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Vimentin

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Vimentin is a cytoskeletal protein that is widely expressed in various cell types. It is a type III intermediate filament protein that plays a crucial role in maintaining the structural integrity of cells and facilitating cellular processes such as migration, signaling, and organelle positioning.

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Lab products found in correlation

E cadherin, by Roche (6 mentions) Benchmark xt, by Roche (3 mentions) Benchmark ultra, by Roche (2 mentions) Pan keratin, by Roche (2 mentions) Synaptophysin, by Roche (2 mentions) Cytoseal xyl, by Thermo Fisher Scientific (1 mentions) Cytokeratin 7, by Agilent Technologies (1 mentions) Cxcl16, by Abcam (1 mentions) Pt link module, by Agilent Technologies (1 mentions) Cd163, by Roche (1 mentions) Autostainer plus, by Agilent Technologies (1 mentions) Fibronectin, by Agilent Technologies (1 mentions) Optiview hq universal linker, by Roche (1 mentions) Cyt387, by Gilead Sciences (1 mentions) P stat3, by Cell Signaling Technology (1 mentions) Gapdh, by Cell Signaling Technology (1 mentions) Cytokeratin ae1 ae3, by Roche (1 mentions) Hematoxylin and eosin, by Bio-Optica (1 mentions) Cox 2, by Abcam (1 mentions) α sma, by Abcam (1 mentions)

21 protocols using vimentin

1

Immunohistochemical Profiling of Lung Tumors

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Immunohistochemical stainings were carried out on paraffin-embedded tissue fixed by formalin. The following antibodies were involved in our work: cytokeratin (CK) 7 (clone: OV-TL12/30), thyroid transcription factor-1 (TTF-1) (clone: SPT24), p40 (clone: BC28), CK5/6 (clone: D5/16B4), p63 (clone: 4A4), ALK (clone: D5F3), Synaptophysin (clone: SP11), chromogranin A (clone: MX018), CD56 (clone: MX039), vimentin (clone: V9), vimentin (clone: EP21), E-cadherin (clone:4A2C7), β-catenin (clone: 17C2), Cdx-2 (clone: EPR2764Y), napsin-A (clone: 1P64), and Ki-67 (clone: MIB1). ALK (D5F3) and vimentin were performed on an automated platform (Benchmark® XT, Ventana). The other stainings were performed on the platform of BOND-MAXTM. Immunohistochemical staining was individually evaluated by two independent pathologists. Both MLCs and the adjacent tumor area of the adenocarcinoma were assessed in the wholes slide.
Wang L.L., Ding L., Zhao P., Guan J.J., Ji X.B., Zhou X.L., Shao S.H., Zou Y.W., Fu W.W, & Lin D.L. (2021). Clinicopathological, Radiological, and Molecular Features of Primary Lung Adenocarcinoma with Morule-Like Components. Disease Markers, 2021, 9186056.
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2

Quantifying Protein Expression in Tissue Microarrays

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Tissue microarray blocks of 1 mm were cut from FFPE blocks and sliced into 3 µm slides, automatically stained, and evaluated as previously described [13 (link)]. In short, the slides were deparaffinized and incubated with primary antibodies E-cadherin, Vimentin (monoclonal, ready-to-use; Ventana Medical Systems, Tucson, AZ, USA), ZEB1, and ZEB2 (polyclonal, 1:400; Sigma-Aldrich). Counterstaining was performed with Hematoxylin II and Blueing Reagent. Next, samples were covered with a series of alcohol (70–99%), Xylol and Cytoseal XYL (Thermo Fisher Scientific) as a cover medium. Quantification of immunohistochemical staining was performed using ImageJ 1.52 (ImageJ Software, National Institutes of Health, Madison, WI, USA). Images of tissue microarrays were taken at 20× magnification with a predefined number of 1,228,800 square pixels. The Color-Threshold function was subsequently used to mark all areas previously stained by immunohistochemistry. The degree of protein expression in tissue microarrays was stated as the mean percentage of square pixels marked by ImageJ for respective images of every protein.
Flammang I., Reese M., Yang Z., Eble J.A, & Dhayat S.A. (2020). Tumor-Suppressive miR-192-5p Has Prognostic Value in Pancreatic Ductal Adenocarcinoma. Cancers, 12(6), 1693.
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3

Immunohistochemical Profiling of Formalin-Fixed Paraffin-Embedded Tissue Sections

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Tumor tissue or cultured cells were fixed in formalin and paraffin embedded according to routine protocol. Deparaffinization and rehydration of tissue sections of 4 μm thickness was performed according to standard procedures. Sections were subjected to epitope retrieval in a PT Link module (Dako, Santa Clara, CA, USA) and immunohistochemical stainings were performed using an Autostainer Plus (Dako) according to the manufacturer’s standard protocol. Antibodies used were: cytokeratin 7 (Dako, M7018, 1:100) cytokeratin 19 (Ventana, Basel, Switzerland, 760-4281, prediluted), vimentin (Ventana, 790-2917, prediluted), CD10 (Ventana, 790-4506, prediluted) CD31 (Ventana, 760-4378, prediluted), CD68 (Dako, M0814, 1:1000), CD163 (Ventana, 760-4437, prediluted), and CXCL16 (Abcam, Cambridge, UK, ab101404, 1:100). Sections were stained with hematoxylin and eosin or counterstained with hematoxylin.
Krawczyk K.M., Nilsson H., Allaoui R., Lindgren D., Arvidsson M., Leandersson K, & Johansson M.E. (2017). Papillary renal cell carcinoma-derived chemerin, IL-8, and CXCL16 promote monocyte recruitment and differentiation into foam-cell macrophages. Laboratory Investigation; a Journal of Technical Methods and Pathology, 97(11), 1296-1305.
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4

Immunohistochemical Staining of FFPE Tissues

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Immunohistochemical staining of 3 µm thick macrodissected and tissue-arrayed formalin-fixed paraffin embedded (FFPE) tissue sections was performed automatically using the Benchmark Ultra (Ventana Medical Systems, Inc., Oro Valley, AZ, USA). This staining machine contains peroxidase, inhibitors, buffer solutions, dye and the secondary antibody (OptiView HQ Universal Linker, Ventana Medical Systems). E-cadherin, vimentin (each monoclonal, ready-to-use, Ventana Medical Systems), fibronectin (polyclonal, 1:1000, Agilent Technologies, Santa Clara, CA, USA) and ZEB-1 (polyclonal, 1:400, Sigma-Aldrich, St. Louis, MO, USA) were used as primary antibodies. Negative controls without primary antibodies and positive controls (pancreas, tonsil, colon and kidney) were included in all experiments using the same experimental conditions. The slides were counterstained with Haematoxylin and dehydrated in graded alcohols. Immunohistochemical staining was evaluated separately in stromal and epithelial tissue by two pathologists in a blinded manner using light microscopy (BX51, Olympus) [89 (link)].
Dhayat S.A., Traeger M.M., Rehkaemper J., Stroese A.J., Steinestel K., Wardelmann E., Kabar I, & Senninger N. (2018). Clinical Impact of Epithelial-to-Mesenchymal Transition Regulating MicroRNAs in Pancreatic Ductal Adenocarcinoma. Cancers, 10(9), 328.
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5

Immunohistochemical Analysis of JAK-STAT Pathway

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Polyclonal antibody against phosphorylated (Tyr-705) STAT3 (P-STAT3), total STAT3 (T-STAT3), phosphorylated (Tyr-1007/1008) JAK2 (P-JAK2), total JAK2 (T-JAK2) and GAPDH were obtained from Cell Signalling Technology (Beverly, MA, USA). Antibodies against cytokeratin 7 (cyt7), Ki67, CA125, E-cadherin, vimentin, Oct4 and CD117 (c-Kit) used for immunohistochemistry were obtained from Ventana (Roche, Arizona, USA). CYT387 was obtained from Gilead Sciences (CA, USA).
Abubaker K., Luwor R.B., Zhu H., McNally O., Quinn M.A., Burns C.J., Thompson E.W., Findlay J.K, & Ahmed N. (2014). Inhibition of the JAK2/STAT3 pathway in ovarian cancer results in the loss of cancer stem cell-like characteristics and a reduced tumor burden. BMC Cancer, 14, 317.
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6

Cytological Analyses of SCI13D

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Cytological analyses of SCI13D were performed with standard hematoxylin and eosin staining or with immunocytochemical probing for vimentin, smooth muscle actin, and cytokeratin AE1–AE3 (Ventana Medical Systems, Inc., Oro Valley, AZ, USA).
Giannoni P., Grosso M., Fugazza G., Nizzari M., Capra M.C., Bianchi R., Fiocca R., Salvi S., Montecucco F., Bertolotto M., Fais F., Salio M., Barisione E, & de Totero D. (2021). Establishment and Characterization of a Novel Fibroblastic Cell Line (SCI13D) Derived from the Broncho-Alveolar Lavage of a Patient with Fibrotic Hypersensitivity Pneumonitis. Biomedicines, 9(9), 1193.
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7

Histological Analysis of BCAF Spheroids

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The BCAF spheroids collected at 72 and 216 h were fixed in 10% neutral buffered formalin. Then, each spheroid was embedded in paraffin (Bio-Optica Milano SpA, Milan, Italy), sliced into serial 4 μm-thick sections and placed on poly-l-lysine-coated glass slides (Menzel-Glaser, Brunswick, Germany). The slides were deparaffinized twice in xylene, rehydrated and immersed in 10 mM of citric acid (Sigma-Aldrich), pH 6, in a microwave oven (VWR) for three cycles of 5 min at 650 Watt to exclude epitope masking owing to fixation. The spheroids deparaffinized sections were hematoxylin and eosin stained (Bio-Optica) according to the manufacturer’s protocol. These sections, on glass slides, were converted into high-resolution digital data through NanoZoomer-2.0RS digital scanner (Hamamatsu, Tokyo, Japan, Asia). Other sections were immunostained with primary antibodies against vimentin (Ventana Medical Systems, Tucson, AZ, USA), COX-2 and α-SMA (Abcam, Cambridge, UK), detected by the ULTRA View UNIVERSAL DAB DETECTION KIT (Ventana Medical Systems), according to the manufacturer’s protocol.
Romano V., Ruocco M.R., Carotenuto P., Barbato A., Venuta A., Acampora V., De Lella S., Vigliar E., Iaccarino A., Troncone G., Calì G., Insabato L., Russo D., Franco B., Masone S., Velotti N., Accurso A., Pellegrino T., Fiume G., Belviso I., Montagnani S., Avagliano A, & Arcucci A. (2022). Generation and Characterization of a Tumor Stromal Microenvironment and Analysis of Its Interplay with Breast Cancer Cells: An In Vitro Model to Study Breast Cancer-Associated Fibroblast Inactivation. International Journal of Molecular Sciences, 23(12), 6875.
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8

Immunohistochemistry for TP53, Vimentin, and Pan-Keratin

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IHC was performed using the Ventana Benchmark XT automated system (Ventana Medical System). Antibodies against the following antigens were used: TP53 (Clone DO-7, N1581, Dako; ready to use), vimentin (Ventana 790-2917; dilution 1:100), and pan-keratin (Ventana 760-2595; dilution 1:100). Aggresome-positivity was considered only for cells exhibiting juxtanuclear staining of vimentin.
Amer N., Taha H., Hesham D., Al-Shehaby N., Mosaab A., Soudy M., Osama A., Mahmoud N., Elayadi M., Youssef A., Elbeltagy M., Zaghloul M.S., Magdeldin S., Sayed A.A, & El-Naggar S. (2021). Aggresomes predict poor outcomes and implicate proteostasis in the pathogenesis of pediatric choroid plexus tumors. Journal of Neuro-Oncology, 152(1), 67-78.
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9

Comprehensive Immunohistochemical Profiling of Tumors

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IHC labeling was performed on the Benchmark XT autostainer (Ventana Medical Systems Inc., Tucson, AZ) using the I-View detection kit. The standard antibodies used, vendors, pretreatments, and dilutions were as follows: cathepsin K (Abcam; steam, 1:800), HMB45 (Novacastra; catalog#ncl-hmb45, steam, 1:100), Melan A (Cell Marque; catalog 281 M-8, clone A103, steam, 1:500), Cam5.2 (Cell Marque; steam, prediluted), AE1/3 (Chemicon; steam, 1:4000), MITF (Dako; steam, 1:50), PAX2 (Zymed; catalog#71 to 6000, steam, 1:100), RCC marker antigen (Leica; steam, 1:50), vimentin (Ventana, 790-2917; prediluted), CD10 (Leica; org-8941, steam, prediluted), racemase (Zeta; P504S, steam, 1:100), SOX10 (Santa; SC-17,342, steam, 1:100), EMA (Ventana; 760-4259, stream, prediluted), inhibin (Serotec; steam, 1:25), PAX8 (ProteinTech Group, Chicago, IL; steam, 1:100), CA IX (Novacastra NCL-L-CA IX; steam, 1:100), EpCAM (Santa Cruz; sc-25,308, steam, 1:200), Ksp-cadherin (Invitrogen, San Francisco, CA; steam, 1:100), CD117 (Cell Marque CMA768; steam, prediluted), and ER (Novacastra; 6F11, 1 μg/mL). For pS6, after a 50-minute steam pretreatment in EDTA buffer, we used the antibody from Cell Signaling (#2215) at 1:200 dilution overnight at 4°C, followed by the Dako Polyclonal Envision + secondary for 30 minutes.
Smith N.E., Illei P.B., Allaf M., Gonzalez N., Morris K., Hicks J., DeMarzo A., Reuter V.E., Amin M.B., Epstein J.I., Netto G.J, & Argani P. (2014). t(6;11) Renal Cell Carcinoma (RCC) Expanded Immunohistochemical Profile Emphasizing Novel RCC Markers and Report of 10 New Genetically Confirmed Cases. The American journal of surgical pathology, 38(5), 604-614.
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10

Immunohistochemical Analysis of EMT Markers

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All surgical samples were fixed in formalin and made into paraffin blocks using standard paraffin embedding procedure. Four µm thick sections were cut from paraffin blocks, mounted on positively-charged slides. The primary antibodies used for immunohistochemical detection were E-cadherin (Ventana, Dako, clone NCH-38, predilute 1:50), N-cadherin (Ventana, Leica, clone IAR06, predilute 1:100), vimentin (Ventana, Dako, clone V9, predilute 1:400) and Ki-67 (Ventana, ready to use). Antigen retrieval was performed in a water bath for 20 min at 97 °C at pH 6 (buffer S1700, Dako, Glostrup, Denmark). Endogenous peroxidase activity was inhibited by immersing the sections in 3% hydrogen peroxide. After incubation with the antibody, the sections were subjected to EnVisionTM FLEX (Dako, Glostrup, Denmark). Finally, slides were counterstained with haematoxylin, mounted and examined.
Skarkova V., Vitovcova B., Matouskova P., Manethova M., Kazimirova P., Skarka A., Brynychova V., Soucek P., Vosmikova H, & Rudolf E. (2022). Role of N-Cadherin in Epithelial-to-Mesenchymal Transition and Chemosensitivity of Colon Carcinoma Cells. Cancers, 14(20), 5146.
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