laser capture
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2022 ◽  
Author(s):  
Rachele A Lubeckyj ◽  
Liangliang Sun

Mass spectrometry (MS)-based spatially resolved top-down proteomics (TDP) of tissues is crucial for understanding the roles played by microenvironmental heterogeneity in the biological functions of organs and for discovering new...


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Aadarsh Patel ◽  
Ganesh Mohan ◽  
Imran Khan ◽  
Mithun Sinha ◽  
Aladdin H. Hassanein

Background:  Lymphedema is characterized by limb swelling secondary to lymphatic dysfunction. Lymphedema most frequently develops following breast cancer treatment due to iatrogenic damage of the lymphatics from surgery and radiation. Lymphedema affects 20-40% of breast cancer survivors. There is no cure for this disease. For determination of successful delivery of gene-based therapies, target cells are often isolated and analyzed via real-time PCR. One method to isolate a region of cells within a tissue section is laser capture microdissection (LCM). This process involves outlining the desired regions, which are cut on membrane slides and captured using a laser. Using LCM requires visualization and identification of the target tissue. In the case of lymphedema therapies, the target tissue is lymphatic vasculature.     Rationale of Project:   While lymphatics can be visualized using immunohistochemistry antibodies specific to lymphatic markers, the process is time consuming and can interfere with RNA levels in the tissue. Another option to visualize lymphatics is to use Lyve1-Cre+ mice. These mice express enhanced green fluorescent protein on lymphatic cells. The purpose of this project is to assess the utility of Lyve1-Cre+ and develop the methodology to capture the lymphatics in the murine tail to enable utilization of this methodology in murine tail model of lymphedema.    Methodology Development:  Samples of Lyve1-Cre+ mouse tails were harvested. Sections (10µm) were captured on LCM slides and dehydrated. The slides were visualized on the LCM microscope system, lymphatics vessels fluoresced green. They were captured via laser dissection. The captured samples were analyzed for the lymphatic specific genes (Prox1 and Lyve1) via quantitative real-time PCR to determine the purity of capture. 


2021 ◽  
Vol 65 (4) ◽  
pp. 519-526
Author(s):  
Agnieszka Jasik ◽  
Anna Kycko ◽  
Monika Olech ◽  
Krzysztof Wyrostek ◽  
Anna Śmiech ◽  
...  

Abstract Introduction Apocrine sweat gland carcinomas (ASGCs) are rare malignant skin tumours in dogs and humans. The literature published so far focuses mostly on the clinico-epidemiological aspect of these tumours, but little is known about their pathogenesis. In this study we aimed to determine whether the p53 gene is involved in the carcinogenesis of the apocrine sweat gland in dogs and whether ultraviolet radiation (UV) is related to it. Material and Methods Forty canine ASGCs were submitted to laser capture microdissection to isolate neoplastic cells, from which DNA was subsequently extracted. PCR amplification and sequencing of p53 exons 2–8 was then performed, followed by computer analysis of the obtained sequences. Results Sixteen mutations within the p53 gene were found in 13 tumours. The mutations involved C → T, T → C, G → A, and CC → TT transitions, C → G transversion and adenine deletion, which are gene alteration types known to be related to UV radiation in the process of skin carcinogenesis in humans. Six of the thirteen tumour cases displayed the C → T transitions in the same location in exon 4 and three of the thirteen cases displayed T → C in the same location in exon 5. Conclusion The results of the present study indicate both the participation of the p53 gene and the influence of UV radiation in the formation of ASGCs in dogs.


2021 ◽  
Author(s):  
Alexander Bury ◽  
Angela Pyle ◽  
Fabio Marcuccio ◽  
Doug Turnbull ◽  
Amy Vincent ◽  
...  

Intracellular heterogeneity contributes significantly to cellular physiology and, in a number of debilitating diseases, cellular pathophysiology. This is greatly influenced by distinct organelle populations and to understand the aetiology of disease it is important to have tools able to isolate and differentially analyse organelles from precise location within tissues. Here we report the development of a subcellular biopsy technology that facilitates the isolation of organelles, such as mitochondria, from human tissue. We compared the subcellular biopsy technology to laser capture microdissection (LCM) that is the state of art technique for the isolation of cells from their surrounding tissues. We demonstrate an operational limit of (>20 micron) for LCM and then, for the first time in human tissue, show that subcellular biopsy can be used to isolate mitochondria beyond this limit.


2021 ◽  
Author(s):  
Kazuki Komiyama ◽  
Keiya Iijima ◽  
Reika Kawabata-Iwakawa ◽  
Kazuyuki Fujihara ◽  
Toshikazu Kakizaki ◽  
...  

Abstract Patients with glioma often demonstrate epilepsy. We previously found burst discharges in the peritumoral area in patents with malignant brain tumors during biopsy. Therefore, we hypothesized that the peritumoral area may possess an epileptic focus and that biological alterations in the peritumoral area may cause epileptic symptoms in patients with glioma. To test our hypothesis, we developed a rat model of glioma and characterized it at the cellular and molecular levels. We first labeled rat C6 glioma cells with tdTomato, a red fluorescent protein (C6-tdTomato) and implanted them into the somatosensory cortex of VGAT-Venus rats, which specifically expressed Venus, a yellow fluorescent protein in GABAergic neurons. We observed that the density of GABAergic neurons was significantly decreased in the peritumoral area of rats with glioma compared with the contralateral healthy side. By using a combination technique of laser capture microdissection and RNA sequencing(LCM-seq) of paraformaldehyde-fixed brain sections, we demonstrated that 19 genes were differentially expressed in the peritumoral area and that five of them were associated with epilepsy and neurodevelopmental disorders. In addition, the canonical pathways actively altered in the peritumoral area were predicted to cause a reduction in GABAergic neurons. These results suggest that biological alterations in the peritumoral area may be a cause of glioma-related epilepsy.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Satoshi Kawakami ◽  
Shinichi Takano ◽  
Mitsuharu Fukasawa ◽  
Hiroko Shindo ◽  
Ei Takahashi ◽  
...  

Abstract Background The genetic changes underlying carcinogenesis in patients with risk factors of gallbladder carcinoma (GBC) remains controversial, especially in patients with pancreaticobiliary maljunction (PBM). This study aimed to clarify the association between risk factors of GBC and genetic changes using next-generation sequencing (NGS). Methods We retrospectively analyzed resected tissues of 64 patients who were diagnosed with GBC (n = 26), PBM [with GBC (n = 8), without GBC (n = 20)], and chronic cholecystitis, used as a control group (n = 10). DNA was extracted from tumors and their surrounding tissues, which were precisely separated by laser-capture microdissection. Gene alterations of 50 cancer-related genes were detected by NGS and compared with clinical information, including PBM status. Results The most frequent gene alterations in GBC tissues occurred in TP53 (50%), followed by EGFR (20.6%), RB1 (17.6%), and ERBB2 (17.6%). Gene alterations that were targetable by molecular targeted drugs were detected in 20 cases (58.8%). Statistical analysis of gene alterations and risk factors revealed that TP53 alteration rate was higher in GBC patients with PBM than those without PBM (p = 0.038), and the TP53 mutation rates in the epithelium of control patients, epithelium of PBM patients without GBC, peritumoral mucosa of GBC patients with PBM, and tumor tissue of GBC patients with PBM were 10, 10, 38, and 75%, respectively (p <  0.01). Conclusions TP53 alteration more than KRAS mutation was revealed to underlie carcinogenesis in patients with PBM.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alba Rudolf Vegas ◽  
Giorgia Podico ◽  
Igor F. Canisso ◽  
Heinrich Bollwein ◽  
Carmen Almiñana ◽  
...  

AbstractDuring the period of maternal recognition of pregnancy (MRP) in the mare, the embryo needs to signal its presence to the endometrium to prevent regression of the corpus luteum and prepare for establishment of pregnancy. This is achieved by mechanical stimuli and release of various signaling molecules by the equine embryo while migrating through the uterus. We hypothesized that embryo’s signals induce changes in the endometrial gene expression in a highly cell type-specific manner. A spatiotemporal transcriptomics approach was applied combining laser capture microdissection and low-input-RNA sequencing of luminal and glandular epithelium (LE, GE), and stroma of biopsy samples collected from days 10–13 of pregnancy and the estrous cycle. Two comparisons were performed, samples derived from pregnancies with conceptuses ≥ 8 mm in diameter (comparison 1) and conceptuses ≤ 8 mm (comparison 2) versus samples from cyclic controls. The majority of gene expression changes was identified in LE and much lower numbers of differentially expressed genes (DEGs) in GE and stroma. While 1253 DEGs were found for LE in comparison 1, only 248 were found in comparison 2. Data mining mainly focused on DEGs in LE and revealed regulation of genes related to prostaglandin transport, metabolism, and signaling, as well as transcription factor families that could be involved in MRP. In comparison to other mammalian species, differences in regulation of genes involved in epithelial barrier formation and conceptus attachment and implantation reflected the unique features of equine reproduction at the time of MRP at the molecular level.


Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3190
Author(s):  
Justine Lai ◽  
Jing Li ◽  
Robert Gniadecki ◽  
Raymond Lai

A subset of patients with mycosis fungoides (MF) progress to the tumor stage, which correlates with a worse clinical outcome. The molecular events driving this progression are not well-understood. To identify the key molecular drivers, we performed gene expression profiling (GEP) using NanoString. Ten formalin-fixed/paraffin-embedded skin biopsies from six patients (six non-tumor and four tumor MF) were included; non-tumor and tumor samples were available in three patients. Laser capture/single cell microdissection of epidermotropic MF cells was used for non-tumor cases. We found that the RNA extracted from 700–800 single cells was consistently sufficient for GEP, provided that multiplexed target enrichment amplification was used. An un-supervised/hierarchical analysis revealed clustering of non-tumor and tumor cases. Many of the most upregulated or downregulated genes are implicated in the PI3K, RAS, cell cycle/apoptosis and MAPK pathways. Two of the targets, HMGA1 and PTPN11 (encodes SHP2), were validated using immunohistochemistry. HMGA1 was positive in six out of six non-tumor MF samples and negative in five out of five tumor MF samples. An opposite pattern was seen with SHP2. Our study has provided a proof-of-concept that single-cell microdissection/GEP can be applied to archival tissues. Some of our identified gene targets might be key drivers of the disease progression of MF.


2021 ◽  
Author(s):  
Jeremy A. Herrera ◽  
Lewis Dingle ◽  
M. Angeles Montero ◽  
Rajesh Shah ◽  
Rajamiyer V. Venkateswaran ◽  
...  

Background: The Fibroblastic Focus (FF) is the signature lesion of Idiopathic Pulmonary Fibrosis (IPF) where myofibroblasts accumulate and extracellular matrix (ECM) is produced. However, the molecular composition and function of the FF and surrounding tissue remain undefined. Methods: Utilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the FF, adjacent mature scar, and adjacent alveoli in 6 IPF specimens plus 6 non-fibrotic alveolar specimens as controls. The data were subject to qualitative and quantitative analysis, and validation by immunohistochemistry. Results: We found that the protein signature of IPF alveoli is defined by immune deregulation as the strongest category. The IPF mature scar was classified as end-stage fibrosis whereas the FF contained an overabundance of a distinctive ECM compared to non-fibrotic control. Conclusion: Spatial proteomics demonstrated distinct protein compositions in the histologically defined regions of IPF tissue. These data revealed that the FF is the main site of collagen biosynthesis and that the alveoli adjacent to the FF are abnormal. This new and essential information will inform future mechanistic studies on mechanisms of IPF progression.


2021 ◽  
Vol 22 (21) ◽  
pp. 12034
Author(s):  
Elizabeth A. Mickler ◽  
Huaxin Zhou ◽  
Tzu L. Phang ◽  
Mark W. Geraci ◽  
Robert S. Stearman ◽  
...  

Defining detailed genomic characterization of early tumor progression is critical to identifying key regulators and pathways in carcinogenesis as potentially druggable targets. In human lung cancer, work to characterize early cancer development has mainly focused on squamous cancer, as the earliest lesions are more proximal in the airways and often accessible by repeated bronchoscopy. Adenocarcinomas are typically located distally in the lung, limiting accessibility for biopsy of pre-malignant and early stages. Mouse lung cancer models recapitulate many human genomic features and provide a model for tumorigenesis with pre-malignant atypical adenomatous hyperplasia and in situ adenocarcinomas often developing contemporaneously within the same animal. Here, we combined tissue characterization and collection by laser capture microscopy (LCM) with digital droplet PCR (ddPCR) and low-coverage whole genome sequencing (LC-WGS). ddPCR can be used to identify specific missense mutations in Kras (Kirsten rat sarcoma viral oncogene homolog, here focused on Kras Q61) and estimate the percentage of mutation predominance. LC-WGS is a cost-effective method to infer localized copy number alterations (CNAs) across the genome using low-input DNA. Combining these methods, the histological stage of lung cancer can be correlated with appearance of Kras mutations and CNAs. The utility of this approach is adaptable to other mouse models of human cancer.


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