Ethical approval and prostate tissue samples
Ethical approval (REC Ref 13/ES/0092) was granted by the joint research office University College London and University College Hospital through East of Scotland Research Ethics Service. Archival prostate tissue samples used primarily for pathological analysis, from Portuguese Oncology Institute of Porto (Porto, Portugal), were used to make tissue arrays utilized in this study. Samples were collected from patients with a median age of 64 (interquartile range of 61,68). Most recent PSA levels (ng/mL) at prostatectomy were also recorded as 9.30 (with an interquartile range 5.61,11.80). A total of 29 individual prostate tissue samples classified by an expert uropathologist as cancerous and further sub-classified for Gleason scores were used; 29 cancer adjacent, non-cancerous, tissue samples were also extracted. The experiment was conducted as a double blind study with neither the experimenter (who performed antibody staining) nor the data analysts being aware of identity of the condition of the tissue samples or that of the antibody used. The data was only decoded after the anonymized, quantitative analysis was completed (Symes et al., 2013).
TA construction
TA were constructed in our laboratory using a manual tissue arrayer (MTA1, Beechers Instruments, Sun Prairie, WI, USA) as described in detail elsewhere (Nariculam et al., 2009; Symes et al., 2013). Individual tissue cores (1mm in diameter), were extracted from the marked regions of prostate cancer and cancer adjacent (normal) prostate tissue blocks and moved to a recipient block using a Beechers MTA1 manual tissue arrayer (Beechers Instruments, Sun Prairie, WI, USA). Five recipient blocks were populated with samples (five to six tissue samples) from both prostate cancer (N=29, n=91) cancer adjacent region (N=29; n=67) of the whole tissue blocks (N= the number of patients, n= number of cores). The following distribution of Gleason grades were used: 3+3 (n=15); 3+4/4+3 (n=11); 4+4 (n=43); and 4+5/5+4 (n=22).
TA blocks were sectioned at 6-8μm thickness on glass slides using a Thermo ScientificTM HM355S automatic microtome. Sections on slides were stained with Hematoxylin and Eosin (H&E) and imaged at 40x magnification using NanoZoomer Digital Pathology Scanner 2.0 RS (Hamamatsu, Hertfordshire, UK) and re-examined by the pathologist.
Immunohistochemistry
Multiplex staining of TAs, using anti-clathrin (Abcam, Cat. No. ab21679), anti-caveolin-1 (Abcam, Cat. No. ab2910) and EGFR (Leica, NCL-EGFR) antibodies on the same TA section, was conducted using Bond Max automated staining system (Leica, UK) (Arthurs et al., 2020; Symes et al., 2013). Each antibody was optimized for pH and concentration dependence, antigen retrieval and temperature parameters; nuclei were counterstained with 4’,6-diamidino-2-phenylindole (DAPI). Antibodies were used at a dilution of 1:2000, 1:4000 and 1:500 for anti-clathrin, anti-caveolin-1 and EGFR, on TAs and labelled with Opal-650 (red), Opal-520 (green) and Opal-570 (yellow), respectively.
Imaging of immunofluorescently labelled TAs
Tissue cores from multi-labelled immunofluorescence TAs were imaged using AxioScan Z1 scanner (Zeiss, Cambridge, UK) at 20x magnification for protein expression analysis, as described previously (Arya et al., 2015). The excitation/emission setting of different channels were 353/465nm (DAPI); 493/517nm (caveolin-1); 653/668nm (clathrin) and 550/570nm (EGFR). Fluorescent signals were optimized to avoid saturation and for comparative analysis. The power settings and integration times of Hamamatsu ORCA Flash4 camera (Hamamatsu Photonics, Japan) on AxioScan were kept constant for all tissue cores imaged. For standardization, all imaging was conducted on the same day with all other image settings kept the same. Images of individual tissue cores (scenes in AxioScan Z1) were extracted from multiple 5712x5712 pixel, 300dpi, 24-bit single color images and stored as tiff files.
For the measurement of colocalization coefficients (Global Intersection Coefficient, GIC) between different fluorescent labels, high magnification confocal imaging on a Leica SP8 microscope (Leica, UK) with a 63x 1.4-NA oil objective and 6x optical zoom at a 1024x1024 pixel format, was also conducted on sub-sets of different prostate tissue samples. The Z-stack scan was performed at 0.17μm (at 600Hz), yielding approximately 26-30 Z-sections for each tissue core.
Quantitation of clathrin and caveolin-1 signal in prostate tissue
The expression levels for clathrin and caveolin-1 were quantified using an unbiased, quantitative analysis developed in our laboratory (Arya et al., 2015; Symes et al., 2013) using an adapted ImageJ plugin (Rasband, 2011). Briefly, the images were separated into red (Opal 650, clathrin), green (Opal 520, caveolin-1) and yellow (Opal-570, EGFR) channels and were exported from ZEN 3.1 (blue edition) software, opened in ImageJ software and were converted to 8-bit greyscale; a threshold and segmentation routine was then applied. Lower and upper threshold parameters were set to include the median to maximum grey values of a range of samples across the sample cohort. The grey values were then used to perform semi-automated analysis of the whole tissue array. A similar approach was implemented to quantify the amount of tissue in each core and this value was divided by the intensity to obtain a standardized signal for each label in prostate tissue samples.
Statistical analysis was performed using MedCalc software (version 19.7.2, www.medcalc.org) using Mann-Whitney U test and boxplots were made using both GraphPad Prism 9 software (GraphPad Software, CA, USA) and Origin pro software (OriginLab, MA, USA).
Deconvolution and colocalization analysis using high magnification confocal images
158 individual tissue cores (67 normal, 91 malignant cores including 15 Gleason score 3+3, 11 Gleason score 3+4, 43 Gleason score 4+4 and 22 Gleason score 4+5 with at least 4 ROIs for each core) were identified for areas of cancer visually on the serial H&E section of the tissue array. These areas were approximated on the fluorescently labelled tissue array and tissue cores were imaged using a Leica SP8 confocal system as described above.
The resulting image files were deconvolved using Huygens Professional software (version 20.04, Netherlands). Deconvolved images were saved as Huygens specific (HDF5) files for each channel (excitation/emission (nm) DAPI 405 / 429, Opal-520 = 488/517, Opal-570 = 561 / 595 and Opal-650 = 635 / 668). The HDF5 files were imported into Huygens co-localization module and were background subtracted using ‘Gaussian minimum’ method; up to 4-16 regions of interest/image were analyzed to calculate the global intersection coefficient for co-localization (Arthurs et al., 2020). Colocalization analysis was conducted using Huygens professional software to calculate GICs.