bluuebunny/crossref_metadata_2025_split huggingface dataset:
A digital imaging analysis (DIA) platform for identifying tertiary lymphoid structures (TLS) in lung adenocarcinoma (LUAD).
Authors: Kushnarev Vladimir , Belozerova Anna , Dymov Daniil , Popov Yuriy , Lukashevich Nadezhda , Valiev Ivan , Shamsutdinova Diana , Akaeva Aida , Galkin Ilia , Popyvanov Lev , Svekolkin Viktor , Nomie Krystle , Love Anna , Bagaev Alexander , Postovalova Ekaterina , Fowler Nathan 
Published: June 2022

3142 Background: Previous studies of non-small cell lung cancer (NSCLC) have shown that TLS can be predictive of therapy response and a positive prognostic factor for survival. Currently, TLS identification is manually performed by pathologists with limited morphological criteria. Standardizing TLS detection with an automated DIA workflow could guide clinical trials in precision medicine by improving patient stratification. Here, we investigate the reproducibility and sensitivity of our DIA platform for evaluating TLS in LUAD using digital histopathology and machine learning. Methods: TLS were assessed by 3 pathologists on whole slide images (WSI) in a validation cohort of 22 LUAD samples using current TLS characterization criteria of dense lymphoid structures, the presence/absence of a germinal center, and high endothelial venules (HEVs). The intraclass correlation coefficient (ICC) was used to measure reproducibility between pathologists. The BostonGene DIA platform was used to train models for automated TLS detection. Quantitative measurements of area, lymphocyte number, and density of each TLS were obtained. A prospective cohort of 8 samples was used to compare pathologist and DIA identification of TLS. Normalized numbers of TLS in the tumor area were used for cohort stratification for overall survival (OS) analysis using the Kaplan-Meier method in an independent clinical cohort of 104 TCGA-LUAD patients. Results: A panel of 3 pathologists identified 326 unique TLS from 22 samples. Between-pathologist detection of TLS, independent of germinal center or HEV criteria, resulted in good reproducibility with an ICC of 0.77. Our DIA platform exhibited excellent reproducibility with an ICC of 0.94 when compared to validated prospective cohort annotation. In total, 155 and 189 TLS were identified by pathologists and our DIA platform, respectively. The DIA platform demonstrated a markedly improved sensitivity of 0.91 for TLS identification. Furthermore, OS analysis revealed that a TLS density greater than 0.94 TLS per mm2 of tumor assessed by DIA is a statistically significant independent biomarker of better OS in the LUAD cohort from TCGA. Conclusions: These results demonstrate the BostonGene DIA platform detects TLS in LUAD, with improved reproducibility and sensitivity over previous methods. Additionally, the DIA platform showed a TLS density greater than 0.94 TLS per mm2 of tumor is a positive prognostic marker for OS in LUAD. Standardized TLS DIA identification can be exploited in digital pathology applications for future clinical trials, informing clinicians of predictive and prognostic information during the decision-making process.
BRAF-targeted therapy for locally advanced ameloblastoma of the mandible: A potential neoadjuvant strategy.
Authors: Grynberg Shirly , Steinberg Yael , Asher Nethanel , Ben-betzalel Guy , Stoff Ronen , Markel Gal , Shapira-Frommer Ronnie , Schachter Jacob , Hirschhorn Ariel 
Published: June 2022

3149 Background: Ameloblastoma is a rare benign but locally aggressive odontogenic neoplasm, with 2% of cases representing ameloblastic carcinoma or metastatic ameloblastoma. It affects young adults with high recurrence rates after surgery. The standard therapy is radical bone resection with subsequent functional, aesthetic & psychological impairments. Therefore, other therapeutic options, including neoadjuvant approach, should be considered. Sixty to 70% of mandible Ameloblastoma carry a BRAF mutation, usually V600E, and previous case reports have shown durable responses to treatment with BRAF inhibitors in these patients. We sought to explore the possibility of neoadjuvant BRAF or BRAF+MEK inhibition as neoadjuvant treatment in mandible Ameloblastoma. Here we present results of 12 patients with locally advanced disease who were treated with BRAF with or without MEK inhibitors. Methods: Patients who were unable to undergo jaw preservation surgery for locally advanced Ameloblastoma with a BRAF V600E mutation were treated with Dabrafenib or Dabrafenib-Tratmetinib in an EAP form. Patient records were analyzed for baseline parameters, treatment regimen, toxicity, response to therapy and the ability to convert to a mandible preservation surgery. Data were collected and analyzed in accordance with Sheba Medical Center IRB approval. Statistical analyses were done with STATA v.17. Results: Twelve patients were treated with Dabrafenib/ Dabrafenib-Tratmetinib between 2017-2021. Five patients received BRAF-MEK inhibitors and 7 BRAF inhibitor alone. Median age was 21. Ten patients(83%) showed excellent response to therapy and have successfully converted from planned radical bone resection to mandible preservation surgery. The other 2 patients are still on therapy and have also showed deep responses that enable conversion to mandible preservation. Median time to surgery was 10 months. With median follow up of 18 months, no cases of recurrence were documented. Rate of adverse events was as expected with only 1 case of G3-4 (hepatitis). Conclusions: Targeted therapy with BRAF with or without MEK inhibition may serve as an important therapeutic tool for locally advanced Ameloblastoma with the potential of organ preservation treatment, and is an important example of oncological therapy assisting in non-cancerous tumors.
Contact x-ray brachytherapy (Papillon) in addition to chemoradiotherapy to improve organ preservation in early cT2-T3 rectal adenocarcinoma: The 3-year results of OPERA randomized trial (NCT02505750).
Authors: Gerard Jean-Pierre , Barbet Nicolas N. , Pacé-Loscos Tanguy , Magné Nicolas , Serrand Jessica , Mineur Laurent , Deberne Melanie , Zilli Thomas , Dhadda Amandeep Singh , Sun Myint Arthur 
Published: June 2022

3512 Background: The OPERA trial was testing the hypothesis that Contact x-ray brachytherapy (CXB) 50 kV boost will increase the rectal preservation rate in early T2-T3ab rectal adenocarcinoma. We present the 3 years clinical results. Methods: Inclusion criteria were: Age > 18 years, PS: 0-1, adenocarcinoma, distal - middle rectum, cT2-T3ab cN0-N1 < 8mm staged using MRI, M0. Stratification: T < vs ≥ 3 cm diameter. Control arm (A) was chemoradiotherapy (CRT) 45Gy/ 5 weeks with concurrent chemotherapy (Capecitabine 825 mg / m2) and external beam radiotherapy boost (9Gy/ 5 fr/ 1 week). Experimental arm used the same CRT (Cape 45) but the boost used CXB (90 Gy/ 3 fr/ 4 weeks). CXB was given first (B1) for tumor < 3 cm and after cap 45 (B2) for tumor ≥ 3 cm. Response assessment was made at week 14 after treatment start using palpation, endoscopy and MRI. A new assessment could be made at week 20 and 24 with a second MRI.TME was recommended in case of Partial response, Watch& Wait in case of clinical complete response (cCR). Bowel function measurement used LARS score. Main end- point was: Rate of organ preservation at 3 years. The hypothesis (in 2014) was 20% arm A vs 40% arm B (HR:0.53). Results: Between 5-2015 and 6-2020, 144 patients were included (France 96, UK 44, Switzerland 4). The analysis was made in 01-2022 with a median Follow-up time of 34 months. Treatment compliance was good in ≥ 90% of patients. Table gives main patients characteristics and clinical outcome. At three years the OP rate (Kaplan Meier estimate) was respectively arm A vs B: 60% vs 81% (HR 0.34 [95% CI 0.19 – 0.73]; p= 0.005). At three years OP for group A1 and B1 were: 65% vs 97% (HR 0.081 [95% CI 0.01-0.64]; p= 0.02). Conclusions: A CXB boost, when combined with chemoradiotherapy, increases the rate of organ preservation in early rectal adenocarcinoma. Starting with CXB in T < 3 cm appears as an attractive option. A B A1 (T < 3cm) B1 (T < 3cm) N° patient 71 73 30 32 Median age 68 69 69 70 Gender M/F 45/26 43/30 18/12 18/14 T2/T3 45/26 47/26 25/5 29/3 Distal/middle 53/18 53/20 21/9 27/5 cCR (W 14-24) 61% 90% p < 0.001 70% 94% p = 0.027 TME 26 12 8 1 Death 2 2 1 0 LARS < 30 80% 83% 87% 86%.
Short-term outcomes of laparoscopy-assisted versus open surgery for low rectal cancer (LASRE): A multicenter, randomized, controlled trial.
Authors: Chi Pan , Su Xiangqian , Xu Jianmin , Qiu Huizhong , Wang Ziqiang , Kang Liang , Deng Haijun , Chen Weiping , Zhang Qingtong , Du Xiaohui , Yang Chunkang , Guo Yincong , Zhong Ming , Ye Kai , You Jun , Xu Dongbo , Li Xinxiang , Xiong Zhiguo , Tao Kaixiong , Ding Ke-Feng ,   The LASRE Trial Investigators
Published: June 2022

3516 Background: The efficacy of laparoscopic versus open surgery for low rectal cancer has not yet been established. We aimed to evaluate whether laparoscopic surgery is non-inferior to open surgery for low rectal cancer in terms of oncologic outcomes. Methods: LASRE trial (NCT01899547) is a multicenter, noninferiority, randomized controlled trial being conducted in 22 tertiary hospitals across China. Patients with low rectal cancer and without evidence of pelvic lateral lymph nodes or distant metastasis were randomly assigned (2:1) to laparoscopic or open surgery. The primary outcome was 3-year disease-free survival (DFS). Secondary outcomes included pathological outcomes, 30-day postoperative complications, 30-day mortality, overall survival (OS), and quality of life. The target sample size was 1065 patients. The short-term pathological, surgical, and postoperative recovery outcomes, analyzed in a modified intention-to-treat population (mITT). Results: Between November 12, 2013, and June 6, 2018, 1070 patients were randomized into laparoscopic (n = 712) or open surgery (n = 358) groups; 1039 were included in the mITT analysis (685 in laparoscopic and 354 in open group). Seventeen patients (2.5%) in the laparoscopic group required conversion to open surgery. There were no significant between-group differences in the rates of complete mesorectal excision (85.3% vs. 85.8%; p = 0.777), negative circumferential resection margins (98.2% vs. 99.7%; p = 0.085), negative distal resection margins (99.4% vs. 100%; p = 0.362), and numbers of retrieved lymph nodes (13.0 vs. 12.0; p = 0.394). The laparoscopic surgery group exhibited a shorter time to first flatus (40.4 vs. 44.8 hours; p = 0.006), time to first defecation (61.2 vs. 66.3 hours; p = 0.031), duration of analgesic use (45.0 vs. 48.0 hours; p = 0.001), and duration of hospitalization (8.0 vs. 9.0 days; p = 0.008) compared to the open surgery group. The postoperative complication rates were 13.0% and 17.2% in the laparoscopic and open surgery groups, respectively (p = 0.065). There was no incidence of 30-day mortality. Conclusions: In patients with low rectal cancer, laparoscopic surgery performed by experienced surgeons can provide pathological outcomes comparable with those of open surgery in terms of complete mesorectal excision and negative resection margins, rapid postoperative recovery, and fewer postoperative complications. Clinical trial information: NCT01899547.
Metagenomic analysis of the fecal microbiome in patients with colorectal cancer compared to healthy controls as a function of age.
Authors: Kharofa Jordan , Apewokin Senu , Alenghat Theresa , Ollberding Nicholas 
Published: June 2022

3532 Background: Colorectal cancer (CRC) incidence is increasing in young patients ( < 50 years old) without a clear etiology. Emerging data has implicated the fecal microbiome in CRC carcinogenesis. However, its impact on young onset CRC (YO-CRC) is poorly defined. Colibactin producing E. Coli and fadA producing Fusobacterium nucleatum can drive CRC carcinogenesis, however their effects across the age spectrum are unknown. Methods: We performed a meta-analysis of fecal metagenomics sequencing from n = 692 patients with CRC and n = 602 healthy controls from eleven studies to evaluate species and known microbial derived factors (colibactin and FadA) associated with CRC as a function of age. Generalized linear mixed effects regression was used to model the predicted prevalence of gene families and taxa as a non-linear function of age. Two-stage individual patient data meta-analysis (IPDMA) with adjustment for gender, CRC status, and body mass index was also used to estimate summary odds ratios for colibactin, F. nucleatum, and E. Coli. Interaction ORs were obtained to assess the difference in the effect of each gene or taxa on CRC case status in YO-CRC. Shannon Diversity index and metabolic pathway differences in the fecal metagenome for YO-CRC patients were assessed using phyloseq and MetaCyc respectively using an IPDMA approach. Results: Summary odds ratios (OR) for CRC were increased relative to controls with the presence of colibactin (OR 1.92 95%CI 1.08-3.38), fadA (OR 4.57 95%CI 1.63-12.85), and F. nucleatum (OR 6.93 95%CI 3.01-15.96) in models of all patients adjusted for age, gender, and body mass index. The OR for CRC for the presence of E.coli was 2.02 (0.92-4.45). An increase in the prevalence of F. nucleatum (OR = 1.40 [1.18; 1.65] and Escherichia coli (OR = 1.14 [1.02; 1.28]) per 10-year increase in age was observed in models including samples from both CRC and healthy controls. No difference was observed for Shannon Diversity (OR 1.36 95%CI 0.68-2.72) or MetaCyc pathways in YO-CRC patients. Species relative abundance was differentially enriched in YO-CRC relative to old CRC patients and controls for five species- Intestinimonas butyriciproducens, Holdemania filiformis, Firimicutues bacterium CAG 83, Bilophilia wadsworthia, and Alistipes putredinis. Conclusions: Strong associations with CRC status were observed for colibactin, fadA, and F. nucleatum with increased F. nucleatum in older patients. Several species were enriched in YO-CRC patients including B. wadsworthia which can produce carcinogenic sulfur metabolites and is increased with adherence to a sulfur microbial diet-low in vegetables and legumes. A sulfur microbial diet has also been associated with higher incidence of YO-CRC in population studies (Nguyen Gastroenterology 2021). Additional study is warranted to understand causal mechanisms of enriched species observed in YO-CRC patients.
Clinical outcomes of immune checkpoint inhibitor (ICI) therapy among Veterans Affairs patients with colorectal cancer and discordant dMMR/MSI-H status.
Authors: Isaacs James , Guo Aixia , Vashistha Vishal , Katsoulakis Evangelia , Boswell Elizabeth , Strickler John H , Ahmed Sara , Kelley Michael J. 
Published: June 2022

3534 Background: Clinical trials have demonstrated improvements in survival with immune checkpoint inhibitors (ICIs) for advanced colorectal cancer patients with MSI-H/dMMR detected using PCR-based assays (PCR) or immunohistochemistry (IHC), respectively. MSI-H can also be assessed by next-generation sequencing (NGS). Evaluation of real-world outcomes among MSI-H patients by NGS treated with ICIs are warranted, particularly when results are discordant between these tests. Methods: The VA National Precision Oncology Program Database was accessed to select veterans with colorectal cancer and an MSI-H biomarker by NGS. Baseline patient variables, disease characteristics, and duration of ICI treatment were obtained from the VA’s Corporate Data Warehouse. Concordance between NGS and IHC or PCR testing was computed, and the response rate and duration of ICI treatment in patients with discordant test results were recorded from chart review. Results: Among 1,276 colorectal cancer patients, 71 (5.6%) were found to have MSI-H by NGS. Of these, 22 (30.1%) received ICI. Among 49 patients who did not receive ICI, 36 had stage I-III disease, 5 had limited performance status, 5 were actively being treated with chemotherapy and 3 had completely resected stage IV disease. Of the 71 patients, 29 had dMMR IHC testing, 8 had MSI-H PCR testing, 1 had both IHC and PCR testing, and 34 patients had only NGS testing. No PCR tests were discordant with NGS but 8 of 29 IHC tests were discordant. Among these 8 patients with discordant IHC MMR and MSI-H by NGS, 5 received pembrolizumab. There were 3 partial responses, 1 stable disease and 1 progressive disease. Durable responses were seen with 3 of 5 patients remaining on therapy without progression at the time of this analysis at a median follow up of 8.5 months. Conclusions: In a cohort of NGS MSI-H colorectal cancer patients, there was a high rate of discordant IHC results. Clinical benefit is seen in patients treated with ICI with discordant testing results, suggesting that NGS testing identifies patients with false negative dMMR IHC testing in the real-world clinical setting.
Consensus molecular subtypes (CMS) as prognostic and predictive biomarkers of panitumumab (Pmab), fluorouracil and folinic acid (FU/FA) or FU/FA maintenance therapy following Pmab-FOLFOX induction in RAS wildtype metastatic colorectal cancer (mCRC): PANAMA trial (AIO-KRK-0212).
Authors: Hoppe Beeke , Modest Dominik Paul , Keilholz Luisa , Na Il-Kang , Karthaus Meinolf , Fruehauf Stefan , Graeven Ullrich , Von Weikersthal Ludwig Fischer , Goekkurt Eray , Reinacher-Schick Anke C. , Kasper Stefan , Kind Andreas Jay , Kurreck Annika , Held Swantje , Heinemann Volker , Horst David , Jarosch Armin , Stintzing Sebastian , Trarbach Tanja , Stahler Arndt 
Published: June 2022

3537 Background: Consensus molecular subtypes (CMS1-4) of colorectal cancer were evaluated as prognostic and predictive biomarkers in the PANAMA trial. PANAMA compared maintenance therapy with panitumumab (Pmab) and fluorouracil/folinic acid (FU/FA) vs. FU/FA alone after Pmab-FOLFOX induction therapy in RAS wildtype mCRC. Methods: Gene expression was measured after mRNA isolation in 179 of 248 patients of the full analysis set. The analysis was conducted using a customized Nanostring PanCancer Progression Panel. The original CMS classifier was re-derived for Nanostring data using a multinomial regression analysis.Median progression-free (PFS) and overall survival (OS) since start of maintenance were estimated by Kaplan-Meier-method and Cox-regression, using the log rank test. Objective response rates (ORR) of maintenance therapy were compared by Chi-square-test. Results: Prevalence of CMS was: CMS1, n = 15 (8.4 %); CMS2, n = 82 (45.8 %); CMS3, n = 20 (11.2 %) and CMS4, n = 62 (34.6 %). A prognostic impact of CMS regardless of treatment was not evident for PFS (p = 0.245) and OS (p = 0.169), but for ORR (p = 0.022), with CMS1 and CMS3 being associated with unfavourable efficacy during maintenance therapy. Potential predictive effects of CMS were observed in patients with CMS2 and CMS4 tumours. In CMS2 and CMS4 tumours, ORR was significantly higher when treated with Pmab-FU/FA in maintenance therapy (CMS2: 56.5% vs 30.6%, p = 0.026; CMS4: 55.6% vs. 28.6%, p = 0.040). In patients with CMS2 mCRC, this translated into a significant effect on PFS (Hazard ratio: 0.61 (95% CI 0.38 – 0.99) p = 0.046 (Table). Conclusions: CMS have limited prognostic impact for pmab-based maintenance therapy. However, CMS2 and CMS4 are positively associated with Pmab efficacy during maintenance therapy in the PANAMA trial. Further trials are necessary to confirm these results. [Table: see text]
Discovering colorectal cancer biomarkers with individual fragments analysis of cell-free DNA using attention-based deep multi-instance learning.
Authors: Lee Eunsaem , Shin Seungho , Park Seungtae , Yu Seunghyeon , Jo Shin-Sang , Jeon Hee Joon , Yoon Na Ri , Kim Jinho , Park Donghyun , Hwang Hyung Ju 
Published: June 2022

3539 Background: Cell-free DNA(cfDNA) are DNA fragments circulating in blood stream. Among these fragments, there are tumor-derived DNA(ctDNA) fragments which can be a significant biomarker for cancer diagnostics. Recently, there are evidences that reveals methylation patterns of ctDNAs facilitate statistical models to diagnose cancers with plausible accuracy than mutation patterns. Despite of such promising facts, an early detection of cancers with methylation patterns of ctDNAs is still statistically difficult since proportion of ctDNAs to cfDNAs is marginal. As a result, it is difficult to set differential threshold on ctDNA proportion to successfully classify early cancer patients. For such a reason, we develop a high-throughput classifier whose classification resolution is per-fragment unlike per-batch approach in existing models. Methods: Targeted methylation sequencing was performed with DNA extracted from plasma cfDNA of 141 colon adenocarcinoma (COAD) patients and 200 healthy individuals. To extract DNA fragment-level methylation status, we profiled the methylation status using Bismark software and home-built python scripts were used to recover methylation status of DNA fragments. We implement an attention based multi-instance learning model which is permutation-invariant with fragments to analyze the impact of individual fragments on COAD prediction. Our models were trained using k-fold cross-validation and to assess generalization performance. Results: We first trained on local differentially methylated regions (DMRs) that contain 80 to 200 CpG sites using our deep learning model. With a single local region, we achieved a mean sensitivity of 87.2% (mean 95% CI 75.8–93.2%) at 97.7% (mean 95% CI 88.3–99.1%) specificity. By analyzing attention weights, we scored on each fragment according to the model contribution to predicting cancers. To find biomarkers, we added up scores according to methylation of each CpG site. Top 10 high scored CpG sites were validated with tissue sample DNA and almost all of them are overlapped with the 10 CpG sites with the highest statistical differences between cancer and normal tissue in the region. For the global region analysis, we combined local DMRs to confirm collaboration between distant regions and other chromosomes in the colorectal cancer prediction. We achieved a mean sensitivity of 93.4% (95% CI 80.1–98.1%) at 98.3% (95% CI 90.4–99.3%) specificity for the global region prediction. Conclusions: Our study shows a potential of targeted sequencing cell-free DNA as a cancer biomarker. An attention based deep learning model allowed for the analysis of individual fragments and showed the potential for biomarker discovery. The model uses only cell-free DNA and excludes tissue sample DNA, which makes our model less sensitive to the tumor heterogeneity.