Medical diagnosis of biopsies performed by fine needle aspiration has to be very reliable. Therefore, pathologists/cytologists need additional biochemical information on single cancer cells for an ...accurate diagnosis. Accordingly, we applied three different classification models for discriminating various features of six breast cancer cell lines by analyzing Raman microspectroscopic data. The statistical evaluations are implemented by linear discriminant analysis (LDA) and support vector machines (SVM). For the first model, a total of 61,580 Raman spectra from 110 single cells are discriminated at the cell-line level with an accuracy of 99.52% using an SVM. The LDA classification based on Raman data achieved an accuracy of 94.04% by discriminating cell lines by their origin (solid tumor versus pleural effusion). In the third model, Raman cell spectra are classified by their cancer subtypes. LDA results show an accuracy of 97.45% and specificities of 97.78%, 99.11%, and 98.97% for the subtypes basal-like, HER2+/ER−, and luminal, respectively. These subtypes are confirmed by gene expression patterns, which are important prognostic features in diagnosis. This work shows the applicability of Raman spectroscopy and statistical data handling in analyzing cancer-relevant biochemical information for advanced medical diagnosis on the single-cell level.
─ To determine the quality and mechanical stability of composite materials, a defect detection whilst in the processing chain as well as active monitoring during use is inevitable. This can be ...achieved via the application of millimeter-wave radars, with the tomographic information extractable from the reflected signal. Due to clutter effects present in the reflected signal, the extracted tomographic image quality diminishes. Therefore, a method to reduce the impact of these clutter sources in the post-processing of the measurement while retaining the information of possible structure defects is presented. The method is based on singular value decomposition with the singular values determined through the comparison of the measured reflected signal with an ideal signal reference. With this method, the singular values do not have to be defined by hand, which represents a major advantage when considering automatic data evaluation possibilities.
Abstract Early detection of tumor activity in clinically asymptomatic patients has the potential to improve quality of life and prevent unnecessary exposure to toxic therapies. DNA methylation is one ...of the most studied, stable, and fundamental epigenetic marks and represents a prominent alteration in most cancers. Analysis of DNA methylation, particularly in liquid biopsies has been introduced in cancer diagnosis and risk stratification. Despite indisputable achievements, translation into clinical practice is lagging behind, primarily due to 1) challenges associated with the analysis of DNA methylation, 2) the fragmented nature of cell-free DNA (cfDNA), aggravated by bisulfite treatment, 3) lack of clinical validation of reported cfDNA methylation marks, and 4) the paucity of knowledge about the functional consequences of cfDNA methylation marks within tumors. Using a sample pooling strategy, complemented with robust whole genome and reduced representation methylation sequencing, we establish a pan-cancer cfDNA methylation resource encompassing 12 cancer entities with diverse clinical phenotypes and treatment modalities. We built this compendium using a robustly performing whole genome and reduced representaion enzymatic methylation sequencing of more than 150 cfDNA and tumor DNA. We complement our data by analyzing DNA methylation data from 15 cancer entities (more than 7,000 patients) within the TCGA. We developed an enzymatic digital PCR (dPCR) approach for pan-cancer but also entity-specific analysis of cfDNA methylation at single base-resolution. Using this dPCR assay, we analyzed cfDNA and tumor DNA samples from more than 400 patients and compared enzymatic digestion with bisulfite treatment. We demonstrate that this resource can allow for the identification of entity-agnostic and specific markers, and that cfDNA methylation patterns are mirrored in tumor samples. The approach can be applied for methylation profiling of yet unanalyzed entities. Finally, we demonstrate unconventional epigenetic regulation of gene expression by methylated DNA-binding transcription factors whose activities are tissue- and context-specific and dosage-dependent. This work, therefore, provides a reference resource to identify minimally invasive, entity-specific and pan-cancer markers applicable for diagnostics, surveillance and patient stratification. It also sets the stage for further investigation of tissue- and context-specific epigenetic regulation of gene expression in health and disease by methylated DNA-binding transcription factors. Citation Format: Smiths Sengkwawoh Lueong, Martin Metzenmacher, Gregor Zaun, Gina Lauren Mayer, Erik Jan Hemmer, Katharina Lückerath, Kelsey Pomykala, Balazs Hegedüs, Peter A. Horn, Marija Trajkovic-Arsic, Tibor Szarvas, Renáta Váraljai, Corinna Keup, Ingeborg Tinhofer, Stephen George, Sabine Kasimir-Bauer, Samuel Peña-Llopis, Alexander Roesch, Cornelius Kürten, Lukas Boosfeld, Kirsten Bruderek, Christopher Darr, Thomas Hilser, Viktor Grünwald, Sven Brandau, Boris Hadaschik, Hans Neubauer, Irene Irene Esposito Irene Esposito, Tanja Fehm, Csilla Oláh, Anita Csizmarik, Fabinshy Thangarajah, Laura Reetz, Ghanam Jamal, Basant Kumar Thakur, Halime Kalkavan, Alexander Schramm, Martin Schuler, Jens T. Siveke. Comprehensive pan-cancer analysis of cfDNA methylation marks in tumors reveals complex epigenetic regulatory circuits and diagnostic biomarkers abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5019.
Despite success with BRAFV600E inhibitors, therapeutic responses in patients with metastatic melanoma are short-lived because of the acquisition of drug resistance. We identified a mechanism of ...intrinsic multidrug resistance based on the survival of a tumor cell subpopulation. Treatment with various drugs, including cisplatin and vemurafenib, uniformly leads to enrichment of slow-cycling, long-term tumor-maintaining melanoma cells expressing the H3K4-demethylase JARID1B/KDM5B/PLU-1. Proteome-profiling revealed an upregulation in enzymes of mitochondrial oxidative-ATP-synthesis (oxidative phosphorylation) in this subpopulation. Inhibition of mitochondrial respiration blocked the emergence of the JARID1Bhigh subpopulation and sensitized melanoma cells to therapy, independent of their genotype. Our findings support a two-tiered approach combining anticancer agents that eliminate rapidly proliferating melanoma cells with inhibitors of the drug-resistant slow-cycling subpopulation.
•Slow-cycling melanoma cells expressing JARID1B show intrinsic multidrug resistance•Slow-cycling melanoma cells show upregulation of OXPHOS•Inhibition of OXPHOS sensitizes slow-cycling cells to therapy•OXPHOS inhibition can overcome drug resistance, irrespective of melanoma genotypes
Abstract Cognitive deficits in schizophrenia, especially those related to prefrontal cortex (PFC) functions, influence functional outcome. There is evidence for sex differences in cognition in ...schizophrenia, but the results in the literature are still controversial. Objective This study evaluated different modalities of working memory (WM) and executive control (EC), functions that are both associated with the PFC, between sexes in schizophrenic patients and controls. Methods We used a battery of neuropsychological tests for assessing auditory, spatial, and visual-matching WM and used a dual task for assessing EC. The study included 50 inpatients (25 female) partially remitted and taking atypical neuroleptics, as well as 40 controls (20 female) matched for age and education. Results Significant sex differences were found in the dual task; female patients detected fewer correct trials than male patients and controls did. Moreover, female patients performed significantly worse in the single visual subtest of the dual task. For the controls, no sex differences were found. Males showed higher positive symptoms than females, but no other differences in psychopathology, disease characteristics, or extrapyramidal symptoms were found between sexes. Conclusion The present study shows an absence of sex differences in WM in healthy subjects and in patients with schizophrenia. However, in the dual task and in the single visual subtest, female patients performed worse than males. This finding suggests that in contrast to males, nonacute female inpatients show an underlying attentional deficit that may contribute to impairment in higher-order functions such as EC.
This contribution provides a new approach for single blood cell analysis in cerebrospinal fluid (CSF) with the possibility of utilizing simultaneously on the same sample the unique capabilities of ...the two methods fluorescence staining and Raman spectroscopy. By doing so this technique enables the potential of accurate and rapid cell identification in order to determine cell parameters immediately (e.g. the study of the level of activation or phagocytosis activity of single blood cells). Fluorescence labeling of blood cells offers the great possibility of differentiating easily between the subtypes of white blood cells, while Raman spectroscopy reveals molecular fingerprint information with a spatial resolution down to the diffraction limit. Compared to an unstained cell, the presented results nicely demonstrate that the selected fluorescence dye does not influence the Raman spectrum of a labeled blood cell notably. By the combined application of Raman spectroscopy and statistical data analysis a distinction between white blood cell substructures could be performed. Since several blood cell types also differ in the amount of their cell components, differentiation between several blood cell types is also possible when one blood cell is described in the database by several Raman spectra according their presented sub-microscopic structures. This capability with the possibility of accurate and rapid blood cell identification in cerebrospinal fluid is extremely promising for implementation in clinical diagnostics.
Background Preclinical data implicate the reinforcing effects of alcohol to be mediated by interaction between the opioid and dopamine systems of the brain. Specifically, alcohol-induced release of ...β-endorphins stimulates μ-opioid receptors (MORs), which is believed to cause dopamine release in the brain reward system. Individual differences in opioid or dopamine neurotransmission have been suggested to be responsible for enhanced liability to abuse alcohol. In the present study, a single dose of the MOR agonist remifentanil was administered in detoxified alcohol-dependent patients and healthy control subjects to mimic the β-endorphin-releasing properties of ethanol and to assess the effects of direct MOR stimulation on dopamine release in the mesolimbic reward system. Methods Availability of D2/3 receptors was assessed before and after single-dose administration of the MOR agonist remifentanil in 11 detoxified alcohol-dependent patients and 11 healthy control subjects with positron emission tomography with the radiotracer 18 Ffallypride. Severity of dependence as assessed with the Alcohol Use Disorders Identification Test was compared with remifentanil-induced percentage change in 18 Ffallypride binding (Δ%BPND ). Results The 18 Ffallypride binding potentials (BPND s) were significantly reduced in the ventral striatum, dorsal putamen, and amygdala after remifentanil application in both patients and control subjects. In the patient group, ventral striatum Δ%BPND was correlated with the Alcohol Use Disorders Identification Test score. Conclusions The data provide evidence for a MOR-mediated interaction between the opioid and the dopamine system, supporting the assumption that one way by which alcohol unfolds its rewarding effects is via a MOR-(γ-aminobutyric acid)-dopamine pathway. No difference in dopamine release was found between patients and control subjects, but evidence for a patient-specific association between sensitivity to MOR stimulation and severity of alcohol dependence was found.
Classic bladder exstrophy (CBE) is the most common form of the bladder exstrophy and epispadias complex. Previously, we and others have identified four patients with a duplication of 22q11.21 among a ...total of 96 unrelated CBE patients.
Here, we investigated whether this chromosomal aberration was commonly associated with CBE/bladder exstrophy and epispadias complex in an extended case-control sample. Multiplex ligation-dependent probe amplification and microarray-based analysis were used to identify 22q11.21 duplications in 244 unrelated bladder exstrophy and epispadias complex patients (including 217 CBE patients) and 665 healthy controls.
New duplications of variable size were identified in four CBE patients and one control. Pooling of our previous and present data (eight duplications in 313 CBE patients) yielded a combined odds ratio of 31.86 (95% confidence interval, 4.24-1407.97). Array-based sequence capture and high-throughput targeted re-sequencing established that all breakpoints resided within the low-copy repeats 22A to 22D. Comparison of the eight duplications revealed a 414 kb phenocritical region harboring 12 validated RefSeq genes. Characterization of these 12 candidate genes through whole-mount in situ hybridization of mouse embryos at embryonic day 9.5 suggested that CRKL, THAP7, and LZTR1 are CBE candidate genes.
Our data suggest that duplication of 22q11.21 increases CBE risk and implicate a phenocritical region in disease formation.
Coherent anti-Stokes Raman scattering (CARS) gained a lot of importance in chemical imaging. This is due to the fast image acquisition time, the high spatial resolution, the non-invasiveness, and the ...molecular sensitivity of this method. By using the single-line CARS in contrast to the multiplex CARS, different signal contributions stemming from resonant and non-resonant light-matter interactions are indistinguishable. Here a numerical method is presented in order to extract more information from univariate CARS images: vibrational composition, morphological information, and contributions from index-of-refraction steps can be separated from single-line CARS images. The image processing algorithm is based on the physical properties of CARS process as reflected in the shape of the intensity histogram of univariate CARS images. Because of this the comparability of individual CARS images recorded with different experimental parameters is achieved. The latter is important for a quantitative evaluation of CARS images.
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