scholarly journals 6. Label-free selective plane illumination microscopy of tissue samples

2017 ◽  
Vol 29 (4) ◽  
pp. 326
Author(s):  
Muteb Alharbi ◽  
Saleh Khonezan ◽  
Melissa Mather ◽  
Abdulrahman Almaymn
Keyword(s):  
Label Free ◽  
Tissue Samples ◽  
Selective Plane Illumination Microscopy

scholarly journals Alteration of protein expression and spliceosome pathway activity during Barrett’s carcinogenesis

2021 ◽  
Author(s):  
Christoph Stingl ◽  
Angela Bureo Gonzalez ◽  
Coşkun Güzel ◽  
Kai Yi Nadine Phoa ◽  
Michail Doukas ◽  
...  
Keyword(s):  
Micro Rna ◽  
Differentially Expressed ◽  
Epithelial Tissue ◽  
Label Free ◽  
Tissue Samples ◽  
Damage Repair ◽  
Inter Observer Variability ◽  
Stromal Tissue ◽  
The Face ◽  
Abundance And Diversity

Abstract Background Barrett’s esophagus (BE) is a known precursor lesion and the strongest risk factor for esophageal adenocarcinoma (EAC), a common and lethal type of cancer. Prediction of risk, the basis for efficient intervention, is commonly solely based on histologic examination. This approach is challenged by problems such as inter-observer variability in the face of the high heterogeneity of dysplastic tissue. Molecular markers might offer an additional way to understand the carcinogenesis and improve the diagnosis—and eventually treatment. In this study, we probed significant proteomic changes during dysplastic progression from BE into EAC. Methods During endoscopic mucosa resection, epithelial and stromal tissue samples were collected by laser capture microdissection from 10 patients with normal BE and 13 patients with high-grade dysplastic/EAC. Samples were analyzed by mass spectrometry-based proteomic analysis. Expressed proteins were determined by label-free quantitation, and gene set enrichment was used to find differentially expressed pathways. The results were validated by immunohistochemistry for two selected key proteins (MSH6 and XPO5). Results Comparing dysplastic/EAC to non-dysplastic BE, we found in equal volumes of epithelial tissue an overall up-regulation in terms of protein abundance and diversity, and determined a set of 226 differentially expressed proteins. Significantly higher expressions of MSH6 and XPO5 were validated orthogonally and confirmed by immunohistochemistry. Conclusions Our results demonstrate that disease-related proteomic alterations can be determined by analyzing minute amounts of cell-type-specific collected tissue. Further analysis indicated that alterations of certain pathways associated with carcinogenesis, such as micro-RNA trafficking, DNA damage repair, and spliceosome activity, exist in dysplastic/EAC.

scholarly journals Label-Free Rapid Separation and Enrichment of Bone Marrow-Derived Mesenchymal Stem Cells from a Heterogeneous Cell Mixture Using a Dielectrophoresis Device

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 3007 ◽  
Author(s):  
Junya Yoshioka ◽  
Yu Ohsugi ◽  
Toru Yoshitomi ◽  
Tomoyuki Yasukawa ◽  
Naoki Sasaki ◽  
...  
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Stem Cell ◽  
Gradient Method ◽  
Label Free ◽  
Rapid Separation ◽  
Isolation System ◽  
Tissue Samples ◽  
Cell Based Therapy

Bone marrow-derived mesenchymal stem cells (BMSCs) are an important cell resource for stem cell-based therapy, which are generally isolated and enriched by the density-gradient method based on cell size and density after collection of tissue samples. Since this method has limitations with regards to purity and repeatability, development of alternative label-free methods for BMSC separation is desired. In the present study, rapid label-free separation and enrichment of BMSCs from a heterogeneous cell mixture with bone marrow-derived promyelocytes was successfully achieved using a dielectrophoresis (DEP) device comprising saw-shaped electrodes. Upon application of an electric field, HL-60 cells as models of promyelocytes aggregated and floated between the saw-shaped electrodes, while UE7T-13 cells as models of BMSCs were effectively captured on the tips of the saw-shaped electrodes. After washing out the HL-60 cells from the device selectively, the purity of the UE7T-13 cells was increased from 33% to 83.5% within 5 min. Although further experiments and optimization are required, these results show the potential of the DEP device as a label-free rapid cell isolation system yielding high purity for rare and precious cells such as BMSCs.

scholarly journals Label-free redox imaging of patient-derived organoids using selective plane illumination microscopy

2020 ◽  
Vol 11 (5) ◽  
pp. 2591 ◽  
Author(s):  
Peter F. Favreau ◽  
Jiaye He ◽  
Daniel A. Gil ◽  
Dustin A. Deming ◽  
Jan Huisken ◽  
...  
Keyword(s):  
Label Free ◽  
Selective Plane Illumination Microscopy

scholarly journals Addressing cellular heterogeneity in tumor and circulation for refined prognostication

2019 ◽  
Vol 116 (36) ◽  
pp. 17957-17962 ◽  
Author(s):  
Su Bin Lim ◽  
Trifanny Yeo ◽  
Wen Di Lee ◽  
Ali Asgar S. Bhagat ◽  
Swee Jin Tan ◽  
...  
Keyword(s):  
Risk Model ◽  
Expression Profiles ◽  
Metastatic Potential ◽  
Cellular Heterogeneity ◽  
Intratumor Heterogeneity ◽  
Specific Gene ◽  
Label Free ◽  
Tissue Samples ◽  
Inertial Focusing ◽  
Gene Signatures

Despite pronounced genomic and transcriptomic heterogeneity in non–small-cell lung cancer (NSCLC) not only between tumors, but also within a tumor, validation of clinically relevant gene signatures for prognostication has relied upon single-tissue samples, including 2 commercially available multigene tests (MGTs). Here we report an unanticipated impact of intratumor heterogeneity (ITH) on risk prediction of recurrence in NSCLC, underscoring the need for a better genomic strategy to refine prognostication. By leveraging label-free, inertial-focusing microfluidic approaches in retrieving circulating tumor cells (CTCs) at single-cell resolution, we further identified specific gene signatures with distinct expression profiles in CTCs from patients with differing metastatic potential. Notably, a refined prognostic risk model that reconciles the level of ITH and CTC-derived gene expression data outperformed the initial classifier in predicting recurrence-free survival (RFS). We propose tailored approaches to providing reliable risk estimates while accounting for ITH-driven variance in NSCLC.

scholarly journals Zinc Phthalocyanine Photochemistry by Raman Imaging, Fluorescence Spectroscopy and Femtosecond Spectroscopy in Normal and Cancerous Human Colon Tissues and Single Cells

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2688 ◽  
Author(s):  
Beata Brozek-Pluska ◽  
Arkadiusz Jarota ◽  
Rafal Kania ◽  
Halina Abramczyk
Keyword(s):  
Single Cells ◽  
Blue Shift ◽  
Human Colon ◽  
Raman Imaging ◽  
Zinc Phthalocyanine ◽  
Label Free ◽  
Colon Tissue ◽  
Tissue Samples ◽  
Colon Cells ◽  
Normal Human

Photodynamic therapy is a clinically approved alternative method for cancer treatment in which a combination of nontoxic drugs known as photosensitizers and oxygen is used. Despite intensive investigations and encouraging results, zinc phthalocyanines (ZnPcs) have not yet been approved as photosensitizers for clinical use. Label-free Raman imaging of nonfixed and unstained normal and cancerous colon human tissues and normal human CCD18-Co and cancerous CaCo-2 cell lines, without and after adding ZnPcS4 photosensitizer, was analyzed. The biochemical composition of normal and cancerous colon tissues and colon cells without and after adding ZnPcS4 at the subcellular level was determined. Analyzing the fluorescence/Raman signals of ZnPcS4, we found that in normal human colon tissue samples, in contrast to cancerous ones, there is a lower affinity to ZnPcS4 phthalocyanine. Moreover, a higher concentration in cancerous tissue was concomitant with a blue shift of the maximum peak position specific for the photosensitizer from 691–695 nm to 689 nm. Simultaneously for both types of samples, the signal was observed in the monomer region, confirming the excellent properties of ZnPcS4 for photo therapy (PDT). For colon cell experiments with a lower concentration of ZnPcS4 photosensitizer, c = 1 × 10−6 M, the phthalocyanine was localized in mitochondria/lipid structures; for a higher concentration, c = 9 × 10−6 M, localization inside the nucleus was predominant. Based on time-resolved experiments, we found that ZnPcS4 in the presence of biological interfaces features longer excited-state lifetime photosensitizers compared to the aqueous solution and bare ZnPcS4 film on CaF2 substrate, which is beneficial for application in PDT.

scholarly journals Intraoperative discrimination of native meningioma and dura mater by Raman spectroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Finn Jelke ◽  
Giulia Mirizzi ◽  
Felix Kleine Borgmann ◽  
Andreas Husch ◽  
Rédouane Slimani ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Dura Mater ◽  
Vibrational Analysis ◽  
Histopathological Analysis ◽  
Label Free ◽  
Fresh Tissue ◽  
Tissue Samples ◽  
Surgical Specimen ◽  
Additional Processing ◽  
External Test

AbstractMeningiomas are among the most frequent tumors of the central nervous system. For a total resection, shown to decrease recurrences, it is paramount to reliably discriminate tumor tissue from normal dura mater intraoperatively. Raman spectroscopy (RS) is a non-destructive, label-free method for vibrational analysis of biochemical molecules. On the microscopic level, RS was already used to differentiate meningioma from dura mater. In this study we test its suitability for intraoperative macroscopic meningioma diagnostics. RS is applied to surgical specimen of intracranial meningiomas. The main purpose is the differentiation of tumor from normal dura mater, in order to potentially accelerate the diagnostic workflow. The collected meningioma and dura mater samples (n = 223 tissue samples from a total of 59 patients) are analyzed under untreated conditions using a new partially robotized RS acquisition system. Spectra (n = 1273) are combined with the according histopathological analysis for each sample. Based on this, a classifier is trained via machine learning. Our trained classifier separates meningioma and dura mater with a sensitivity of 96.06 $$\pm $$ ± 0.03% and a specificity of 95.44 $$\pm $$ ± 0.02% for internal fivefold cross validation and 100% and 93.97% if validated with an external test set. RS is an efficient method to discriminate meningioma from healthy dura mater in fresh tissue samples without additional processing or histopathological imaging. It is a quick and reliable complementary diagnostic tool to the neuropathological workflow and has potential for guided surgery. RS offers a safe way to examine unfixed surgical specimens in a perioperative setting.

scholarly journals Digital Staining of High-Definition Fourier Transform Infrared (FT-IR) Images Using Deep Learning

2019 ◽  
Vol 73 (5) ◽  
pp. 556-564 ◽  
Author(s):  
Mahsa Lotfollahi ◽  
Sebastian Berisha ◽  
Davar Daeinejad ◽  
David Mayerich
Keyword(s):  
Fourier Transform ◽  
Fourier Transform Infrared ◽  
Cellular Level ◽  
Label Free ◽  
High Definition ◽  
Tissue Samples ◽  
Ft Ir ◽  
Downstream Analysis ◽  
Ir Spectroscopic ◽  
Multiple Samples

Histological stains, such as hematoxylin and eosin (H&E), are routinely used in clinical diagnosis and research. While these labels offer a high degree of specificity, throughput is limited by the need for multiple samples. Traditional histology stains, such as immunohistochemical labels, also rely only on protein expression and cannot quantify small molecules and metabolites that may aid in diagnosis. Finally, chemical stains and dyes permanently alter the tissue, making downstream analysis impossible. Fourier transform infrared (FT-IR) spectroscopic imaging has shown promise for label-free characterization of important tissue phenotypes and can bypass the need for many chemical labels. Fourier transform infrared classification commonly leverages supervised learning, requiring human annotation that is tedious and prone to errors. One alternative is digital staining, which leverages machine learning to map IR spectra to a corresponding chemical stain. This replaces human annotation with computer-aided alignment. Previous work relies on alignment of adjacent serial tissue sections. Since the tissue samples are not identical at the cellular level, this technique cannot be applied to high-definition FT-IR images. In this paper, we demonstrate that cellular-level mapping can be accomplished using identical samples for both FT-IR and chemical labels. In addition, higher-resolution results can be achieved using a deep convolutional neural network that integrates spatial and spectral features.

scholarly journals Molecular and proteomic signatures associated with preservation related graft injury: insight from human liver normothermic machine perfusion (NMP)

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Fungai Dengu
Keyword(s):  
Differential Expression ◽  
Cold Storage ◽  
Liver Perfusion ◽  
Molecular Signature ◽  
Label Free ◽  
Significant Differential Expression ◽  
Tissue Samples ◽  
University Of Oxford ◽  
Novel Technology ◽  
The Impact

Fungai Dengu1; Sadr Shaheed1; Letizia Lo Faro1; Adam Thorne1; Honglei Huang1; Peter Friend1,Rutger Ploeg1. 1. Oxford Organ Perfusion Lab, Nuffield Department of Surgical Sciences and Oxford BiomedicalResearch Centre, University of Oxford, Oxford, UK     BackgroundContinuous liver NMP is a novel technology associated with safe extension of organ preservation time, increased organ utilisation and reduced early graft injury1. Increasingly, it is utilised as a ‘back to base’ application with cold storage for organ transport and NMP initiated at the implanting centre prior to transplantation2. We aimed to evaluate the impact of additional cold ischaemia time (CIT) on the proteomic and molecular signature of NMP livers. Methods Liver tissue samples (N= 57) from a prospective clinical trial of ‘back to base’ NMP were analysed. Collection occurred at the end of cold storage (LT1), end of NMP/total preservation (LT2) and after organ reperfusion (LT3). Unbiased, label-free-quantitative (LFQ) proteomic analysis was conducted using liquid chromatography with tandem mass spectrometry and trapped ion mobility spectrometry (TIMS) to time-of-flight (TOF) mass analysis (LC-MS/MS TIMS-TOF). Differential expression and Gene Ontology/Pathway analysis were performed. Results LT2 samples with prolonged CIT (>6hr) prior to NMP had significant differential expression of proteins associated with liver-specific oxidative stress, cellular haemostasis and removal of damaged or misfolded proteins (e.g. CYP3A5, PSMB1). LT3 samples, similarly, had reduced proteins involved in autophagy and cell-cycle regulation (e.g. STBD1, CD2AP, GADD45GIP1,) and increased expression of proteins involved in neutrophil chemotaxis, adhesion and aggregation (e.g. S100A9). Discussion The molecular signature of grafts at LT2 and LT3 varies depending on the length of CIT prior to NMP. Further exploration of the molecular signatures associated with preservation related graft injury is required to determine how best to apply this novel technology clinically. References: 1. Nasralla, D. et al. A randomized trial of normothermic preservation in liver transplantation. Nature 557, 50–56 (2018).2. Ceresa, C. D. L. et al. Transient Cold Storage Prior to Normothermic Liver Perfusion May Facilitate Adoption of a Novel Technology. Liver Transplant. lt.25584 (2019).doi:10.1002/lt.25584

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