Journal: STAR Protocols

Article Title: Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing

doi: 10.1016/j.xpro.2025.104296

Figure Lengend Snippet: 3D light sheet and 2D multi-cyclic imaging data comparison (Human OvCa) (A) Imaris 3D surface rendering of autofluorescence (cyan) and CD326 positive cells (red). (B) Imaris 3D surface rendering of autofluorescence (cyan) with target plane in yellow. (C) Light sheet guided target plane selection representing CD326 positive cell (purple), CD45 positive cells (red), and CD3 positive cells (green). (D) DAPI overview image of selected tissue slice for 2D MACSima™ imaging. (E) Magnified merged six color multiparameter MICS image with CD45 (green), CD326 (cyan), FOLR1 (purple), Collagen III (red), Collagen IV (red), and CD31 (yellow). (F–L) Single staining MICS images (white) of DAPI (F), CD45 (G), CD326 (H), FOLR1 (I), Collagen III (J), Collagen IV (K), and CD31 (L) (gray) (see “Antibodies”). Scale bars: (A–F) 1 mm; (E) 250 μm; (F–L) 500 μm.

Article Snippet: Collagen III antibody, anti-human, PE, REAdye_lease , Miltenyi Biotec B.V. & Co. KG , Cat# 130-127-357 RRID: AB_2905171.

Techniques: Imaging, Comparison, Selection, Staining

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Violin plots graphs showing proteins of the epithelial-mesenchymal transition process, matricellular, and the Wnt signaling pathway expression analyzed by QuPath (N=120). The protein expression was demonstrated between three different histologic types in non-small cells lung cancer for (A) E-cadherin, (B) β-catenin, (C) Heparan sulfate, (D) Chondroitin sulfate, (E) Col I, (F) Col III, (G) Col IV, (H) Col V, (I) WNT1, (J) WNT3A, (K) WNT5A, (L) WNT5B, and (M) SPARC. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC, lung squamous cell carcinoma; Col, collagen type.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Co-analysis of immunofluorescence of chondroitin sulfate (green; C , G , K ) and collagen type I (red; B , F , J ) in three different histological subtypes of non-small cell lung carcinoma (N=120). The stained nuclei are represented in blue (DAPI; A , E , I ). Images D , H , L represent the merge of the same field of these three stains. White arrows indicate positive expression of the markers. Original magnification: 40x. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC: lung squamous cell carcinoma.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Immunofluorescence, Staining, Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Co-analysis of immunofluorescence of chondroitin sulfate (green; C , G , K ) and collagen type V (red; B , F , J ) in three different histological subtypes of non-small cell lung carcinoma (N=120). The stained nuclei are represented in blue (DAPI; A , E , I ). Images D , H , L represent the merge of the same field of these three stains. White arrows indicate positive expression of the markers. Original magnification: 40x. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC: lung squamous cell carcinoma.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Immunofluorescence, Staining, Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Co-analysis of immunofluorescence of chondroitin sulfate (green; C , G , K ) and collagen type III (red; B , F , J ) in three different histological subtypes of non-small cell lung carcinoma (N=120). The stained nuclei are represented in blue (DAPI; A , E , I ). Images D , H , L represent the merge of the same field of these three stains. White arrows indicate positive expression of the markers. Original magnification: 40x. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC: lung squamous cell carcinoma.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Immunofluorescence, Staining, Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Co-analysis of immunofluorescence of heparan sulfate (green; C , G , K ) and collagen type IV (red; B , F , J ) in three different histological subtypes of non-small cell lung carcinoma (N=120). The stained nuclei are represented in blue (DAPI; A , E , I ). Images D , H , L represent the merge of the same field of these three stains. White arrows indicate positive expression of the markers. Original magnification: 40x. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC: lung squamous cell carcinoma.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Immunofluorescence, Staining, Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Association between clinicopathologic characteristics and mean expression (% positive expression) of GAGs and collagen types ( t test and ANOVA, P <0.05).

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Variables associated with overall survival in 120 non-small cell lung cancer patients.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing

Journal: The Journal of pathology

Article Title: A 3D tri-culture system reveals that activin receptor-like kinase 5 and connective tissue growth factor drive human glomerulosclerosis

doi: 10.1002/path.4960

Figure Lengend Snippet: (A) MC 3D monoculture without the addition of TGFβ, and (B) in the presence of TGFβ, shown by H&E staining of paraffin-embedded sections. Human collagen type I/III (immunostained with an antibody that recognises both collagen type I and III) (C) and human collagen type IV (D) can be demonstrated in nodules by immunoperoxidase staining. (E) High-power view of MC nodule by scanning electron microscopy in cross section. (F) MC nodule count and collagen type I alpha1 (COL1a1), and collagen type IV alpha1 (COL4a1) RNA quantification (n=3). (G) Effect of ALK5 inhibition (Alk5i) on MC nodule formation (n=3). (H) Effect of SMAD2 or SMAD3 siRNA knockdown in MCs on nodule formation (n=3) with immunoblots demonstrating degree of knockdown. [DharmaFECT (DH), non-targeting siRNA control (siCP), siSMAD2 (siS2), siSMAD3 (siS3), total SMAD2 (tSMAD2), total SMAD3 (tSMAD3)]. Error bars represent 1 s.d. NS, not significant; ***, p<0.001; **, p<0.01: 2-tailed Student’s t test.

Article Snippet: After culture, matrices were embedded in HistoGel, fixed in 4% paraformaldehyde and paraffin wax-embedded for sectioning and staining for human collagen type IV (mouse anti-human collagen IV monoclonal antibody 2150–0121, Bio-Rad, CA, USA) and human collagen type I/III (rabbit anti-human collagen I/III polyclonal antibody 2150–2210, Bio-Rad, CA, USA).

Techniques: Staining, Immunoperoxidase Staining, Electron Microscopy, Inhibition, Western Blot

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Violin plots graphs showing proteins of the epithelial-mesenchymal transition process, matricellular, and the Wnt signaling pathway expression analyzed by QuPath (N=120). The protein expression was demonstrated between three different histologic types in non-small cells lung cancer for (A) E-cadherin, (B) β-catenin, (C) Heparan sulfate, (D) Chondroitin sulfate, (E) Col I, (F) Col III, (G) Col IV, (H) Col V, (I) WNT1, (J) WNT3A, (K) WNT5A, (L) WNT5B, and (M) SPARC. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC, lung squamous cell carcinoma; Col, collagen type.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Co-analysis of immunofluorescence of chondroitin sulfate (green; C , G , K ) and collagen type V (red; B , F , J ) in three different histological subtypes of non-small cell lung carcinoma (N=120). The stained nuclei are represented in blue (DAPI; A , E , I ). Images D , H , L represent the merge of the same field of these three stains. White arrows indicate positive expression of the markers. Original magnification: 40x. LCC, large cell carcinoma; ADC, lung adenocarcinoma; SqCC: lung squamous cell carcinoma.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Immunofluorescence, Staining, Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Association between clinicopathologic characteristics and mean expression (% positive expression) of GAGs and collagen types ( t test and ANOVA, P <0.05).

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: Modeling extracellular matrix through histo-molecular gradient in NSCLC for clinical decisions

doi: 10.3389/fonc.2022.1042766

Figure Lengend Snippet: Variables associated with overall survival in 120 non-small cell lung cancer patients.

Article Snippet: The specimens were incubated overnight at 4°C with antibodies against: E-cadherin (1:100; Boster Biological), β-catenin (1:100; Santa Cruz), heparan sulfate (1:500; Santa Cruz), chondroitin sulfate (1:100, Santa Cruz), anti-human collagen type I (1:700; Rockland Inc.), anti-human collagen type III (1:200; Rockland Inc.), anti-human collagen type IV (1:100; Dako), and anti-human collagen type V (1:1000; Rockland Inc.).

Techniques: Expressing