Tissue drying oven

Haematoxylin and eosin (H&E)-stained slides from formalin-fixed, paraffin-embedded tissue blocks were used to identify specific areas of normal squamous epithelium, SIM, LGD, HGD and EAC. The areas of interest were marked by a Pathologist (B.D.) and 0.6 mm cores were taken from the blocks and TMAs were constructed. Several representative cores (mean 2, range 1 to 6) were taken from diagnostic biopsies to construct the TMAs. 4 µm sections were placed onto Superfrost Plus poly-L-lysine coated glass slides (Thermo Fisher Scientific, Waltham, MA, USA), and baked overnight at 37 °C in a tissue-drying oven (Binder, Tuttlingen, Germany). Slides were then stored at 4 °C until stained.
Diagnoses of SIM, LGD, HGD and EAC were all previously made by a specialist upper gastrointestinal consultant pathologist. All selected samples were subsequently marked and reviewed on two separate occasions (pre- and post-TMA construction) by the Gastrointestinal Pathologist (BD), in order to ensure the accuracy of the histology samples selected. In addition, as sections were taken deeper into these blocks and the H&E slides were further examined by the pathologist. In some incidences, the pathology of interest cut-out on deeper levels, and following re-examination of H&E and immunohistochemically stained slides, these cores required removal from statistical analysis, thus affecting sample size.

Three sets of TMA were constructed for this study from paraffin-embedded tissue blocks, with pathological expertise from consultant pathologists (Dr. Brendan Doyle, Professor Elaine Kay). TMA set 1 consists of tissue cores taken from a cohort of patients with normal squamous epithelium (n = 15), esophagitis (n = 32), BE intestinal metaplasia (n = 36), LGD (n = 16), HGD (n = 9), and EAC (n = 7). TMA set 2 included tissue cores from EAC patients where tumor, BE lesions and matched normal mucosa were present in resected tissue (n = 29) in patients undergoing esophagectomy at Beaumont Hospital, Dublin. TMA set 3 included tissues from 70 EAC patients undergoing surgical resection at St James’s Hospital, using tissue from both tumor core (n = 70) and leading edge tissue (n = 41). Areas of interest were marked by a pathologist and 0.6 or 1 mm cores were taken from the blocks and TMA were constructed. Several representative cores (mean n = 2, range 1–6) were taken from diagnostic biopsies to construct the TMA. 4 μm sections were placed onto Superfrost Plus poly-L-lysine coated glass slides (Thermo Fisher Scientific, IL, USA), and baked overnight at 37 °C in a tissue drying oven (Binder, Tuttlingen, Germany).