Abstract To date, characterization of the Barrett’s esophagus (BE) immune microenvironment in patients with known progression status to determine how the microenvironment may influence BE progression to esophageal adenocarcinoma (EAC) has been understudied, hindering both the biological understanding of progression and the development of novel diagnostics and therapies. Therefore, this study’s aim was to determine if highly multiplex interrogation of the immune microenvironment can be performed on endoscopic formalin-fixed, paraffin-embedded (FFPE) samples utilizing the Nanostring GeoMx digital spatial profiling (GeoMx DSP) platform. We performed spatial proteomic analysis of 49 proteins expressed in the microenvironment and epithelial cells of histologically identical FFPE endoscopic biopsies from patients with non-dysplastic BE (NDBE) who later progressed to high-grade dysplasia (HGD) or EAC (N=7) or from patients who after at least 5 years follow up did not (N=8). In addition, we performed RNA analysis of 1,812 cancer related transcripts on a series of three endoscopic mucosal resections containing regions of normal tissue, BE, dysplasia (DYS), and EAC. Our primary goal was to determine feasibility of this approach and begin to identify the types of specific immune cell populations that may mediate the progression of pre-neoplastic BE to EAC. Spatial proteomic and transcriptomic profiling with GeoMx DSP showed reasonable quality metrics and detected expected differences between epithelium and stroma. Several proteins were found to have increased expression within non-dysplastic BE biopsies from progressors compared to non-progressors, suggesting further studies on the BE microenvironment are warranted. Summary New biological insights into the stepwise development and progression of esophageal adenocarcinoma (EAC) from Barrett’s esophagus (BE) are imperative to develop tailored approaches for early detection and optimal clinical management of the disease. This study aimed to determine the feasibility to spatially profile stromal and immunologic properties that accompany malignant transformation of BE to EAC in formalin-fixed, paraffin-embedded (FFPE) tissues. NanoString’s Digital Spatial Profiling (DSP) technology can detect and quantify protein and RNA transcripts in a highly multiplexed manner with spatial resolution, within specific regions of interest on FFPE tissue. Here, we performed a pilot study using the Nanostring GeoMx DSP, for measurement of protein and ribonucleic acid (RNA) expression on a series of FFPE slides from endoscopic biopsies and endoscopic mucosal resections (EMR) of BE. We compare a small series of biopsies of non-dysplastic BE (NDBE) from patients who progressed to more advanced disease to patients with NBDE who did not progress and then perform RNA profiling on EMRs with a range of histologic diagnoses.
Low-grade dysplasia (LGD) is associated with an increased risk of progression in Barrett's esophagus (BE); however, the diagnosis of LGD is limited by substantial interobserver variability. Multiple studies have shown that an objective tissue systems pathology test (TissueCypher Barrett's Esophagus Test, TSP-9), can effectively predict neoplastic progression in patients with BE. This study aimed to compare the risk stratification performance of the TSP-9 test vs benchmarks of generalist and expert pathology.
Aims Current risk prediction for malignant progression in Barrett’s Esophagus (BE) is based on the histological diagnosis of dysplasia, which is limited by several factors. Genomic abnormalities precede dysplasia and may allow for objective and early risk stratification. We aimed to identify genomic factors to develop a clinically applicable targeted sequencing panel predicting progression in BE.
Eradication of early Barrett's neoplasia by endoscopic resection and radiofrequency ablation is safe and effective. In T1b adenocarcinoma, standard of care remains controversial. We investigated the therapeutic outcome between high-grade dysplasia (HGD)/mucosal adenocarcinoma and submucosal adenocarcinoma in Barrett's patients. We hypothesised similar outcome in low-risk (LR) T1b compared to T1a/HGD.Patients with endoscopically treated Barrett's esophagus were included in a Swiss tertiary center cohort study. Primary outcome parameter was complete eradication of early neoplasia. Secondary outcome parameters were recurrence-free survival and safety of endoscopic treatment.Forty-eight patients (1 female) with median Barrett's length C4M6 and mean age of 66 years were included. Complete endoscopic eradication of HGD/T1a was achieved in 33 out of 35 and in 11 out of 13 T1b adenocarcinoma. During a median follow-up of 41 (interquartile range 28-63) months no systemic recurrence was observed in endoscopically treated HGD/T1a and LR -T1b and one in a high-risk T1b adenocarcinoma after surgery. Local recurrences were amenable to surgical or endoscopic re-treatment. No lymphnode metastasis was detected in initial staging with esophageal endosonography/positron emission tomography-CT.Comparable endoscopic eradication and recurrence rate were observed in HGD/T1a and LR T1b adenocarcinoma. Carefully selected LR T1b cancer may receive endoscopic treatment in an expert center without any negative impact on recurrence.
Abstract Esophageal adenocarcinoma (EAC), a significant cause of morbidity and mortality, develops from its metaplastic precursor lesion termed Barrett’s esophagus (BE). BE progresses to EAC within an inflammation rich environment, however a detailed understanding of the types of inflammatory cells present, how that population changes over time or diagnosis, and the related immunomodulatory pathways that may mediate BEs progression is still understudied. Traditional immunohistochemistry is often inadequate to provide detailed information about a broad number of cells, local cellular proportions, and cellular heterogeneity; while bulk or single cell RNA sequencing lose the spatial context and relationships between the stroma and epithelium. Utilizing modern multiplex profiling technologies such as Nanostring’s GeoMx digital Profiler (DSP) aid in identifying both cellular composition and distribution of cells within the epithelium and stroma. Therefore, our aim of this study was to determine the suitability of the DSP platform for analyzing formalin fixed paraffin embedded (FFPE) endoscopic samples of BE and determine any differences between non-dysplastic BE (NDBE) samples from patients who eventually progressed (progressors) compared to those who did not (non-progressors), with the goal to gain deeper insights about cellular composition and spatial distribution of immune cells that may dictate progression of BE. Our secondary goal was to investigate the relationship of these cells to the BE epithelial cells through understanding the immune signaling and regulatory pathways. Our pilot study utilizing a 49-plex antibody panel on 7 NDBE samples from progressors and 8 NDBE samples from non-progressors showed good quality metrics and deciphered an immune rich microenvironment in BE with several immune markers including CD66b (neutrophils), CD14 (monocytes), CD68 (macrophages) and CD56 (NK cells) being overexpressed in the stroma of progressors compared with non-progressors, corrected p value less than 0.05. The myeloid activation marker CD80 was overexpressed in the BE epithelial cells of progressors. To determine how spatial transcriptomic profiling performed in FFPE endoscopic samples, 1,812 transcripts within 48 regions of interest of four BE, HGD, and EAC samples was interrogated. Only 36 (2%) probes fell below the limit of detection quality threshold. Thus, our pilot results show that robust proteomic and transcriptomic profiling can be obtained from endoscopic BE biopsies using this system. Based on these results, we systematically interrogated the immune cell makeup and distribution as well as their related inflammatory and immunoregulatory pathways in 40 NDBE biopsies (20 progressors and 20 with stable non-progressing disease) within discrete compartments (stroma and epithelium) through spatial whole transcriptome profiling. Citation Format: Qurat ul Ain, Nicola Frei, Amir M. Khoshiwal, Pim Stougie, Robert Odze, Sophie Camilleri-Broet, Lorenzo Ferri, Lucas C. Duits, Jacques Bergman, Matthew D. Stachler. Spatial proteomic and transcriptomic characterization of the inflammatory landscape of formalin fixed paraffin embedded Barrett’s esophagus tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6853.
Aims Patients with non‐dysplastic Barrett's oesophagus (BE) often show a wide range of ‘atypical’ histological features in the bases of the crypts. However, the significance of crypt atypia has never been evaluated, despite prior studies showing the presence of DNA content and other molecular abnormalities in this epithelium. The aim of this study was to evaluate whether the degree of crypt atypia in BE patients without dysplasia correlates with progression to high‐grade dysplasia/adenocarcinoma (HGD/EAC). Methods and results Baseline biopsies from 114 BE patients without dysplasia, 57 who progressed to HGD/EAC (progressors) and 57 who did not progress (non‐progressors), were included in the study. Biopsies were evaluated for the degree of basal crypt atypia on a three‐point scale according to discrete histological criteria. In non‐progressors, 64.9, 31.6 and 3.5% of biopsies had a crypt atypia score of 1, 2 and 3, respectively, with a mean score of 1.39 ± 0.56. The percentage of biopsies with an atypia score of 2 or 3 increased in progressors [42.1, 42.1 and 15.8% of biopsies scored 1, 2 or 3, respectively, with a mean score of 1.74 ± 0.72 ( P = 0.004)]. The odds ratio of grade 3 crypt atypia for progression to HGD/EAC was 5.2 (95% confidence interval = 1.1–25.0, P = 0.04) and the findings did not change significantly when the data were analysed according to progression to either HGD or EAC. Conclusions This study shows that non‐dysplastic crypts in BE are biologically abnormal, suggesting that neoplastic progression begins prior to the onset of dysplasia. The degree of crypt atypia in BE patients without dysplasia correlates with progression.
ABSTRACT Background Variant‐adapted COVID‐19 vaccines are recommended for patients with inflammatory bowel disease (IBD). However, many patients rely on pre‐existing immunity by original vaccines or prior infections. Aim To assess whether such immunity sufficiently combats the highly immune‐evasive SARS‐CoV‐2 JN.1 variant. Methods Utilising two longitudinal cohorts, we evaluated immunity against JN.1 induced by original vaccines (IBD: n = 98; healthy: n = 48), omicron breakthrough infection (IBD: n = 55; healthy: n = 57) or XBB.1.5‐adapted vaccines (IBD: n = 18). Neutralisation and anti‐receptor‐binding domain (RBD) IgG levels against wild‐type SARS‐CoV‐2 and JN.1 were assessed using multiplex immunoassays. Study outcomes were wild‐type and JN.1 neutralisation following three doses of original mRNA vaccines, stratified by immunosuppressive therapy (primary outcome), and JN.1 neutralisation following third‐dose breakthrough infection or a fourth dose of XBB.1.5‐adapted mRNA vaccines (secondary outcomes). Results Following original vaccines, JN.1 neutralisation was lower than wild‐type neutralisation in all study groups (healthy, anti‐TNF and non‐anti‐TNF; each p < 0.001); most individuals lacked JN.1 neutralisation (healthy: 97.9%; anti‐TNF: 98.3% and non‐anti‐TNF: 92.3%). Confounder‐adjusted multivariable modelling strongly associated anti‐TNF therapy with low levels of anti‐JN.1‐RBD IgG (fold‐change 0.48 [95% CI 0.39–0.59]). JN.1 neutralisation was similar in patients with or without breakthrough infection (anti‐TNF, non‐anti‐TNF; each p > 0.05); neutralisation failure was 100% despite breakthrough infection. XBB.1.5‐adapted vaccines enhanced JN.1 neutralisation ( p < 0.001) and reduced neutralisation failure rates in patients with IBD (94.4% pre‐vaccination vs. 44.4% post‐vaccination; p = 0.003). Conclusions Only variant‐adapted vaccines protect against emerging SARS‐CoV‐2 variants. Patients with IBD and healthy individuals without recent vaccination may lack protection against the JN.1 subvariant KP.3 which causes current COVID‐19 surges.
<b><i>Background:</i></b> A histological diagnosis of dysplasia is our current best predictor of progression in Barrett’s esophagus (BE), the precursor of esophageal adenocarcinoma (EAC). Despite periodic endoscopic surveillance and assessment of dysplastic changes, we fail to identify the majority of those who progress before the development of EAC, whereas the majority of patients undergo endoscopy without showing progression. <b><i>Summary:</i></b> Low-grade dysplasia (LGD), confirmed by expert pathologists, identifies BE patients at higher risk for progression, but the diagnosis of LGD is challenging. Recent research indicates that progression from BE to EAC is heterogeneous and can accelerate via genome doubling and genome catastrophes, resulting in different ways to progression. We identified 3 target areas, which may help to overcome the current lack of an accurate biomarker: (1) the implementation of somatic point mutations, chromosomal alterations, and epigenetic changes (genomics and epigenomics), (2) evaluate and develop biomarkers over space and time, (3) use new sampling methods such as noninvasive self-expandable sponges and endoscopic brushes. This review focus on the state of the art in risk stratifying BE and on recent advances which may overcome the limitations of current strategies. <b><i>Key Messages:</i></b> A panel of clinical factors, genomics, epigenomics, and/or proteomics will most likely lead to an assay that accurately risk stratifies BE patients into low- or high-risk for progression. This biomarker panel needs to be developed and validated in large cohorts containing a sufficient number of progressors, with testing samples over space (spatial distribution) and time (temporal distribution). For implementation in clinical practice, the technique should be affordable and applicable to formalin-fixed paraffin-embedded samples, which represent standard of care.
