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https://www.readbyqxmd.com/read/28109428/a-protocol-for-large-scale-proteomic-analysis-of-microdissected-formalin-fixed-and-paraffin-embedded-tissue
#1
P Ostasiewicz, J R Wiśniewski
Extensive use of biomarkers in diagnostic and therapeutic procedures is probably the hallmark of future medicine. Biomarkers can be of different chemical nature-most frequently DNA, RNA, and proteins are considered as molecules of interest. As the most rational approach appears analysis of proteins, because these are the "effector" molecules directly involved for cell homeostasis. There is no commonly accepted standard procedure in proteomic-based biomarker search. In this chapter, we described a protocol for proteomic analysis of formalin-fixed and paraffin-embedded tissue, which has been proven to be highly effective for proteomics-based biomarker discovery...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109170/comparative-proteomic-analysis-of-urine-and-laser-microdissected-glomeruli-in-iga-nephropathy
#2
Xiaoyuan Ning, Zhong Yin, Zuoxiang Li, Jiayun Xu, Linna Wang, Wanjun Shen, Yang Lu, Guangyan Cai, Xueguang Zhang, Xiangmei Chen
The purpose of the present study was to identify the differential proteins that synchronously change in urine and glomeruli and could be used to monitor glomerular lesions of IgA nephropathy (IgAN). The proteomes of urine and glomeruli from 4 IgAN patients who were graded III/IV according to the grading system of Lee et al were compared to the urine proteomes of 4 healthy volunteers and the glomeruli proteomes of adjacent normal tissue from 4 patients with renal tumors, respectively. Western blot, enzyme-linked immunosorbent assay and immunofluorescence assay were applied to verify the results of the proteomic analysis...
January 21, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28108651/roflumilast-and-aquaporin-2-regulation-in-rat-renal-inner-medullary-collecting-duct
#3
Ezigbobiara N Umejiego, Yanhua Wang, Mark A Knepper, Chung-Lin Chou
Roflumilast is a cyclic nucleotide phosphodiesterase inhibitor that is FDA-approved for treatment of chronic obstructive pulmonary disease. With a view toward possible use for treatment of patients with X-linked nephrogenic diabetes insipidus (NDI) due to hemizygous mutations in the V2 vasopressin receptor, this study sought to determine the effect of roflumilast on aquaporin-2 (AQP2) phosphorylation, AQP2 trafficking, and water permeability in the rat inner medullary collecting duct (IMCD). In the presence of the vasopressin analog dDAVP (0...
January 2017: Physiological Reports
https://www.readbyqxmd.com/read/28100869/gonadotoropin-actions-on-spermatogenesis-and-hormonal-therapies-for-spermatogenic-disorders-review
#4
Koji Shiraishi, Hideyasu Matsuyama
Microdissection testicular sperm extraction and intracytoplasmic sperm injection have made it possible for men with non-obstructive azoospermia (NOA) to conceive a child. A majority of men cannot produce sperm because spermatogenesis per se is believed to be "irreversibly" disturbed. For these men, it and has been thought that any hormonal therapy will be ineffective. Further understandings of endocrinological regulation of spermatogenesis are needed and LH or FSH receptor knock out (KO) mice have revealed the roles of gonadotropin separately...
January 19, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28093272/a-method-for-obtaining-simian-immunodeficiency-virus-rna-sequences-from-laser-capture-microdissected-and-immune-captured-cd68-and-cd163-macrophages-from-frozen-tissue-sections-of-bone-marrow-and-brain
#5
Jaclyn Mallard, Emily Papazian, Caroline Soulas, David J Nolan, Marco Salemi, Kenneth C Williams
Laser capture microdissection (LCM) is used to extract cells or tissue regions for analysis of RNA, DNA or protein. Several methods of LCM are established for different applications, but a protocol for consistently obtaining lentiviral RNA from LCM captured immune cell populations is not described. Obtaining optimal viral RNA for analysis of viral genes from immune-captured cells using immunohistochemistry (IHC) and LCM is challenging. IHC protocols have long antibody incubation times that increase risk of RNA degradation...
January 13, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28088687/whole-genome-dna-methylation-profiling-identifies-epigenetic-signatures-of-uterine-carcinosarcoma
#6
Jing Li, Xiaoyun Xing, Daofeng Li, Bo Zhang, David G Mutch, Ian S Hagemann, Ting Wang
Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic basis of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with those of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma...
January 12, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28078450/genome-wide-methylation-profiles-in-primary-intracranial-germ-cell-tumors-indicate-a-primordial-germ-cell-origin-for-germinomas
#7
Shintaro Fukushima, Satoshi Yamashita, Hisato Kobayashi, Hirokazu Takami, Kohei Fukuoka, Taishi Nakamura, Kai Yamasaki, Yuko Matsushita, Hiromi Nakamura, Yasushi Totoki, Mamoru Kato, Tomonari Suzuki, Kazuhiko Mishima, Takaaki Yanagisawa, Akitake Mukasa, Nobuhito Saito, Masayuki Kanamori, Toshihiro Kumabe, Teiji Tominaga, Motoo Nagane, Toshihiko Iuchi, Koji Yoshimoto, Masahiro Mizoguchi, Kaoru Tamura, Keiichi Sakai, Kazuhiko Sugiyama, Mitsutoshi Nakada, Kiyotaka Yokogami, Hideo Takeshima, Yonehiro Kanemura, Masahide Matsuda, Akira Matsumura, Kazuhiko Kurozumi, Keisuke Ueki, Masahiro Nonaka, Akio Asai, Nobutaka Kawahara, Yuichi Hirose, Tatusya Takayama, Yoichi Nakazato, Yoshitaka Narita, Tatsuhiro Shibata, Masao Matsutani, Toshikazu Ushijima, Ryo Nishikawa, Koichi Ichimura
Intracranial germ cell tumors (iGCTs) are the second most common brain tumors among children under 14 in Japan. The World Health Organization classification recognizes several subtypes of iGCTs, which are conventionally subclassified into pure germinoma or non-germinomatous GCTs. Recent exhaustive genomic studies showed that mutations of the genes involved in the MAPK and/or PI3K pathways are common in iGCTs; however, the mechanisms of how different subtypes develop, often as a mixed-GCT, are unknown. To elucidate the pathogenesis of iGCTs, we investigated 61 GCTs of various subtypes by genome-wide DNA methylation profiling...
January 11, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28073359/whole-transcriptome-analysis-of-pre-invasive-and-invasive-early-squamous-lung-carcinoma-in-archival-laser-microdissected-samples
#8
Andre Koper, Leo A H Zeef, Leena Joseph, Keith Kerr, John Gosney, Mark A Lindsay, Richard Booton
BACKGROUND: Preinvasive squamous cell cancer (PSCC) are local transformations of bronchial epithelia that are frequently observed in current or former smokers. Their different grades and sizes suggest a continuum of dysplastic change with increasing severity, which may culminate in invasive squamous cell carcinoma (ISCC). As a consequence of the difficulty in isolating cancerous cells from biopsies, the molecular pathology that underlies their histological variability remains largely unknown...
January 10, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28072477/recurrent-nab2-stat6-gene-fusions-and-estrogen-receptor-alpha-expression-in-pulmonary-adenofibromas
#9
Nicola Fusco, Elena Guerini-Rocco, Claudia Augello, Andrea Terrasi, Giulia Ercoli, Caterina Fumagalli, Davide Vacirca, Paola Braidotti, Antonina Parafioriti, Marta Jaconi, Letterio Runza, Vijayalakshmi Ananthanarayanan, Fabio Pagni, Silvano Bosari, Massimo Barberis, Stefano Ferrero
AIMS: Pulmonary adenofibromas are rare benign fibroepithelial tumours of the lung with unknown histogenesis and an indolent clinical behaviour. Their stroma resembles that of solitary fibrous tumours, while the glands are composed of respiratory epithelium organized in a phyllodes-like architecture. Differentiation of pulmonary adenofibromas from other more aggressive intrathoracic tumours is clinically relevant. However, their biology is unknown. Here, we sought to characterize pulmonary adenofibromas at a clinicopathologic level and to define whether they could be underpinned by a highly recurrent somatic genetic alteration akin to tumours with similar morphology...
January 10, 2017: Histopathology
https://www.readbyqxmd.com/read/28067867/germline-brca2-mutations-drive-prostate-cancers-with-distinct-evolutionary-trajectories
#10
Renea A Taylor, Michael Fraser, Julie Livingstone, Shadrielle Melijah G Espiritu, Heather Thorne, Vincent Huang, Winnie Lo, Yu-Jia Shiah, Takafumi N Yamaguchi, Ania Sliwinski, Sheri Horsburgh, Alice Meng, Lawrence E Heisler, Nancy Yu, Fouad Yousif, Melissa Papargiris, Mitchell G Lawrence, Lee Timms, Declan G Murphy, Mark Frydenberg, Julia F Hopkins, Damien Bolton, David Clouston, John D McPherson, Theodorus van der Kwast, Paul C Boutros, Gail P Risbridger, Robert G Bristow
Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and increased risk of aggressive disease. To understand this aggression, here we profile the genomes and methylomes of localized PCa from 14 carriers of deleterious germline BRCA2 mutations (BRCA2-mutant PCa). We show that BRCA2-mutant PCa harbour increased genomic instability and a mutational profile that more closely resembles metastastic than localized disease. BRCA2-mutant PCa shows genomic and epigenomic dysregulation of the MED12L/MED12 axis, which is frequently dysregulated in metastatic castration-resistant prostate cancer (mCRPC)...
January 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28067829/the-cause-of-death-of-a-child-in-the-18th-century-solved-by-bone-microbiome-typing-using-laser-microdissection-and-next-generation-sequencing
#11
Valeria D'Argenio, Marielva Torino, Vincenza Precone, Giorgio Casaburi, Maria Valeria Esposito, Laura Iaffaldano, Umberto Malapelle, Giancarlo Troncone, Iolanda Coto, Paolina Cavalcanti, Gaetano De Rosa, Francesco Salvatore, Lucia Sacchetti
The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative "infection" at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most "informative" area to be examined...
January 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28063057/quantitative-assessment-of-cerebral-basement-membranes-using-electron-microscopy
#12
Matthew MacGregor Sharp, Anton Page, Alan Morris, Roy O Weller, Roxana O Carare
In this chapter we describe in detail the tissue processing techniques we employ for the study of cerebral tissue by transmission electron microscopy (TEM). In particular, we explain a technique that enables quantification of changes in cerebral basement membranes at the ultrastructural level. This is significant, as age related pathological conditions affecting the brain are often accompanied by ultrastructural changes in the cerebral vasculature.Briefly, experimental mice are fixed by perfusion and their brains removed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28062322/mir-23b-controls-tgf-%C3%AE-1-induced-airway-smooth-muscle-cell-proliferation-via-direct-targeting-of-smad3
#13
Ming Chen, Jianting Shi, Wei Zhang, Linjie Huang, Xiaoling Lin, Zhiqiang Lv, Wei Zhang, Ruiyun Liang, Shanping Jiang
BACKGROUND: MicroRNAs are small yet versatile gene tuners that regulate a variety of cellular processes, including cell growth and proliferation. Here we report that miR-23b inhibited airway smooth muscle cells (ASMCs) proliferation through directly targeting of Smad3. METHODS: We obtained ASMCs by laser capture microdissection of normal and asthmatic mice lung tissues. Mice ASMCs were cultured and induced by TGF-β1. The implication between TGF-β1 and miR-23b in ASMCs were detected by RT-PCR...
January 3, 2017: Pulmonary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28059096/colorectal-mixed-adenoneuroendocrine-carcinomas-and-neuroendocrine-carcinomas-are-genetically-closely-related-to-colorectal-adenocarcinomas
#14
Moritz Jesinghaus, Björn Konukiewitz, Gisela Keller, Matthias Kloor, Katja Steiger, Magdalena Reiche, Roland Penzel, Volker Endris, Ruza Arsenic, Gratiana Hermann, Albrecht Stenzinger, Wilko Weichert, Nicole Pfarr, Günter Klöppel
Colorectal mixed adenoneuroendocrine carcinomas are rare and clinically aggressive neoplasms with considerable morphological heterogeneity. Data on their genomic characteristics and molecular associations to either conventional colorectal adenocarcinomas or poorly differentiated neuroendocrine neoplasms is still scarce, hampering optimized patient treatment and care. Tissue from 19 colorectal mixed adenoneuroendocrine carcinomas and eight colorectal poorly differentiated neuroendocrine neoplasms (neuroendocrine carcinomas) was microdissected and subjected to next-generation sequencing using a colorectal adenocarcinoma-specific panel comprising 196 amplicons covering 32 genes linked to colorectal adenocarcinoma, and poorly differentiated neuroendocrine neoplasm tumorigenesis...
January 6, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28058811/proteomic-characterization-of-microdissected-breast-tissue-environment-provides-a-protein-level-overview-of-malignant-transformation
#15
René B H Braakman, Christoph Stingl, Madeleine M A Tilanus-Linthorst, Carolien H M Deurzen, Mieke A M Timmermans, Marcel Smid, John A Foekens, Theo M Luider, John W M Martens, Arzu Umar
Both healthy and cancerous breast tissue is heterogeneous, which is a bottle-neck for proteomics-based biomarker analysis, as it obscures the cellular origin of a measured protein. We therefore aimed at obtaining a protein-level interpretation of malignant transformation through global proteome analysis of a variety of laser capture microdissected cells originating from benign and malignant breast tissues. We compared proteomic differences between these tissues, both from cells of epithelial origin and the stromal environment, and performed string analysis...
January 5, 2017: Proteomics
https://www.readbyqxmd.com/read/28057717/pathology-driven-comprehensive-proteomic-profiling-of-the-prostate-cancer-tumour-microenvironment
#16
Lisa Staunton, Claire Tonry, Rosina Lis, Virginia Espina, Lance Liotta, Rosanna Inziatari, Michaela Bowden, Aurelie Fabre, John O'Leary, Stephen P Finn, Massimo Loda, Stephen R Pennington
: Prostate cancer (PCa) is the second most common cancer in men worldwide. Gleason grading is an important predictor of PCa outcomes and is influential in determining patient treatment options. Clinical decisions based on a Gleason score of 7 are difficult as the prognosis for individuals diagnosed with Gleason 4+3 cancer is much worse than for those diagnosed with Gleason 3+4 cancer. Laser capture microdissection (LCM) is a highly precise method to isolate specific cell populations or discrete microregions from tissues...
January 5, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28056117/alopecia-following-bicoronal-incisions
#17
Sameep Kadakia, Arvind Badhey, Sara Ashai, Thomas S Lee, Yadranko Ducic
Importance: Multiple techniques may be used to perform bicoronal incisions, and alopecia is a known postoperative complication of this procedure. To date, no large studies exist comparing alopecia outcomes among bicoronal incision techniques with and without the use of Raney clips. Objective: To determine (1) whether postoperative alopecia is more common when bicoronal incisions are performed with monopolar cautery, Colorado microdissection tip cautery, or traditional cold steel and (2) whether this outcome is affected by the use of Raney clips...
January 5, 2017: JAMA Facial Plastic Surgery
https://www.readbyqxmd.com/read/28035987/tumor-line-1-methylation-level-in-association-with-survival-of-patients-with-stage-ii-colon-cancer
#18
Marloes Swets, Anniek Zaalberg, Arnoud Boot, Tom van Wezel, Martine A Frouws, Esther Bastiaannet, Hans Gelderblom, Cornelis J H van de Velde, Peter J K Kuppen
Genome-wide DNA hypomethylation is associated with a worse prognosis in early-stage colorectal cancer. To measure genome-wide DNA methylation levels, long interspersed nucleotide element (LINE-1) repeats are used as a surrogate marker. Cohort studies on the clinical impact of genome-wide DNA methylation level in patients with only early-stage colon cancer, are currently lacking. This study aimed to investigate the prognostic value of LINE-1 methylation in a stage II colon cancer cohort (n = 164). Manual needle microdissection of tumor areas was performed on formalin-fixed paraffin-embedded tumor tissue sections followed by DNA extraction...
December 27, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28028135/unique-transcriptional-programs-identify-subtypes-of-aki
#19
Katherine Xu, Paul Rosenstiel, Neal Paragas, Christian Hinze, Xiaobo Gao, Tian Huai Shen, Max Werth, Catherine Forster, Rong Deng, Efrat Bruck, Roger W Boles, Alexandra Tornato, Tejashree Gopal, Madison Jones, Justin Konig, Jacob Stauber, Vivette D'Agati, Hediye Erdjument-Bromage, Subodh Saggi, Gebhard Wagener, Kai M Schmidt-Ott, Nicholas Tatonetti, Paul Tempst, Juan A Oliver, Paolo Guarnieri, Jonathan Barasch
Two metrics, a rise in serum creatinine concentration and a decrease in urine output, are considered tantamount to the injury of the kidney tubule and the epithelial cells thereof (AKI). Yet neither criterion emphasizes the etiology or the pathogenetic heterogeneity of acute decreases in kidney excretory function. In fact, whether decreased excretory function due to contraction of the extracellular fluid volume (vAKI) or due to intrinsic kidney injury (iAKI) actually share pathogenesis and should be aggregated in the same diagnostic group remains an open question...
December 27, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28027905/notochord-isolation-using-laser-capture-microdissection
#20
R G C Santegoeds, Y Yakkioui, A Jahanshahi, G Raven, J J Van Overbeeke, A Herrler, Y Temel
BACKGROUND: Chordoma are malignant tumors of the axial skeleton, which arise from remnants of the notochord. The Notochord (chorda dorsalis) is an essential embryonic structure involved in the development of the nervous system and axial skeleton. Therefore, the notochord seems to be the most biologically relevant control tissue to study chordoma in molecular biology research. Nevertheless, up to now mainly different tissues but not the notochord have been used as control for chordoma, due to difficulty of isolating notochordal tissue...
December 24, 2016: Journal of Chemical Neuroanatomy
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