pancreaticoduodenectomy (PD) survivors. METHODS: Survivors were surveyed via internet-based support groups. The relative importance of longevity, experience, costs, and QOL were assessed. RESULTS: The PD cohort (n = 247, 35%) was 60 ± 12 years, 71% female, and 93% white. With moderate agreement, patients ranked survival most important, followed by functional and emotional well-being; costs and experience were least important (W = 35.7%, p < 0.001). Well-being improved throughout survivorship (P-QOL: 39 ± 12 at ≤3 mo vs 43 ± 12 at >10 y, p = 0.170; M-QOL: 38 ± 13 at ≤3 mo vs 44 ± 16 at >10 y; p = 0.015) but remained below the general population (p < 0.001). PD patients with benign diagnoses ranked functional independence as most important (2.00 ± 1.13 vs 2.63 ± 1.19, p < 0.001, W = 41.1%); PD patients with malignant diagnoses regarded overall survival most important (2.10 ± 1.20 vs 1.82 ± 1.22, p < 0.16, W = 35.1%). The mean rank order of priorities remained concordant between short-term (<1 year) and long-term (>5 years) survivors. CONCLUSION: PD survivors experience long-term mental and physical health impairments, underscoring the importance of functional and emotional support. Survivors place paramount importance on overall survival, functional independence, and emotional well-being. Cancer survivors prioritize longevity, while survivors of chronic benign conditions prioritize functional independence.


Subject(s)
Pancreaticoduodenectomy , Quality of Life , Humans , Pancreaticoduodenectomy/adverse effects , Female , Male , Middle Aged , Aged , Time Factors , Surveys and Questionnaires , Survivors/psychology , Emotions , Mental Health , Functional Status , Treatment Outcome , Longevity
9.
Bioconjug Chem ; 34(1): 162-168, 2023 01 18.
Article in English | MEDLINE | ID: mdl-36534753

ABSTRACT

Herein, we describe a catalyst-free thia-Diels-Alder cycloaddition for the chemoselective labeling of fully deprotected phosphonodithioester-peptides in solution with fluorophores functionalized with an exocyclic diene. The reaction was optimized on the model tripeptide 1 containing a lysine residue, which enabled its rapid and straightforward labeling with three different fluorophores (fluorescein, lissamine rhodamine B, and squaraine) in very mild conditions (H2O/iPrOH, 37 °C, 1 h). The reaction was then successfully applied to the chemoselective labeling of fully deprotected apelin-13 with squaraine dye. The resulting fluorescent ligand 18 exhibited a high affinity (0.17 ± 0.03 nM) for apelinR. It enabled the development of time-resolved FRET-based competition assays for high-throughput screening and drug discovery. Thanks to its fluorogenic properties, ligand 18 was also successfully involved in the live-cell optical imaging of apelinR in no-wash conditions.


Subject(s)
Fluorescent Dyes , Peptides , Apelin , Cycloaddition Reaction , Ligands , Peptides/chemistry , Fluorescent Dyes/chemistry
10.
Ann Surg Oncol ; 30(12): 7825-7832, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37535272

ABSTRACT

BACKGROUND: Advances in treatment of peritoneal surface malignancies including cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CRS±HIPEC) have led to long-term survivorship, yet the subsequent quality of life (QOL) and values of these patients are unknown. PATIENTS AND METHODS: Survivors were offered surveys via online support groups. Novel items assessed how patients prioritized experience, costs, longevity, and wellbeing. RESULTS: Of the 453 gastrointestinal/hepatobiliary (GI/HPB) surgical patients that responded, 74 underwent CRS±HIPEC and were 54±12 years old, 87% female, and 93% white. Respondents averaged 29 months from diagnosis, with a maximum survival of 20 years. With a moderate level of agreement (W = 39%), rankings of value metrics among respondents were predictable (p < 0.001). Longevity and functional independence were ranked highest; treatment experience and cost of treatment were ranked lowest (p < 0.001). Those who underwent CRS±HIPEC or other GI/HPB surgeries reported the same rank order. QOL in CRS±HIPEC survivors, both mental (M-QOL) (44±13) and physical (P-QOL) (41±11) were lower than in the general population (50±10); p < 0.001. Impairments persisted throughout survivorship, but M-QOL improved over time (p < 0.05). When comparing CRS±HIPEC with other GI/HPB cancer surgery survivors, M-QOL (43±13 versus 43±14, p = 0.85) and P-QOL (40±11 versus 42±12, p = 0.41) were similar. CONCLUSIONS: Although CRS±HIPEC survivors experience long-term mental and physical health impairments, they were similar to those experienced by survivors of other GI/HPB cancer surgeries, and their QOL improved significantly throughout survivorship. As CRS±HIPEC survivors prioritize longevity above all other metrics, survival benefit may outweigh a temporary reduction in QOL.


Subject(s)
Cancer Survivors , Hyperthermia, Induced , Neoplasms , Humans , Female , Adult , Middle Aged , Aged , Male , Quality of Life , Cytoreduction Surgical Procedures , Combined Modality Therapy , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Survival Rate , Retrospective Studies
11.
Sensors (Basel) ; 23(2)2023 Jan 05.
Article in English | MEDLINE | ID: mdl-36679407

ABSTRACT

This article provides an overview on the broad topic of biogenic amines (BAs) that are a persistent concern in the context of food quality and safety. They emerge mainly from the decomposition of amino acids in protein-rich food due to enzymes excreted by pathogenic bacteria that infect food under inappropriate storage conditions. While there are food authority regulations on the maximum allowed amounts of, e.g., histamine in fish, sensitive individuals can still suffer from medical conditions triggered by biogenic amines, and mass outbreaks of scombroid poisoning are reported regularly. We review first the classical techniques used for selective BA detection and quantification in analytical laboratories and focus then on sensor-based solutions aiming at on-site BA detection throughout the food chain. There are receptor-free chemosensors for BA detection and a vastly growing range of bio- and biomimetic sensors that employ receptors to enable selective molecular recognition. Regarding the receptors, we address enzymes, antibodies, molecularly imprinted polymers (MIPs), and aptamers as the most recent class of BA receptors. Furthermore, we address the underlying transducer technologies, including optical, electrochemical, mass-sensitive, and thermal-based sensing principles. The review concludes with an assessment on the persistent limitations of BA sensors, a technological forecast, and thoughts on short-term solutions.


Subject(s)
Biogenic Amines , Food Safety , Animals , Biogenic Amines/analysis , Histamine/analysis , Amino Acids
12.
Sensors (Basel) ; 24(1)2023 Dec 26.
Article in English | MEDLINE | ID: mdl-38202993

ABSTRACT

Per- and polyfluoroalkyl substances (PFAS) are a class of materials that have been widely used in the industrial production of a wide range of products. After decades of bioaccumulation in the environment, research has demonstrated that these compounds are toxic and potentially carcinogenic. Therefore, it is essential to map the extent of the problem to be able to remediate it properly in the next few decades. Current state-of-the-art detection platforms, however, are lab based and therefore too expensive and time-consuming for routine screening. Traditional biosensor tests based on, e.g., lateral flow assays may struggle with the low regulatory levels of PFAS (ng/mL), the complexity of environmental matrices and the presence of coexisting chemicals. Therefore, a lot of research effort has been directed towards the development of biomimetic receptors and their implementation into handheld, low-cost sensors. Numerous research groups have developed PFAS sensors based on molecularly imprinted polymers (MIPs), metal-organic frameworks (MOFs) or aptamers. In order to transform these research efforts into tangible devices and implement them into environmental applications, it is necessary to provide an overview of these research efforts. This review aims to provide this overview and critically compare several technologies to each other to provide a recommendation for the direction of future research efforts focused on the development of the next generation of biomimetic PFAS sensors.


Subject(s)
Biomimetics , Fluorocarbons , Humans , Carcinogenesis , Carcinogens , Industry
13.
Carcinogenesis ; 43(9): 842-850, 2022 10 22.
Article in English | MEDLINE | ID: mdl-35552655

ABSTRACT

Esophageal adenocarcinoma (EAC) is a leading cause of cancer deaths. Pexidartinib, a multi-gene tyrosine kinase inhibitor, through targeting colony-stimulating factor 1 (CSF-1) receptor (CSF-1R), down modulates macrophage-mediated pro-survival tumor signaling. Previously, CSF-1R inhibitors have successfully shown to enhance antitumor activity of PD-1/PD-L1 inhibitors by suppressing tumor immune evasion, in solid tumors. In this study, we investigated the antitumor activity of pexidartinib alone or in combination with blockade of PD-1 in a de novo EAC rat model. Here, we showed limited toxicity with significant tumor shrinkage in pexidartinib treated animals compared to controls, single agent and in combination with a PD-1 inhibitor, AUNP-12. Suppression of CSF-1/CSF-1R axis resulted in enhanced infiltration of CD3 + CD8 + T cells with reduced M2 macrophage polarization, in the tumor microenvironment (TME). Endpoint tissue gene expression in pexidartinib treated animals demonstrated upregulation of BAX, Cas3, TNFα, IFNγ and IL6 and downregulation of Ki67, IL13, IL10, TGFß and Arg1 (P < 0.05). Additionally, among the pexidartinib treated animals responders compared to nonresponders demonstrated a significant upregulation of pretreatment CSF-1 gene, confirming that tumor-associated macrophage suppression directly translates to clinical benefit. Moreover, a posttreatment serum cytokine assay exhibited similar systemic trends as the gene expression in the TME, depicting increases in proinflammatory cytokines and decreases in anti-inflammatory cytokines. In conclusion, our study established a promising combinatorial strategy using a CSF-1R inhibitor to overcome resistance to PD-1/PD-L1 axis blockade in an EAC model, providing the rationale for future clinical strategies.


Subject(s)
Adenocarcinoma , CRISPR-Associated Proteins , Rats , Animals , Macrophage Colony-Stimulating Factor/pharmacology , Immune Checkpoint Inhibitors , Programmed Cell Death 1 Receptor , Receptor, Macrophage Colony-Stimulating Factor/metabolism , Ki-67 Antigen , Tumor Necrosis Factor-alpha/pharmacology , B7-H1 Antigen , Interleukin-10 , Interleukin-13/pharmacology , Interleukin-6 , bcl-2-Associated X Protein , Tumor Microenvironment , Adenocarcinoma/drug therapy , Adenocarcinoma/genetics , Protein Kinase Inhibitors/pharmacology , Transforming Growth Factor beta/pharmacology , CRISPR-Associated Proteins/pharmacology , Cell Line, Tumor
14.
Br J Cancer ; 127(11): 2016-2024, 2022 11.
Article in English | MEDLINE | ID: mdl-36097175

ABSTRACT

BACKGROUND: Emerging evidence indicates the potential clinical significance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in oesophageal adenocarcinoma (EAC) patients, particularly as novel non-invasive, early detection, surveillance and prognostic classifiers. METHODS: Metagenome sequencing was performed on 81 serum specimens collected across EAC spectrum, with sequencing reads classified using Bracken and MetaPhlAn3. Followed by the Linear Discriminant Analysis effect size (LEfSe) method to identify microbial profiles between groups. Logistic regression and Kaplan-Meier analyses were used to build classifiers. RESULTS: A significant loss of alpha and beta diversity was identified in serum specimens from EAC patients. We observed a shift in microbial taxa between each group-at the phylum, genus, and species level-with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 (95% CI: 0.78-0.95; P < 0.001) and this panel in conjunction with the TNM stage was a robust predictor of overall survival (≥24 months; AUC = 0.84 (95% CI: 0.66-0.92; P = 0.006)). CONCLUSION: This study firstly describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC. TRANSLATIONAL RELEVANCE: Accumulating data indicates the clinical relevance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in patients with oesophageal adenocarcinoma (EAC). Herein, we performed metagenome sequencing in serum specimens from EAC patients 81 collected across EAC spectrum and observed a significant loss of alpha and beta diversity, with a shift in microbial taxa between each group-at the phylum, genus, and species level-with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 and this panel, in conjunction with the TNM stage, was a robust predictor of overall survival. This study for the first time describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC.


Subject(s)
Adenocarcinoma , Esophageal Neoplasms , Gastroesophageal Reflux , Humans , Metagenome , Early Detection of Cancer , Esophageal Neoplasms/diagnosis , Esophageal Neoplasms/genetics , Adenocarcinoma/diagnosis , Adenocarcinoma/genetics , Adenocarcinoma/pathology , Prognosis , Gastroesophageal Reflux/genetics , Carcinogenesis , Escherichia coli , Biomarkers
15.
Int J Mol Sci ; 23(24)2022 Dec 16.
Article in English | MEDLINE | ID: mdl-36555692

ABSTRACT

Extracellular vesicles (EVs) are cell-derived structures surrounded by a lipid bilayer that carry RNA and DNA as potential templates for molecular diagnostics, e.g., in cancer genotyping. While it has been established that DNA templates appear on the outside of EVs, no consensus exists on which nucleic acid species inside small EVs (<200 nm, sEVs) are sufficiently abundant and accessible for developing genotyping protocols. We investigated this by extracting total intravesicular nucleic acid content from sEVs isolated from the conditioned cell medium of the human NCI-H1975 cell line containing the epidermal growth factor (EGFR) gene mutation T790M as a model system for non-small cell lung cancer. We observed that mainly short genomic DNA (<35−100 bp) present in the sEVs served as a template. Using qEV size exclusion chromatography (SEC), significantly lower yield and higher purity of isolated sEV fractions were obtained as compared to exoEasy membrane affinity purification and ultracentrifugation. Nevertheless, we detected the EGFR T790M mutation in the sEVs' lumen with similar sensitivity using digital PCR. When applying SEC-based sEV separation prior to cell-free DNA extraction on spiked human plasma samples, we found significantly higher mutant allele frequencies as compared to standard cell-free DNA extraction, which in part was due to co-purification of circulating tumor DNA. We conclude that intravesicular genomic DNA can be exploited next to ctDNA to enhance EGFR T790M mutation detection sensitivity by adding a fast and easy-to-use sEV separation method, such as SEC, upstream of standard clinical cell-free DNA workflows.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Cell-Free Nucleic Acids , Circulating Tumor DNA , Lung Neoplasms , Humans , Lung Neoplasms/diagnosis , Carcinoma, Non-Small-Cell Lung/diagnosis , ErbB Receptors/genetics , Mutation , Protein Kinase Inhibitors , Oncogenes , Epidermal Growth Factor/genetics , Chromatography, Gel , Genomics
16.
Bioinformatics ; 36(8): 2401-2409, 2020 04 15.
Article in English | MEDLINE | ID: mdl-31913448

ABSTRACT

MOTIVATION: Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step. RESULTS: We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies. AVAILABILITY AND IMPLEMENTATION: Source code is available under https://github.com/nstrodt/UDSMProt. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Algorithms , Proteins , Amino Acid Sequence , Databases, Protein , Proteins/genetics , Software
17.
Sensors (Basel) ; 21(7)2021 Apr 01.
Article in English | MEDLINE | ID: mdl-33916287

ABSTRACT

The study of cell proliferation is of great importance for medical and biological research, as well as for industrial applications. To render the proliferation process accurately over time, real-time cell proliferation assay methods are required. This work presents a novel real-time and label-free approach for monitoring cell proliferation by continuously measuring changes in thermal properties that occur at the sensor interface during the process. The sensor consists of a single planar resistive structure deposited on a thin foil substrate, integrated at the bottom of a cell culture reservoir. During measurement, the structure is excited with square wave current pulses. Meanwhile, the temperature-induced voltage change measured over the structure is used to derive variations in the number of cells at the interface. This principle is demonstrated first by performing cell sedimentation measurements to quantify the presence of cells at the sensor interface in the absence of cell growth. Later, cell proliferation experiments were performed, whereby parameters such as the available nutrient content and the cell starting concentration were modified. Results from these experiments show that the thermal-based sensor is able to accurately measure variations in the number of cells at the interface. Moreover, the influence of the modified parameters could be observed in the obtained proliferation curves. These findings highlight the potential for the presented thermal method to be incorporated in a standardized well plate format for high-throughput monitoring of cell proliferation.


Subject(s)
Cell Culture Techniques , Cell Proliferation , Physical Phenomena
18.
Molecules ; 26(2)2021 Jan 13.
Article in English | MEDLINE | ID: mdl-33450992

ABSTRACT

Mitogen- and Stress-Activated Kinase 1 (MSK1) is a nuclear kinase, taking part in the activation pathway of the pro-inflammatory transcription factor NF-kB and is demonstrating a therapeutic target potential in inflammatory diseases such as asthma, psoriasis and atherosclerosis. To date, few MSK1 inhibitors were reported. In order to identify new MSK1 inhibitors, a screening of a library of low molecular weight compounds was performed, and the results highlighted the 6-phenylpyridin-2-yl guanidine (compound 1a, IC50~18 µM) as a starting hit for structure-activity relationship study. Derivatives, homologues and rigid mimetics of 1a were designed, and all synthesized compounds were evaluated for their inhibitory activity towards MSK1. Among them, the non-cytotoxic 2-aminobenzimidazole 49d was the most potent at inhibiting significantly: (i) MSK1 activity, (ii) the release of IL-6 in inflammatory conditions in vitro (IC50~2 µM) and (iii) the inflammatory cell recruitment to the airways in a mouse model of asthma.


Subject(s)
Drug Design , Guanidines/pharmacology , Protein Kinase Inhibitors/pharmacology , Ribosomal Protein S6 Kinases, 90-kDa/antagonists & inhibitors , Cells, Cultured , Guanidines/chemical synthesis , Guanidines/chemistry , Humans , Molecular Structure , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry , Ribosomal Protein S6 Kinases, 90-kDa/metabolism
19.
Sensors (Basel) ; 20(6)2020 Mar 17.
Article in English | MEDLINE | ID: mdl-32192226

ABSTRACT

In this review article, we are going to present an overview on possible applications of light-addressable electrodes (LAE) as actuator/manipulation devices besides classical electrode structures. For LAEs, the electrode material consists of a semiconductor. Illumination with a light source with the appropiate wavelength leads to the generation of electron-hole pairs which can be utilized for further photoelectrochemical reaction. Due to recent progress in light-projection technologies, highly dynamic and flexible illumination patterns can be generated, opening new possibilities for light-addressable electrodes. A short introduction on semiconductor-electrolyte interfaces with light stimulation is given together with electrode-design approaches. Towards applications, the stimulation of cells with different electrode materials and fabrication designs is explained, followed by analyte-manipulation strategies and spatially resolved photoelectrochemical deposition of different material types.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Light , Semiconductors , Biosensing Techniques/instrumentation , Biosensing Techniques/methods , Coated Materials, Biocompatible/chemical synthesis , Coated Materials, Biocompatible/chemistry , Coated Materials, Biocompatible/supply & distribution , Coated Materials, Biocompatible/therapeutic use , Electrochemical Techniques/instrumentation , Electrochemical Techniques/methods , Electrodes , Electroplating/instrumentation , Electroplating/methods , Equipment Design , Humans , Lighting/instrumentation , Lighting/methods , Microtechnology/methods
20.
Molecules ; 25(21)2020 Oct 27.
Article in English | MEDLINE | ID: mdl-33121149

ABSTRACT

We report herein an efficient synthesis of furopyran derivatives through a gold(I)-catalyzed domino reaction. The cascade reaction starts with two regioselective cyclizations, a 5-endo-dig and a 8-endo-dig, followed with a Grob-type fragmentation and a hetero Diels-Alder. The obtained furopyran derivatives contain fused and spiro-heterocycles. During this one-pot process, four bonds and four controlled stereogenic centers including a quaternary center are formed.


Subject(s)
Gold/chemistry , Pyrans/chemistry , Pyrans/chemical synthesis , Catalysis , Chemistry Techniques, Synthetic
SELECTION OF CITATIONS
SEARCH DETAIL