julilili42/papers huggingface dataset:
KEYNOTE-905/EV-303: A phase 3 study to evaluate the efficacy and safety of perioperative pembrolizumab or pembrolizumab plus enfortumab vedotin (EV) for muscle-invasive bladder cancer (MIBC).
2023-06-01

TPS4601 Background: Standard of care for MIBC is neoadjuvant cisplatin-based chemotherapy followed by radical cystectomy + pelvic lymph node dissection (RC + PLND), but many patients with MIBC are ineligible for cisplatin-based chemotherapy. In the phase 1b/2 KEYNOTE-869/EV-103 study, combination therapy with the PD-1 inhibitor pembrolizumab and the Nectin-4–directed antibody-drug conjugate EV showed promising antitumor activity in cisplatin-ineligible patients with locally advanced or metastatic urothelial carcinoma. KEYNOTE-905/EV-303 (NCT03924895) is a multicenter, randomized, open-label, phase 3 study to evaluate efficacy and safety of perioperative pembrolizumab alone or combined with EV versus RC + PLND alone in patients with MIBC who are ineligible for or decline cisplatin-based treatment. Methods: Patients with treatment-naive MIBC (T2-T4aN0M0 or T1-T4aN1M0) and predominantly (≥50%) urothelial histology who are cisplatin ineligible or decline cisplatin-based treatment and have an ECOG PS score of 0-2 are eligible. Cisplatin ineligibility will be defined as meeting ≥1 of the following criteria: impaired renal function with calculated creatinine clearance 30-59 mL/min; ECOG PS 2; grade ≥2 audiometric hearing loss per CTCAE v4.0; or NYHA class III heart failure. Patients will receive neoadjuvant pembrolizumab 200 mg intravenously (IV) every 3 weeks (Q3W) for ≤3 cycles followed by RC + PLND and adjuvant pembrolizumab 200 mg IV Q3W for ≤14 cycles (arm A); RC + PLND followed by observation (adjuvant nivolumab permitted based on clinical indication and regulatory approval [arm B]); or neoadjuvant EV 1.25 mg/kg + pembrolizumab 200 mg IV Q3W for ≤3 cycles followed by RC + PLND and adjuvant EV + pembrolizumab for ≤6 cycles and adjuvant pembrolizumab 200 mg IV Q3W for ≤8 cycles (arm C). In the neoadjuvant and adjuvant phases of arm C, pembrolizumab will be administered on day 1 and EV will be administered on days 1 and 8 of each cycle. Enrollment is complete for arm A; patients will continue to be randomly assigned 1:1 to arm B or arm C. Stratification factors are tumor stage (T2N0 vs T3/T4aN0 vs T1-T4aN1), geographic region (United States vs Europe vs most of world), and cisplatin eligibility (cisplatin ineligible or cisplatin eligible but declines treatment). The primary end point is event-free survival between arm B and arm C. Secondary end points are event-free survival (arm A vs arm B) pathologic complete response, overall survival, disease-free survival, pathologic downstaging rates, and safety. Enrollment is planned for 308 patients, and recruitment is ongoing in Africa, Asia, Australia, Europe, North America, and South America. © 2023 American Society of Clinical Oncology, Inc. Reused with permission. This abstract was accepted and previously presented at the 2023 ASCO-GU Annual Meeting. All rights reserved. Clinical trial information: NCT03924895 .
Quality assurance within the context of genome diagnostics (a german perspective)
2023-06-01

Abstract The rapid and dynamic implementation of Next-Generation Sequencing (NGS)-based assays has revolutionized genetic testing, and in the near future, nearly all molecular alterations of the human genome will be diagnosable via massive parallel sequencing. While this progress will further corroborate the central role of human genetics in the multidisciplinary management of patients with genetic disorders, it must be accompanied by quality assurance measures in order to allow the safe and optimal use of knowledge ascertained from genome diagnostics. To achieve this, several valuable tools and guidelines have been developed to support the quality of genome diagnostics. In this paper, authors with experience in diverse aspects of genomic analysis summarize the current status of quality assurance in genome diagnostics, with the aim of facilitating further standardization and quality improvement in one of the core competencies of the field.
visMOP – A Visual Analytics Approach for Multi‐omics Pathways
2023-06-01

Abstract We present an approach for the visual analysis of multi‐omics data obtained using high‐throughput methods. The term “omics” denotes measurements of different types of biologically relevant molecules like the products of gene transcription (transcriptomics) or the abundance of proteins (proteomics). Current popular visualization approaches often only support analyzing each of these omics separately. This, however, disregards the interconnectedness of different biologically relevant molecules and processes. Consequently, it describes the actual events in the organism suboptimally or only partially. Our visual analytics approach for multi‐omics data provides a comprehensive overview and details‐on‐demand by integrating the different omics types in multiple linked views. To give an overview, we map the measurements to known biological pathways and use a combination of a clustered network visualization, glyphs, and interactive filtering. To ensure the effectiveness and utility of our approach, we designed it in close collaboration with domain experts and assessed it using an exemplary workflow with real‐world transcriptomics, proteomics, and lipidomics measurements from mice.
EGFR expression and relapse in patients with melanoma receiving adjuvant PD-1-based immunotherapy.
2023-06-01

e21566 Background: Since 2018, adjuvant immune checkpoint inhibitors (ICI) have been available for patients with resected stage III/IV melanoma. The Checkmate 238 and Keynote 054 studies showed a survival benefit in patients receiving adjuvant ICI. However, there is no validated biomarker to identify patients at high risk of relapse, despite receiving adjuvant therapy. Here we investigated resistance patterns to immune checkpoint inhibition in the adjuvant setting. Methods: In this cohort study, a discovery cohort of 30 patients from the Department of Dermatology, University Hospital Zürich, was used to evaluate resistance patterns to adjuvant ICI. A second cohort of 107 patients from the Department of Dermatology, University Hospital Tuebingen, was used to validate the findings. We measured epidermal growth factor receptor (EGFR) expression in primary tumor and metastatic tissue by immunohistochemistry and digital pathology using QuPath. The primary endpoint was relapse-free survival. Results: We included 137 patients with melanoma receiving adjuvant ICI: 63 (46%) were females, and 52 (38%) patients harbored a BRAFV600 mutation. The median follow-up was 45 and 39 months in the Zürich and Tuebingen cohorts, respectively (95% confidence interval (CI) 41.8-48.2 and 36.8-41.2, respectively). The two cohorts were homogenous in terms of patients' and tumor characteristics, except for the relapse rate, which was significantly higher in the Tuebingen cohort ( p&lt; 0.002). 71 (52%) therapy naïve in transit or lymph node metastasis and 23 (17%) primary tumors were available to evaluate EGFR expression by immunohistochemistry and digital pathology using QuPath. Surprisingly, in both cohorts, patients with high EGFR expression in metastatic tissue had a significantly higher relapse rate than patients with low EGFR expression ( p= 0.0004 and p= 0.0168 for the Zürich and Tuebingen cohorts, respectively). EGFR expression in primary tumors did not correlate with relapse-free survival ( p= 0.7286). Next-generation sequencing revealed that EGFR expression assessed by immunohistochemistry was not associated with the presence of EGFR mutations and/or amplifications. Conclusions: Currently, there are no validated biomarkers to identify patients with melanoma at high risk of recurrence, despite receiving adjuvant ICI. We found in two independent cohorts that EGFR expression in therapy naive metastatic tissue is positively associated with relapse in patients receiving adjuvant ICI. Our data identified EGFR as a prognostic biomarker that can easily be assessed by immunohistochemistry, allowing us to stratify patients for adjuvant ICI therapy according to their risk of relapse. Stratification according to EGFR expression should be considered in future clinical trials in the adjuvant setting.
Clinical development of the bispecific PSMAxCD3 antibody CC-1.
2023-06-01

2534 Background: While being highly efficient in hematological malignancies, bispecific antibodies (bsAbs), alike CAR T cells, are yet not successful in solid tumors. Moreover, all available T cell-mobilizing strategies cause side effects that endanger patients and, in case of bsAbs, limit applicable doses and thus efficacy. We report on the clinical development of CC-1, a PSMAxCD3 bsAb, in an IgG-based format that induces fully target cell-restricted T cell activity (Zekri et al, EMBO Mol Med, 2020). Targeting PSMA, which is expressed on malignant cells and on the neovasculature, improves accessibility of the tumor site for immune effector cells as critical prerequisite for success in solid tumors. Notably, CC-1 binds a unique PSMA epitope which is expressed on malignant cells both of prostate carcinoma (PC) and 50% of patients with squamous cell carcinoma (SCC) of the lung. Methods: A FIH trial evaluating CC-1 with pre-emptive Tocilizumab included patients with metastatic castration resistant prostate carcinoma (mCRPC) (NCT04104607) and consisted of two parts. Dose escalation (n=10-66) using a novel intra-individual dose escalation design to rapidly reach the target dose of 826μg to determine safety, tolerability and maximum tolerated dose (MTD) (Labrenz et al, Pharm Stat, 2022). The dose expansion cohort exposed patients to CC-1 at MTD and explored efficacy to define RP2D (n=14). Our second phase I trial enrolls patients with SCC of the lung (NCT04496674) to receive CC-1 in combination with checkpoint inhibition. Based on the meanwhile available very favorable safety and preliminary efficacy data, a third phase I trial was initiated where CC-1 is evaluated as first line treatment in patients with hormone sensitive biochemical recurrence (BCR) of PC (NCT05646550), where tumor burden is low and accordingly lower side effects and long-lasting efficacy are expected. Results: Recruitment in the dose escalation part of the trial in mCRPC has been completed and the target dose was reached and MTD defined without DLT upon treatment of the 9 th and 14 th patient, respectively. 24 patients completed treatment, with the most frequently observed toxicity being cytokine release syndrome (CRS, max. 2°) (88%). Besides grade 1 to 2 hypertension (46%) and xerostomia (8%), no further CC-1 related toxicities were observed. A rapid and profound decline of elevated PSA levels was observed in all but one patient, with up to 60% reduction compared to baseline. So far 5 patients received multiple treatment cycles at MTD-level. One patient with SCC of the lung has been treated and CC-1 was escalated up to 153μg without occurrence of CRS. In the phase I trial in BCR of PC, the first three patients were enrolled in February 2023. Conclusions: CC-1 is a promising compound with a favourable toxicity profile and promising clinical activity. Details on study designs and updated data from the 3 clinical trials will be presented at the meeting. Clinical trial information: NCT04104607 , NCT04496674 , NCT05646550 .
EO2401 (E) peptide immunotherapy + nivolumab (N) +/- bevacizumab (B) in recurrent glioblastoma (GB): EOGBM1-18/ROSALIE.
2023-06-01

2020 Background: EO2401 was designed to activate/expand existing memory T cells recognizing specific protein sequences from gut bacteria, which cross-react with tumor associated antigens (TAAs). E contains 3 CD8 HLA-A2 epitopes with mimicry to GB-TAAs (IL13Rα2, BIRC5, and FOXM1) and the CD4 epitope UCP2. Methods: Patients (pt) at 1st progression GB received E (300 μg/peptide, q2w x4 then q4w) with N (3 mg/kg q2w) in cohorts: 1a E x2 → EN; 2a/1, 2a/2 and 2b EN from start; 2c EN x2 → surgery → EN; 3/1 and 3/2 EN + B (10mg/kg q2w) (Table). Results: Among 100 treated pt EN+/-B was well tolerated, with E associated events limited to local skin reactions (45% of pt; 96% Grades 1/2, and 4% Grade 3) and N-/B-tox consistent with historical data. EN induced immune response against all 3 mimics in 94% of 35 tested pt (all pt responded against at least 2 mimics), detectable as early as 2 weeks after first EN, and with durations beyond 10 months. Cross-reactivity against human peptides found in 89%. Conclusions: EN +/- B was well tolerated and generated fast and durable immune responses. EN survival like current standards. Delayed N was not advantageous for outcome. sLDB increased trt duration of EN, and improved efficacy. Continuous B plus EN further improved efficacy. Neo-/adjuvant EN was clinically feasible. Updated data, including C3/2 to confirm C3/1, to be presented. Clinical trial information: NCT04116658 . [Table: see text]
Modern Novel Writing in the Eighteenth Century: ‘Classic’ and Later Perspectives
2023-06-01

Abstract This article provides a recapitulation of Ian Watt’s classic account of the rise of the novel in terms of the rise of the middle class which finds its ideological equivalent in the rise of formal realism. While this account has been frequently countered by revisionist approaches in a largely new historicist mode, which insist that the historical multifariousness of modern novel writing in the eighteenth century is not fully captured by Watt (Lennart J. Davis, Michael McKeon, J. Paul Hunter, Jane Spencer, Nancy Armstrong and Janet Todd in the 1980s, Marcie Frank, Jordan Alexander Stein and Mike Goode more recently), it has not really lost its persuasiveness to this day. As the article tries to show, this persuasiveness rests on the ideological implications of Watt’s account of early novelistic practice rather than its actual historical implementation. This diagnosis has recently been confirmed by Mike Goode’s approach to Sir Walter Scott’s and Jane Austen’s ‘synthesis’ of fully developed formal realism in terms of ‘media behaviors’ and their affordances. In the case of Jane Austen, for example, the fact that later media usage in fanfiction tends to turn to narrative techniques from before Austen’s synthesis (letters, journals, etc.) points to the (perceived) ideological limitations of her technical achievement of smooth assimilation of multiple points of view into a naturalized third-person narrator’s discourse. This opens up new perspectives on Smollett’s practice of unassimilated multiperspectivity, especially in his last novel The Expedition of Humphry Clinker (1771).
Hypothalamic volumes predict sleep dysfunction in genetic frontotemporal dementia
2023-06-01

Abstract Background Sleep dysfunction is common in neurodegenerative disorders, however, its neural correlates, remain poorly characterized in genetic frontotemporal dementia (FTD). Atrophy in two hypothalamic nuclei, the suprachiasmatic nucleus and the lateral hypothalamic area, important for sleep regulation, may be related to this dysfunction. Thus, we examined changes in cerebral and hypothalamic structure across the lifespan in genetic FTD and their relations to measures of sleep dysfunction. Method Data was retrieved from the Genetic Frontotemporal Dementia Initiative (GENFI). T1‐weighted structural MRI images and scores on the Cambridge Behavioural Inventory‐Revised (CBI‐R) sleep subscale were obtained from subjects with mutations causative of FTD (n = 491, scan number = 1029) and healthy controls (n = 321, scan number = 739). MRI images were processed for cortical thickness using CIVET 2.1 and hypothalamic volumes using a deep learning segmentation algorithm (Billot et al., NeuroImage 2020). Using linear mixed‐effects models, we examined changes in sleep dysfunction, vertex‐wise differences in cortical thickness, and volumetric changes in hypothalamic regions in mutation carriers compared to controls. Further, using linear mixed‐effects models, we examined associations between cortical and hypothalamic atrophy and changes in the CBI‐R sleep subscale while controlling for age, sex, scanning site, and disease severity based on the MMSE. Result Mutation carriers showed greater sleep dysfunction across the lifespan, and this increased closer to the predicted onset of symptoms, compared to controls (p &lt; 0.01), with MAPT carriers having greater dysfunction overall (figure 1). All mutation carriers showed patterns of cortical thinning (figure 2) commensurate with the literature (p &lt; 0.05, FDR corrected). Further, cortical thinning in frontal and parietal regions were associated with greater sleep disturbance in C9orf72 and GRN mutation carriers (p &lt; 0.05, FDR corrected) (figure 3). Lastly, MAPT mutation carriers showed consistently significant hypothalamic volume loss across the lifespan (figure 4) (p &lt; 0.01) and reduced hypothalamic volumes were related to increased sleep dysfunction (p &lt; 0.05) (Figure 5). Conclusion These findings suggest that while cortical thinning in C9orf72 and GRN carriers non‐specifically correlate with increased sleep dysfunction, the increased sleep dysfunction observed in MAPT carriers may be attributable to increased hypothalamic atrophy.
Interim analysis of MelaRisk, a biomarker assay validation study in stage IB/IIA melanoma tissue.
2023-06-01

e21591 Background: Adjuvant therapy for melanoma patients (pts) is now available for pts from stage IIB onwards. Pts with cutaneous melanoma in early stages stage IB/IIA have low risk of relapse. However, this group still contributes to the most melanoma deaths in absolute numbers. Therefore, it is important to identify pts in stage IB/IIA that could benefit from adjuvant therapy. One promising biomarker is a proprietary 7-protein immunohistochemistry (7-P-IHC) signature (Immunoprint). Based on primary tumor tissue analysis, the 7-P-IHC has shown very high sensitivity and risk enhancement ability in previous prospective and retrospective validations. 1,2 The 7-P-IHC test result indicates a risk score predicting relapse-free and melanoma-free survival (RFS, MSS), thereby allocating most relapses to the high score risk group. To further validate its key parameters, the MelaRisk trial was started in 2022, aiming to analyze up to 500 tissue samples with Immunoprint. Here we present its interim analysis and a combined analysis of all available data for Immunoprint in stage IB/IIA. Methods: All pts with available formalin-fixed paraffin-embedded blocks of the Central German Melanoma Registry diagnosed from 2005-16 and AJCC v8 stage IB/IIA were screened. Tumor tissue samples from 119 pts (83/IB; 36/IIA) were available; the 7-P-IHC was used to determine a risk group. Results: 7-P-IHC assigned 68 pts to the low-risk (57%) and 51 (43%) to the high-risk group. Median follow-up was 76 months. 15/17 relapses after 5-years were detected, resulting in a sensitivity of 88%. 5-years RFS event rate of the cohort according to AJCC v8 was 12% and 19% for stages IB and IIA, respectively. This was enhanced to a risk of recurrence of 30% (stage IB) and 29% (stage IIA) in the respective high score group. 5y-RFS rate was 97% for pts with 7-P-IHC low score risk and 71% for pts with 7-P-IHC high score risk (p=0.0001). 7-P-IHC was the only significant factor in a multivariate Cox analysis for RFS (HR 10.78 (2.38-48.74), p=0.002) and could detect 4/5 MSS events. Combined analysis including these and previous Immunoprint results in stage IB/IIA are summarized in the table. Conclusions: 7-P-IHC could concentrate 88% of stage IB/IIA RFS events in a small high score risk group. This group entails 43% of pts of the total cohort, correctly identifying pts needing adjuvant therapy. Immunoprint should be used to select pts in future studies in the adjuvant setting if these promising interim results can be confirmed in the final analysis. 1. Meyer et al. (2023) EJC; 2. Reschke et al. (2021). [Table: see text]
CAPTOR-BC: Comprehensive analysis of spatial, temporal and molecular biomarkers predicting response and resistance to first-line treatment with ribociclib + ET in HR+, HER2- advanced breast cancer.
2023-06-01

TPS1124 Background: The combination of an oral CDK4/6 inhibitor with endocrine therapy (ET) has become the standard first-line therapy for women with advanced HR+ HER2- breast cancer. In this context, the broadest clinical trial data are available for ribociclib, a highly selective CDK4/6 inhibitor, with three phase III trials (MONALEESA-2, -3 and -7) consistently showing a significant overall survival benefit compared to ET monotherapy regardless of treatment line, menopausal status or combination partner. However, de novo or acquired resistance to CDK4/6 inhibitors does occur and biomarkers predicting treatment response or providing information on resistance mechanisms are only beginning to be understood. Comprehensive identification and validation of biomarkers before and during ribociclib therapy is needed to better understand mechanisms leading to disease progression, which will be the first step towards developing novel therapies and optimizing treatment sequences. Methods: CAPTOR-BC (NCT054552213) is a single-arm, open-label phase IV study evaluating the combination of ribociclib and ET according to SmPC in the first-line treatment of HR+ HER2- advanced breast cancer to identify and validate molecular and non-molecular biomarkers predictive of drug response and resistance. First patient first visit occurred in October 2022 and at least 1000 patients across more than 75 sites in Germany will be enrolled until October 2025. Progression-free survival (PFS) and overall survival (OS) at 12 months are the co-primary endpoints, quality of life (QoL) and toxicity are secondary endpoints. Exploratively, a comprehensive multi-omics biomarker discovery and validation program is integrated into the study: Besides tumor tissue, liquid biopsies profiling circulating tumor (ct)DNA, ctRNA, whole blood RNA, proteins from serum and plasma, and circulating immune cells will be evaluated before, during and after treatment or upon progression to determine correlations with PFS, OS, QoL and adverse events. Clinical trial information: NCT05452213 .
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction
2023-06-01

Abstract Motivation Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently, no such dataset for the exploration of Plasmodium falciparum protein antigen candidates exists. The parasite P.falciparum causes the infectious disease malaria. Thus, identifying potential antigens is of utmost importance for the development of antimalarial drugs and vaccines. Since exploring antigen candidates experimentally is an expensive and time-consuming process, applying machine learning methods to support this process has the potential to accelerate the development of drugs and vaccines, which are needed for fighting and controlling malaria. Results We developed PlasmoFAB, a curated benchmark that can be used to train machine learning methods for the exploration of P.falciparum protein antigen candidates. We combined an extensive literature search with domain expertise to create high-quality labels for P.falciparum specific proteins that distinguish between antigen candidates and intracellular proteins. Additionally, we used our benchmark to compare different well-known prediction models and available protein localization prediction services on the task of identifying protein antigen candidates. We show that available general-purpose services are unable to provide sufficient performance on identifying protein antigen candidates and are outperformed by our models that were trained on this tailored data. Availability and implementation PlasmoFAB is publicly available on Zenodo with DOI 10.5281/zenodo.7433087. Furthermore, all scripts that were used in the creation of PlasmoFAB and the training and evaluation of machine learning models are open source and publicly available on GitHub here: https://github.com/msmdev/PlasmoFAB.