Endoscopic Biopsy Research Articles

Impact of a new dedicated sheath device for tissue sampling of biliary stricture on pathological diagnostic yield: Retrospective study.

Background and study aims Endoscopic transpapillary biliary forceps biopsy (TBFB) is a common method for obtaining specimens from biliary lesions. Its diagnostic yield is unsatisfactory; to overcome this disadvantage, a dedicated sheath has been developed. This study aimed to evaluate the outcomes of conventional TBFB and TBFB with a novel sheath device. Patients and methods Consecutive patients who underwent TBFB between January 2020 and December 2021 were retrospectively evaluated. The rate of obtaining adequate samples, failed attempts at forceps insertion into the bile duct, and sensitivity were compared between the two groups. Results Ninety-two patients who underwent 115 endoscopic retrograde cholangiopancreatographies (76 in the conventional group vs. 39 in the dedicated sheath group) were included. The rates of obtaining adequate samples, failed attempts of the forceps into the bile duct, and sensitivity were 72.4% vs. 89.7% ( P = 0.03), 28.3% vs. 0% ( P < 0.01), and 66.7% vs. 88.9% ( P = 0.02), respectively. Conclusions TBFB with the novel sheath device contributed to improved sensitivity for diagnosis of biliary stricture without insertion of forceps outside the bile duct.

Clinical Decision Making in Inflammatory Bowel Disease Mimics: Practice Management from Inflammatory Bowel Disease LIVE.

Since 2009, inflammatory bowel disease (IBD) specialists have utilized "IBD LIVE," a weekly live video conference with a global audience, to discuss the multidisciplinary management of their most challenging cases. While most cases presented were confirmed IBD, a substantial number were diseases that mimic IBD. We have categorized all IBD LIVE cases and identified "IBD-mimics" with consequent clinical management implications. Cases have been recorded/archived since May 2018; we reviewed all 371 cases from May 2018-February 2023. IBD-mimics were analyzed/categorized according to their diagnostic and therapeutic workup. Confirmed IBD cases made up 82.5% (306/371; 193 Crohn's disease, 107 ulcerative colitis, and 6 IBD-unclassified). Sixty-five (17.5%) cases were found to be mimics, most commonly medication-induced (n = 8) or vasculitis (n = 7). The evaluations that ultimately resulted in correct diagnosis included additional endoscopic biopsies (n = 13, 21%), surgical exploration/pathology (n = 10, 16.5%), biopsies from outside the GI tract (n = 10, 16.5%), genetic/laboratory testing (n = 8, 13%), extensive review of patient history (n = 8, 13%), imaging (n = 5, 8%), balloon enteroscopy (n = 5, 8%), and capsule endoscopy (n = 2, 3%). Twenty-five patients (25/65, 38%) were treated with biologics for presumed IBD, 5 of whom subsequently experienced adverse events requiring discontinuation of the biologic. Many patients were prescribed steroids, azathioprine, mercaptopurine, or methotrexate, and 3 were trialed on tofacitinib. The diverse presentation of IBD and IBD-mimics necessitates periodic consideration of the differential diagnosis, and reassessment of treatment in presumed IBD patients without appropriate clinical response. The substantial differences and often conflicting treatment approaches to IBD versus IBD-mimics directly impact the quality and cost of patient care.

Imprint Cytology of Gastrointestinal Endoscopic Tissue Biopsies at Kenyatta National Hospital, East Africa, Kenya

Imprint Cytology of Gastrointestinal Endoscopic Tissue Biopsies at Kenyatta National Hospital, East Africa, Kenya

Somatic Mutational Analysis in Endoscopic Ultrasound-Guided Biopsy of Pancreatic Adenocarcinoma: Assessing Yield and Impact.

We sought to determine the yield of somatic mutational analysis from endoscopic ultrasound (EUS)-guided biopsies of pancreatic adenocarcinoma compared with that of surgical resection and to assess the impact of these results on oncologic treatment. We determined the yield of EUS sampling and surgical resection. We evaluated the potential impact of mutational analysis by identifying actionable mutations and its direct impact by reviewing actual treatment decisions. Yield of EUS sampling was 89.5%, comparable with the 95.8% yield of surgical resection. More than a quarter in the EUS cohort carried actionable mutations, and of these, more than 1 in 6 had treatment impacted by mutational analysis. EUS sampling is nearly always adequate for somatic testing and may have substantial potential and real impact on treatment decisions.

Evaluation of two liver biopsy and rectal sealing techniques in dog cadavers undergoing Natural Orifices Transluminal Endoscopic Surgery (NOTES) by transrectal access

The aim of this study was to evaluate two liver biopsy techniques by transrectal Natural Orifice Transluminal Endoscopic Surgery (NOTES) and compare tensiometric parameters of rectal sealing using 2-octyl cyanoacrylate glue or conventional rectal sutures in a dog cadaver model. In sixteen dog cadavers two liver biopsy techniques were performed via transrectal NOTES using either polypectomy diathermy forceps or endoscopic oval biopsy forceps. The cadavers were divided into two groups: Glue Group (GG) where rectal sealing was performed with 2-octyl cyanoacrylate glue and Suture Group (SG) with the rectal defect sealed with simple continuous extracorporeal 3-0 polydioxanone sutures. The rupture pressure of the seals was measured on a rectal burst test. The diathermy polypectomy endoscopic forceps biopsy technique was significantly faster (p&lt;0.001) and provided larger diameter samples. Rectal sealing was significantly faster (p&lt;0.001) in the GG. There was no difference between the two groups with regard to rupture pressure (258.5 mmHg) with air insufflation. Using endoscopic oval biopsy forceps, biopsy samples can only be collected from the surface of the liver, whereas polypectomy forceps with a diathermy loop can be used to collect samples from the tip of the hepatic lobe. There was no difference in rectal rupture pressure in the burst test between the cadavers where sealing was performed with rectal sutures and those where cyanoacrylate adhesive was used.

The impact of surgical resection on prognosis in gastric neuroendocrine tumors

Aims: This study aimed to investigate the pathological factors influencing prognosis in patients undergoing surgical resection for GNETs, in the context of the World Health Organization 2010 staging system. Methods: This retrospective study included 27 patients who underwent surgical resection for GNETs diagnosis between 2001 and 2015. Patients were clinically categorized into four types based on gastric NET characteristics: type 1 tumors, which are typified by hypergastrinemia and develop on a background of atrophic gastritis; type 2 tumors, which are related with gastrinomas; type 3 tumors, which have low serum gastrin levels and no underlying mucosal pathology, and type 4, which are characterized by neuroendocrine carcinoma. Additionally, all patients were classified according to the TNM staging system. Results: The median age of the patients was 56 years (range: 33-81), and most patients were identified as type I (55.6%), with subsequent groups being type IV (25.9%) and type III (18.5%). The majority of type I patients were classified as stage I, while the majority of type III patients were in stage IIA, and most type IV patients were in stage IIIB. Type III and type IV groups exhibited a higher rate of lymph node metastasis compared to type I group (Type I: 13.3% vs. Type II: 80.0% vs. Type IV: 57.1%, p &lt; 0.001). The mortality rate was higher in the Type IV group compared to other groups (Type I: 0% vs. Type II: 20% vs. Type IV: 57.1%, p &lt; 0.001). The Ki-67 levels were higher in patients with lymph node metastasis than in those without. Conclusion: Type III and IV GNETs are at a higher risk of lymph node metastasis and mortality. The Ki-67 value assessed through preoperative endoscopic biopsy may serve as a guide for deciding on the necessity of lymph node dissection.

Differential diagnosis of gastric low- and high grade dysplasia using C6orf15 protein

ObjectiveTo investigate the expression of C6orf15 protein in gastric endoscopic biopsy specimens and its usage as an ancillary diagnostic biomarker in determining the grade of gastric dysplasia. MethodsWe selected 102 patients with gastric endoscopic biopsy specimens from Jinling Hospital. These were divided into four groups: 22 cases of gastric mucosal benign lesions, 28 with low-grade dysplasia (LGD, intestinal-type: 21 cases，foveolar-type: 7cases), 28 with high-grade dysplasia (HGD, intestinal-type: 20 cases，foveolar-type: 8 cases), and 24 cases of gastric adenocarcinoma. We examined the expressions of C6orf15, P53, and Ki67 in 102 gastric endoscopic biopsy specimens, including 47 cases with accompanying endoscopic submucosal dissection (ESD) specimens, using immunohistochemistry. ResultsIn gastric HGD and gastric adenocarcinoma, the c6orf15 protein exhibits diffuse and strong cytoplasmic expression in tumor cells. Conversely, in gastric LGD and benign gastric mucosal lesions, the c6orf15 protein shows negative or faint yellow cytoplasmic staining. The expression rate of C6orf15 in high-grade gastric dysplasia (HGD, 93 %) and gastric adenocarcinoma (100 %) was significantly higher than in the gastric mucosal benign lesion group (0 %) and the low-grade dysplasia (LGD, 7 %) group (P < 0.001). ConclusionThe detection of C6orf15 protein expression could serve as a valuable adjunctive diagnostic tool for distinguishing between gastric HGD, LGD, and benign lesions. The combined assessment of C6orf15, P53, and Ki67 expressions may be beneficial in determining the grade of gastric dysplasia and evaluating the risk of progression in gastric mucosal lesions in clinical practice.

Propensity score matching analysis of the short-term efficacy of Kamikawa versus double- tract reconstruction in laparoscopic proximal gastric cancer surgery

Objective: To compare the short-term efficacy of Kamikawa anastomosis and double-tract reconstruction (DTR) after proximal gastrectomy. Methods: This was a propensity score matched, retrospective, cohort study. Inclusion criteria comprised age 20-70 years, diagnosis of gastric cancer by pathological examination of preoperative endoscopic biopsies, tumor diameter ≤4 cm, and location in the upper 1/3 of the stomach (including the gastroesophageal junction), and TNM stage IA, IB, or IIA. The study cohort comprised 73 patients who had undergone laparoscopic proximal gastric cancer radical surgery in the Department of Gastroenterology, Tangdu Hospital, Air Force Medical University between June 2020 and February 2023, 19 of whom were in the Kamikawa group and 54 in the DTR group. After using R language to match the baseline characteristics of patients in a ratio of 1:2, there were 17 patients in the Kamikawa group and 34 in the DTR group. Surgery-related conditions, postoperative quality of life, and postoperative complications were compared between the two groups. Results: After propensity score matching, there were no statistically significant differences in baseline data between the two groups (P>0.05). Compared with the DTR group, the Kamikawa group had longer operative times (321.5±15.7 minutes vs. 296.8±26.1 minutes, t=32.056, P<0.001), longer anastomosis times (93.0±6.8 minutes vs. 45.3±7.7 minutes, t=56.303, P<0.001), and less bleeding (76 [54~103] mL vs.112 [82~148) mL, Z=71.536, P<0.001); these differences are statistically significant. There were no statistically significant differences between the two groups in tumor size, time to first postoperative passage of gas, postoperative hospital stay, number of lymph nodes removed, duration of lymph node dissection, or total hospitalization cost (all P>0.05). The median follow-up time was 6.1 ± 1.8 months. As to postoperative quality of life, the Kamikawa group had a lower rate of upper gastrointestinal contrast reflux than did the DTR group (0 vs. 29.4% [10/34], χ2=6.220, P=0.013); this difference is statistically significant. However, differences between the two groups in quality of life score on follow-up of 3 months and 6 months on the Gastroesophageal Reflux Disease (GERD) scale were not statistically significant (all P>0.05). The incidence of postoperative complications was 2/17 in the Kamikawa group, which is significantly lower than the 41.2% (14/34) in the DTR group (χ2=4.554, P=0.033). Conclusion: Kamikawa anastomosis and DTR are equally safe and effective procedures for reconstructing the digestive tract after proximal gastric surgery. Although Kamikawa anastomosis takes slightly longer and places higher demands on the surgical team, it is more effective at preventing postoperative reflux.

Immunocompetent isolated cerebral mucormycosis presenting with obstructive hydrocephalus: illustrative case.

Isolated cerebral mucormycosis is rare in immunocompetent adults and is only sparsely reported to be associated with obstructive hydrocephalus. Here, the authors report a case of obstructive hydrocephalus secondary to central nervous system mucormycosis without other systems or rhino-orbital involvement and its technical surgical management. A 23-year-old, incarcerated, immunocompetent patient with history of intravenous (IV) drug use presented with syncope. Although clinical and radiographic findings failed to elucidate an infectious pathology, endoscopy revealed an obstructive mass lesion at the level of the third ventricle, which, on microbiological testing, was confirmed to be Rhizopus fungal ventriculitis. Perioperative cerebrospinal fluid diversion, endoscopic third ventriculostomy, endoscopic biopsy technique, patient outcomes, and the literature are reviewed here. The patient received intrathecal and IV amphotericin B followed by a course of oral antifungal treatment and currently remains in remission. The patient's unique presentation and diagnosis of isolated cerebral mucormycosis reveal this pathogen as a cause of ventriculitis and obstructive hydrocephalus in immunocompetent adult patients, even in the absence of infectious sequelae on neuroimaging.

Endoscopic Surveillance of the Intestinal Allograft: Recommendations From the Intestinal Rehabilitation and Transplant Association Working Group.

Intestinal transplant (ITx) rejection lacks a reliable noninvasive biomarker and rejection surveillance relies on serial endoscopies and mucosal biopsies followed by histologic assessment. Endoscopic biopsies are also essential for identifying other ITx-related complications such as infectious, allergic, and inflammatory graft enteritis as well as post-transplant lymphoproliferative disease or graft versus host disease. In spite of its central role in ITx, published guidelines on endoscopy and biopsy are lacking and significant variability between centers in terms of timing and technical performance exists. Therefore, an international expert group convened and discussed several aspects related to the surveillance endoscopy after ITx with the aim to summarize and standardize its practice. This article summarizes these considerations on endoscopic ITx monitoring and highlights practices of surveillance and for-cause endoscopy, biopsy techniques, pathologic evaluation, potential risks and complications, outsourcing, and less-invasive monitoring techniques.

Liquid biopsy of wash samples obtained via endoscopic ultrasound-guided fine-needle biopsy: Comparison with liquid biopsy of plasma in pancreatic cancer.

Pancreatic cancer (PC) has a poor prognosis and limited treatment options. Liquid biopsy, which analyzes circulating tumor DNA (ctDNA) in blood, holds promise for precision medicine; however, low ctDNA detection rates pose challenges. This study aimed to investigate the utility of wash samples obtained via endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) as a liquid biopsy for PC. A total of 166 samples (42 formalin-fixed paraffin-embedded [FFPE] tissues, 80 wash samples, and 44 plasma samples) were collected from 48 patients with PC for genomic analysis. DNA was extracted and quantified, and 60 significantly mutated genes were sequenced. The genomic profiles of FFPE tissues, wash samples, and plasma samples were compared. Finally, the ability to detect druggable mutations in 80 wash samples and 44 plasma samples was investigated. The amount of DNA was significantly lower in plasma samples than in wash samples. Genomic analysis revealed a higher detection rate of oncogenic mutations in FFPE tissues (98%) and wash samples (96%) than in plasma samples (18%) and a comparable detection rate in FFPE tissues and wash samples. Tumor-derived oncogenic mutations were detected more frequently in wash samples than in plasma samples. Furthermore, the oncogenic mutations detection rate remained high in wash samples at all PC stages but low in plasma samples even at advanced PC stages. Using wash samples was more sensitive than plasma samples for identifying oncogenic and druggable mutations. The wash sample obtained via EUS-FNB is an ideal specimen for use as a liquid biopsy for PC.

Abstract 6099: Identification of intrinsic precursors of Barrett's and gastric intestinal metaplasia

Abstract The origin of Barrett's esophagus (BE) and gastric intestinal metaplasia (GIM), obligate precursors of esophageal adenocarcinoma (EAC) and intestinal gastric cancer (iGC), has intrigued investigators for decades and would likely guide preemptive strategies. From endoscopic biopsies of clinically confirmed BE and GIM, we have cloned stem cells committed to intestinal metaplasia in vitro. Remarkably, the gene expression profiles of BE and GIM stem cells are highly related down to broad arrays of transcription factors compared with stem cells of the normal gastric mucosa. Using cell surface markers in common between BE and GIM stem cells, we have identified clusters of cells at the squamocolumnar junction and the distal stomach in mice and have used Fluorescence-activated cell sorting (FACS) to clone these cells from both sites. These murine clones can be differentiated in air-liquid interface cultures, and both are committed to intestinal metaplasia marked by goblet cells and Alcian blue staining. To ask whether similar cells exist in humans, we generated stem cell libraries from endoscopic biopsies taken from the gastroesophageal junction (GEJ) and the antrum-body junction (ABJ) in patients without BE or GIM. FACS sorting of these stem cell libraries using the same cell surface markers common to BE and GIM stem cells and the murine precursors, we have identified stem cells from the GEJ and ABJ that show similar gene expression profiles and share a commitment to intestinal metaplasia upon in vitro differentiation. Using identical transformation protocols involving retrovirally transduced protooncogenes, we find that these transformed intrinsic cells give rise to tumors with expression profiles similar to EAC and iGC in TCGA datasets, whereas transformed gastric mucosal stem cells yield tumors marked by signet ring cells typical of diffuse gastric cancer. Lastly, we find that drugs we have developed that target the stem cells of BE and GIM also eliminate the putative precursor cells of BE and GIM, suggesting the potential of therapeutics that might eliminate the emergence of intestinal metaplasia and the cancers derived from them. Citation Format: Wa Xian, Frank McKeon, Yusuke Yamamoto, Melika Khorrami, Melina Khorrami, Zaal Mory, Jeremy Siegelman, Amber Su, Raul Caballero Montes, Ashley Hoffman, Jaffer Ajani, Christopher Crum, William Bachovchin, Shan Wang, Matthew Vincent, Crystal Nguyen. Identification of intrinsic precursors of Barrett's and gastric intestinal metaplasia [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 6099.

Abstract 6853: Spatial proteomic and transcriptomic characterization of the inflammatory landscape of formalin fixed paraffin embedded Barrett’s esophagus tissues

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.

Abstract 1028: Assessment of the diagnostic accuracy of Oncuria-Detect® for detection of upper tract urothelial carcinoma

Abstract Introduction and Objective: Due to insufficient accuracy, urine-based assays currently have a limited role in the management of patients with upper tract urothelial carcinoma (UTUC). The application of a robust urine-based multiplex assay, Oncuria-Detect®, to aid in the detection of UTUC has the potential to address this deficiency and to assist with accurate, non-invasive diagnosis. Methods: To evaluate the performance of Oncuria-Detect®, a multiplex immunoassay capable of querying a voided urine sample for 10 protein biomarkers associated with urothelial carcinoma (A1AT, APOE, ANG, CA9, IL8, MMP9, MMP10, PAI1, SDC1 and VEGFA). Its application to UTUC was evaluated in a multi-institutional cohort of 35 prospectively collected subjects presenting for evaluation of upper tract mass along with 46 prospective collected matched controls (i.e., non-tumor bearing). The ability of the test to identify patients harboring UTUC was assessed. UTCU status was confirmed by endoscopy and tissue biopsy or definitive surgery. Diagnostic performance was assessed using ROC curves. Results: Oncuria-Detect® provided an AUC of 0.886 (95% CI: 0.807-0.964) with an overall sensitivity of 91.4%, specificity of 73.9%, NPV 91.9% and PPV 72.7%. Sensitivity values of the diagnostic panel for low-grade UTUC, high-grade UTUC, non-invasive UTUC and invasive UTUC were 86.7%, 90.9%, 88.9% and 94.1%, respectively. Urinary cytology or selective ureteral washing/cytology was associated with an overall sensitivity of 54.2%, specificity of 100%, NPV 63.3% and PPV 100%. Sensitivity values of cytology for low-grade UTUC, high-grade UTUC, non-invasive UTUC and invasive UTUC were 100%, 100%, 100%, and 77.8%, respectively. Conclusions: Urinary levels of a biomarker panel enabled the accurate discrimination of UTUC and controls non-tumor bearing individuals. The multiplex Oncuria-Detect® test can achieve the efficient and accurate detection of UTUC in a non-invasive patient setting. Citation Format: Toru Sakatani, Sunao Tanaka, Kazutoshi Fujita, Jennifer Linehan, Kaoru Murakami, Riko Lee, Ian Pagano, Charles J. Rosser, Hideki Furuya. Assessment of the diagnostic accuracy of Oncuria-Detect® for detection of upper tract urothelial carcinoma [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 1028.

Abstract 6184: A novel approach to Barrett's esophagus risk stratification: Whole-slide image analysis for aneuploidy detection

Abstract Background Barrett’s esophagus (BE) is the only known precursor of esophageal adenocarcinoma (EAC) and there is a need for biomarkers in BE for risk stratification for cancer progression. Aneuploidy has been suggested as a factor in the development, initiation or progression of EAC in patients with BE, and it has been found predictive for EAC progression (Hadjinicolaou, et al. 2020, Sikkema, et al. 2009). However, current assays for detecting aneuploidy require valuable tissue, hence validation studies are limited. We hypothesise that routine histology images can be used to detect ploidy status. We aim to develop a sensitive, accurate, and easy-to-use deep learning tool for this purpose. Methods We used a weakly supervised deep learning-based approach called clustering-constrained-attention multiple-instance learning (CLAM) (Lu et al., 2021) to detect aneuploidy on hematoxylin and eosin-stained whole slide images of endoscopical biopsies from BE, for which the ploidy status had been determined by flow cytometry. To benchmark the model’s performance, we also trained a traditional fully supervised algorithm, ResNet50 (He et al., 2016), with the same dataset. The models were trained on 388 slides (51 aneuploid) from the Seattle Barrett’s Esophagus Annotated Resource (BEAR) and then applied to an independent test cohort of BEAR patients, consisting of 279 slides (36 aneuploid). Results The multi-attention-branch CLAM model achieved AUC of 0.82 and 76.4% balanced accuracy for aneuploidy on the internal test subset (10% of the cohort). On the independent test dataset, the model achieved AUC of 0.85 and 79.3% balanced accuracy, while performance of the fully supervised model was AUC of 0.65 and 33.1 balanced accuracy. In a challenging subset for image-based diagnosis, including 253 samples (29 aneuploid) without dysplasia or atypical mitosis (a major feature of aneuploidy samples) the model achieved a 67.6% accuracy and an AUC of 0.83. Both the flow results (p=2.84e-7) and the model's predictions (p=2.18e-3) revealed a correlation between progression to EAC and ploidy status. Conclusion We developed a deep learning model for predicting aneuploidy in BE biopsies. The weakly-supervised approach can perform much better compared to the traditional fully-supervised model. Aneuploidy is correlated with cancer progression and stands as a promising candidate for the prediction of cancer progression in BE patients. Although atypical mitosis is the primary histological indicator of aneuploidy, our model can still make aneuploid predictions in the absence of atypical mitosis, as it doesn't rely solely on a single parameter. Our model is efficient, capable of processing hundreds of samples resource-effectively, and thus an ideal adjunct to standard histologic evaluation. This classifier may facilitate molecular-based improvements in identifying individuals at high risk of progression. Citation Format: Caner Ercan, Xiaoxi Pan, Thomas G. Paulson, Matthew D. Stachler, Carlo C. Maley, Yinyin Yuan. A novel approach to Barrett's esophagus risk stratification: Whole-slide image analysis for aneuploidy detection [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 6184.

Abstract 7623: Biomarker study to personalized neoadjuvant chemotherapy using preoperative gastric cancer specimens of biopsy from the COMPASS trial, a phase II randmazed controlled trial

Abstract Background and Aim: The results of COMPASS, a randomized phase II trial, suggest that preoperative adjuvant chemotherapy (NAC) regimen or course for locally advanced gastric cancer (GC) does not affect overall survival (OS). However, we hypothesized that some NAC regimens may be more effective for OS on a case-by-case basis. Furthermore, we searched for biomarkers, assuming that further improvement in the outcome of locally advanced GC could be expected if appropriate NAC regimens could be selected using biomarkers before treatment initiation. Materials and Methods: RNA was extracted from endoscopic biopsy specimens of primary tumors collected prior to NAC administration in COMPASS patients, and real-time polymerase chain reaction (PCR) of 127 genes was performed to identify genes with significant (P &amp;lt; 0.05) interaction P values for survival with each regimen and stratified OS with each regimen. Genes were identified and biomarkers were searched at the protein level using immunohistochemical analysis. Results: The THBS1, MSI1, and IGF2BP3 genes were identified as genes whose expression levels significantly (P &amp;lt; 0.05) stratified survival for each regimen and had significant (P &amp;lt; 0.05) interaction P values. Furthermore, a strong correlation was observed between each gene and THBS1, MSI1, and IGF2BP protein expression by immunohistochemical analysis, confirming that protein expression levels by immunohistochemical analysis are also useful as biomarkers. Conclusion: Using endoscopic biopsy specimens prior to NAC for locally advanced GC, biomarkers were identified to select NAC regimens over predicted OS. The results of this study may guide the conduct of clinical trials of individualized treatment of NAC using biomarkers. Citation Format: Takashi Oshima. Biomarker study to personalized neoadjuvant chemotherapy using preoperative gastric cancer specimens of biopsy from the COMPASS trial, a phase II randmazed controlled trial [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 7623.

Abstract 1023: Whole-genome methylation analysis using liquid biopsy for pancreatic cancer diagnosis

Abstract Objective: Pancreatic cancer is one of the highly malignant tumors. Its diagnosis requires invasive ultrasound endoscopic biopsy or endoscopic retrograde cholangiopancreatography (ERCP). However, these methods are limited by false-positive results and complications. Liquid biopsy, which uses blood to detect KRAS mutations in cancer, can be used to overcome these hurdles. However, only about 30% of cases can be detected as a diagnostic marker by KRAS mutations using plasma from patients with stage I-II pancreatic cancer, and its clinical application remains a challenge. Therefore, in this study, we focused on diagnosing pancreatic cancer using methylated DNA in plasma cell-free DNA (cfDNA) obtained from pancreatic cancer and non-cancer patients. Subjects: Plasma was collected before the start of the treatment from six patients diagnosed with pancreatic cancer from 2019 to 2023 at our hospital, and six non-cancer patients simultaneously. Methods: Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing (NGS) was performed using the cfDNA obtained from the plasma of pancreatic cancer and non-cancer patients. Results: The cfDNA fragments obtained by WGBS revealed that promoter regions were mostly deleted, and no difference was observed between cancer and non-cancer patients. The methylation rate of cfDNA fragments by WGBS differed between cancer and non-cancer patients, with multiple methylation sites (&amp;gt;100 sites) in intergenic regions. Discussion: Although attempts have been made to diagnose cancer using genetic mutations and liquid biopsy, only a few studies are available on using methylation markers in the plasma cfDNA of pancreatic cancer patients, and the effectiveness of this method remains unclear. In the present study, we found that promoter regions were deleted by WGBS, and several distinct hypermethylated regions were present in the intergenic region between pancreatic cancer and non-cancer samples, suggesting the presence of certain markers that can distinguish between pancreatic cancer and non-cancer patients. Conclusion: This small number of cases suggests that hypermethylation of the intergenic regions could be helpful in the diagnosis of pancreatic cancer. We will need more cases in the future to verify the usefulness of hypermethylation of intergenic regions in the diagnosis of pancreatic cancer. Citation Format: Tomoaki Ito, Takuya Iwasawa, Satoshi Takeda, Chikako Okamoto, Tomoko Motohashi, Shuhei Ueda, Hisaki Kato, Riku Yamamoto, Akihiro Koizumi, Yuta Murai, Kosaku Nihei, Moe Itakura, Ryunosuke Akima, Mutsumi Sakurada, Kenichiro Tanaka, Tomoyuki Kushida, Koichi Sato. Whole-genome methylation analysis using liquid biopsy for pancreatic cancer diagnosis [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 1023.

Abstract 1172: Association between CD8+ PD-1+ T cell infiltration levels and improved response to total neoadjuvant therapy in mismatch-repair proficient locally advanced rectal cancer

Abstract Background: The tumor microenvironment plays a major role in colorectal cancer progression, dissemination, and response to therapy. As a mechanism of tumor immunity, CD8+ tumor infiltrating lymphocytes have been shown to express PD-1 in response to clonal neoantigens of tumors. We hypothesized that high levels of CD8+ PD-1+ T cell infiltration prior to treatment initiation may correlate with improved response to total neoadjuvant therapy (TNT) in patients with locally advanced rectal cancer (LARC). Methods: We analyzed untreated endoscopic biopsies from 159 patients diagnosed with stage II (n=25) or III (n=134), mismatch-repair proficient rectal adenocarcinoma. All patients were treated with TNT, consisting of either induction chemotherapy followed by chemoradiation (n=108) or chemoradiation followed by consolidative chemotherapy (n=51). FFPE blocks from each biopsy were sectioned into slides for H&amp;E and immunohistochemistry staining with antibodies for CD8 and PD-1 in a CLIA certified lab. CD8+ and PD-1+ cells were quantified using established protocols from the College of American Pathologists. We evaluated associations between response to TNT and tertiles of intratumoral CD8 and PD-1 expression (low/mid/high). Disease free survival (DFS) from the start of TNT and rate of sustained complete response (CR, either clinical or pathologic) were used as primary endpoints. Results: Median follow-up was 40.3 months. The overall CR rate was 42% and the 5-year DFS rate was 77%. Intratumoral CD8 levels were significantly correlated with improved response rates (56% in the top tertile vs. 27% in the bottom tertile, p=0.003, Fisher’s test) and improved 5-year DFS (92% vs. 67% for the top vs. bottom tertiles, respectively; p=0.006, log-rank test). Patients in the highest tertile of intratumoral PD-1 expression also had improved response (56% vs. 25%, p=0.002) and DFS (88% vs. 67%, p=0.034). CD8 and PD-1 levels were strongly correlated with each other (R=0.72, p&amp;lt;0.001, Spearman correlation). Finally, the 41 patients who met criteria for top tertiles of CD8 and PD-1 expression had higher CR rates (66% vs. 32%, p&amp;lt;0.001) and better 5-year DFS (97% vs. 70%, p=0.002) than the other patients. Conclusions: Higher levels of CD8+ and PD-1+ tumor infiltrating lymphocytes on pre-treatment biopsies are associated with improved response to TNT and disease free survival in LARC patients. Citation Format: Christina Lee, Chin-Tung Chen, Nil Urganci, Fan Wu, Canan Firat, Hannah Williams, Evan Seffar, Parisa Malekzadeh, Walid K. Chatila, Jinru Shia, Julio Garcia-Aguilar, Francisco Sanchez-Vega. Association between CD8+ PD-1+ T cell infiltration levels and improved response to total neoadjuvant therapy in mismatch-repair proficient locally advanced rectal cancer [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 1172.

EUS-guided FNA and biopsy for cytohistologic diagnosis of gallbladder cancer: a multicenter retrospective study

EUS-guided FNA and biopsy (EUS-FNAB) is a standard diagnostic procedure for pancreatic masses but not gallbladder (GB) cancer (GBC). The aim of this study was to investigate the efficacy and safety of EUS-FNAB for patients with suspected GBC. Data were analyzed from patients who underwent EUS-FNAB for suspected GBC in 3 hospitals between 2010 and 2023. The diagnostic performance and safety of EUS-FNAB according to characteristic factors were calculated and compared. Of 170 patients, 163 had GBC. EUS-FNAB samples were obtained from the GB in 125 patients and sites other than the GB in 45 patients. The overall sensitivity, specificity, and accuracy were 83.4%, 100%, and 84.1%, respectively. The sensitivity and accuracy for patients with GB samples were 80.8% and 81.6%; for patients without GB samples, these values were 90.7% and 91.1%. The sensitivity and accuracy were higher with fine-needle biopsy needles than with FNA needles and with≤22-gauge needles than with 25-gauge needles. However, no significant differences were observed between the GB and lymph node samples. GB lesions<40mm in size, wall-thickening type, fundal location, absence of extensive liver invasion, and distant metastasis were more frequent in patients without GB samples than in patients with GB samples. Four mild bleeding events were the only reported adverse events. EUS-FNAB was safe and showed high diagnostic performance for patients with suspected GBC, regardless of the target site. When appropriate GB targeting is difficult, targeting the lymph nodes would be a good strategy with comparable outcomes.

Unveiling the challenges of UTUC biopsies and cytology: insights from a global real-world practice study

PurposeDiagnostic ureteroscopy (dURS) is optional in the assessment of patients with upper tract urothelial carcinoma (UTUC) and provides the possibility of obtaining histology.MethodsTo evaluate endoscopic biopsy techniques and outcomes, we assessed data from patients from the CROES-UTUC registry. The registry includes multicenter prospective collected data on diagnosis and management of patients suspected having UTUC.ResultsWe assessed 2380 patients from 101 centers. dURS with biopsy was performed in 31.6% of patients. The quality of samples was sufficient for diagnosis in 83.5% of cases. There was no significant association between biopsy techniques and quality (p = 0.458). High-grade biopsy accurately predicted high-grade disease in 95.7% and high-risk stage disease in 86%. In ureteroscopic low-grade tumours, the prediction of subsequent low-grade disease was 66.9% and low-risk stage Ta-disease 35.8%. Ureteroscopic staging correctly predicted non-invasive Ta-disease and ≥ T1 disease in 48.9% and 47.9% of patients, respectively. Cytology outcomes did not provide additional value in predicting tumour grade.ConclusionBiopsy results adequately predict high-grade and high-risk disease, but approximately one-third of patients are under-staged. Two-thirds of patients with low-grade URS-biopsy have high-risk stage disease, highlighting the need for improved diagnostics to better assess patient risk and guide treatment decisions.Clinical trial registration: The study was registered at ClinicalTrials.gov (ClinicalTrials.gov NCT02281188; https://clinicaltrials.gov/ct2/show/NCT02281188).