Clinical Context Research Articles

Integrated image and location analysis for wound classification: a deep learning approach

The global burden of acute and chronic wounds presents a compelling case for enhancing wound classification methods, a vital step in diagnosing and determining optimal treatments. Recognizing this need, we introduce an innovative multi-modal network based on a deep convolutional neural network for categorizing wounds into four categories: diabetic, pressure, surgical, and venous ulcers. Our multi-modal network uses wound images and their corresponding body locations for more precise classification. A unique aspect of our methodology is incorporating a body map system that facilitates accurate wound location tagging, improving upon traditional wound image classification techniques. A distinctive feature of our approach is the integration of models such as VGG16, ResNet152, and EfficientNet within a novel architecture. This architecture includes elements like spatial and channel-wise Squeeze-and-Excitation modules, Axial Attention, and an Adaptive Gated Multi-Layer Perceptron, providing a robust foundation for classification. Our multi-modal network was trained and evaluated on two distinct datasets comprising relevant images and corresponding location information. Notably, our proposed network outperformed traditional methods, reaching an accuracy range of 74.79–100% for Region of Interest (ROI) without location classifications, 73.98–100% for ROI with location classifications, and 78.10–100% for whole image classifications. This marks a significant enhancement over previously reported performance metrics in the literature. Our results indicate the potential of our multi-modal network as an effective decision-support tool for wound image classification, paving the way for its application in various clinical contexts.

Organoid-based personalized medicine: from tumor outcome prediction to autologous transplantation.

Inter-individual variation largely influences disease susceptibility, as well as response to therapy. In a clinical context, the optimal treatment of a disease should consider inter-individual variation and formulate tailored decisions at an individual level. In recent years, emerging organoid technologies promise to capture part of an individual's phenotypic variability and prove helpful in providing clinically relevant molecular insights. Organoids are stem cell-derived three-dimensional models that contain multiple cell types that can self-organize and give rise to complex structures mimicking the organization and functionality of the tissue of origin. Organoids represent thus a more faithful recapitulation of the dynamics of the tissues of interest, compared to conventional monolayer cultures, thus supporting their use in evaluating disease prognosis, or as a tool to predict treatment outcomes. Additionally, the individualized nature of patient-derived organoids enables the use of autologous organoids as a source of transplantable material not limited by histocompatibility. An increasing amount of preclinical evidence has paved the way for clinical trials exploring the applications of organoid-based technologies, some of which are in phase I/II. This review focuses on the recent progress concerning the use of patient-derived organoids in personalized medicine, including (1) diagnostics and disease prognosis, (2) treatment outcome prediction to guide therapeutic advice and (3) organoid transplantation or cell-based therapies. We discuss examples of these potential applications and the challenges associated with their future implementation.

STRUCTURE-ACTIVITY RELATIONSHIP OF 5,6-DIHYDRO-TETRAZOLO[1,5-c]QUINAZOLINES TARGETING CANDIDA GLABRATA

Candida species cause both disseminated and superficial fungal infections in humans. Although azole antifungals have historically proven effective in treating such infections, recent epidemiological studies highlight a crucial concern in the clinical context. Some Candida species exhibit inherent resistance to azoles and echinocandins, and the emergence of high-level resistance poses a significant problem. Consequently, derivatives of 5,6-dihydrotetrazolo[1,5-c]quinazolines have shown potent inhibitory properties against C. glabrata at concentrations range of 0.4 – 55.0 μM, leading to the identification of a structure-activity relationship.

Interprofessional practice and person-centred care: moral contexts and ethical conflicts in the US and Canada

Health and social care services and systems increasingly promote both interprofessional practice and person-centred care. This discussion first examines the clinical and community-based contexts for providing interprofessional practice and person-centred care through the lens of personal, interpersonal, interprofessional and organisational values. Emerging conflicts among values are highlighted using the concept of moral distress, with examples from US and Canadian settings. The comparison then moves to the systems level, examining different US and Canadian contexts for improving the quality and reducing the cost of care. Finally, implications and applications are presented, focusing on interrelationships among the individual, interprofessional team and organisation.

Public Health Risks of PFAS-Related Immunotoxicity Are Real.

The discovery of per- and polyfluoroalkyl substances (PFAS) in the environment and humans worldwide has ignited scientific research, government inquiry, and public concern over numerous adverse health effects associated with PFAS exposure. In this review, we discuss the use of PFAS immunotoxicity data in regulatory and clinical decision-making contexts and question whether recent efforts adequately account for PFAS immunotoxicity in public health decision-making. Government and academic reviews confirm the strongest human evidence for PFAS immunotoxicity is reduced antibody production in response to vaccinations, particularly for tetanus and diphtheria. However, recent events, such as the economic analysis supporting the proposed national primary drinking water regulations and clinical monitoring recommendations, indicate a failure to adequately incorporate these data into regulatory and clinical decisions. To be more protective of public health, we recommend using all relevant immunotoxicity data to inform current and future PFAS-related chemical risk assessment and regulation. Biological measures of immune system effects, such as reduced antibody levels in response to vaccination, should be used as valid and informative markers of health outcomes and risks associated with PFAS exposure. Routine toxicity testing should be expanded to include immunotoxicity evaluations in adult and developing organisms. In addition, clinical recommendations for PFAS-exposed individuals and communities should be revisited and strengthened to provide guidance on incorporating immune system monitoring and other actions that can be taken to protect against adverse health outcomes.

Care complexity, perceptions of complexity and preferences for interprofessional collaboration: an analysis of relationships and social networks in paediatrics

BackgroundIn the context of increasingly intricate healthcare systems, professionals are compelled to collaborate within dynamically changing interprofessional teams. Moreover, they must adapt these collaborative processes to effectively and efficiently manage the evolving complexity of care needs. It remains unclear how professionals determine care complexity and relate this complexity to their preferences for interprofessional collaboration (IPC). This study investigated the relationships between care complexity, professionals’ perceived complexity and IPC preferences, and examined the variation in individual and team characteristics of IPC-practices across different levels of complexity in paediatric care.MethodsIn an online questionnaire, 123 healthcare professionals working at an academic tertiary children’s hospital scored their perceptions of complexity and preferences for IPC. They also selected family and various professions as members of the interprofessional (IP-) team based on thirteen patient cases. We employed conjoint analysis to systematically model the complexity of case descriptions across the five domains of the International Classification of Functioning, Disability and Health (ICF). Additionally, we applied social network analysis to identify important professions, crucial connectors and influential professions in the IP-team, and to describe the cohesiveness of IP-teams.ResultsModelled case complexity, professionals’ perceived complexity and IPC preferences were positively associated. We found large inter-individual variations in the degree of these associations. Social network analysis revealed that the importance and influence of professions was more equally distributed when case complexity increased. Depending on the context and complexity of the case, different professions (e.g. medical doctors, social professionals, extramural professionals) were considered to be more crucial connectors within the IP-team. Furthermore, team cohesion was positively associated with modelled and perceived care complexity.ConclusionsIn conclusion, our study contributes to the existing knowledge by integrating task-specific insights and broadening the use of conjoint and social network analysis in the context of IPC. The findings substantiate the contingency theory that relates characteristics of IPC to care complexity, offering quantified insights into how IP-teams adapt to situational needs. This understanding of relationships and variations within IPC holds crucial implications for designing targeted interventions in both clinical and health profession education contexts. Consequently, it contributes to advancements in healthcare systems.

Don't Overlook Syphilis: An Atypical Rash in a Woman With Neurologic, Ocular, and Otic Involvement.

The manifestations of syphilis, a sexually transmitted infection caused by Treponema pallidum, can be divided into primary, secondary, or tertiary stages. In addition, syphilis can cause a latent infection with no clinical manifestations and be diagnosed solely by serologic testing. Secondary syphilis is especially known for causing a rash and diverse clinical manifestation which can make its diagnosis challenging-particularly in patients whose medical and sexual histories do not align with the classical epidemiologic and textbook description of secondary syphilis. We present a case of a 20-year-old immunocompetent heterosexual woman who presented with a rash atypical for secondary syphilis and accompanied by neurologic, ocular, and otic manifestations. This case highlights the importance of considering syphilis in the differential diagnosis of sexually active patients with a rash, even when their clinical presentations do not align with the textbook description of a syphilitic rash. Health care providers must remain vigilant for the diagnosis of syphilis in diverse clinical contexts, as early recognition and treatment are vital to prevent further syphilitic complications and transmission in military and civilian populations. Timely identification and intervention are crucial for both patient care and public health.

Defibrillator Lead Perforation Leading to Concerning Electrocardiogram Findings: Case Report

Introduction: Implantable cardioverter-defibrillator (ICD) lead perforation through the myocardium may result in chest pain and electrocardiogram (ECG) changes concerning for ST-segment elevation myocardial infarction. The clinical context of the ECG aids in appropriate management.Case Report: We report the case of a 71-year-old woman experiencing chest pain after an ICD placement two weeks earlier. On presentation, she exhibited ST-segment elevation on her ECG. Computed tomography confirmed ICD lead migration. The patient’s hemodynamics were normal, and she was discharged home after a five-day hospital stay following a lead revision.Conclusion: Although rare, ICD lead perforation is a potential cause of chest pain and ischemic ECG changes. Emergency physicians should consider lead perforation as a potential differential diagnosis when evaluating chest pain in patients with ICDs, taking into account the potential complications of coronary angiography.

Individual and Contextual Factors Associated with Adolescents' Self-Perceived Need for Treatment.

The present study aimed to investigate associations between the self-perceived dental treatment need and clinical factors, familial characteristics, and school context in adolescents. A cross-sectional study was conducted with a representative sample of 746 students aged 15 to 19 years in a medium-sized city in Brazil. Data collection involved the use of a sociodemographic questionnaire, an oral health questionnaire, and the Family Adaptability and Cohesion Scales (FACES III) instrument. Clinical examinations were performed by two trained and calibrated examiners (Kappa > 0.80) using the Nyvad criteria. A robust logistic regression analysis for complex samples was performed using a multilevel approach (α = 5%). The individual factors associated with the self-perceived treatment need were dental pain (OR = 1.08; 95% CI: 1.01-1.16), the loss of the first molars (OR = 1.09; 95% CI: 1.03-1.15), and disengaged family cohesion (OR = 1.15; 95% CI: 1.01-1.31). In terms of context, attending a public school was associated with the self-perceived treatment need (OR = 1.17; 95% CI: 1.02-1.33). Thus, the individual factors of toothache, tooth loss, and a disengaged family, as well as the school context, exerted an influence on the self-perceived treatment need.

Application of the ICF on students with disabilities at school in India

ICF serve as the basis for both the assessment and measurement of disability in many scientific, clinical, administrative and social policy contexts. However, few studies have used the application of ICF on students with disabilities in scientific and clinical context in India. The objective of this study is to identify the problems and record information by implementing the ICF as the basis for both the assessment and measurement of barriers/facilitator in students with disability in educational setting on clinical and social policy contexts. Method & procedure - A focus group of participants selected as to represent each level of school and each type of disability service provider working in rehabilitation institute. The group for the Identification Card included only teachers; that for the Functional Diagnosis was constituted only by multi-disciplinary health professionals from Disability Services; that for the Achievable Functional Goal Setting Profile and the Individual Educational Action Plan were mixed, including both teachers and operators from Disability Services. Results- In the school year 2021-23, the school sent 206 identification cards to disability services using the ICF model; the disability services issued 118 new disability certifications (57.3% of the received 206 identification cards). The school received 220 Functional Diagnosis from the disability services. The number of achievable functional goal setting profile stands at 132 and reached 54 number of Individual Educational Action Plan. Conclusion- In summary, the study suggested that to make any treatment effective for students with disabilities the medical, allied health expert like occupational therapist and the skilled teacher need to work hand in hand.

Abstract 6625: Development of novel mixed-cell models to capture heterogeneity in castration-resistant prostate cancer

Abstract Heterogeneity is ubiquitous in cancer and treatment responses among patient cohorts are highly variable, leading to drug resistance and disease relapse. Yet, preclinical drug screening is usually performed in cell lines or patient cells, one at a time, without consideration of cancer heterogeneity. Consequentially, positive outcomes obtained in the preclinical stage do not translate well into subsequent clinical successes. Castration-resistant prostate cancer (CRPC) is a highly lethal form of prostate cancer (PC) exhibiting a high degree of genetic and phenotypic heterogeneity with very few therapeutic options. Therefore, we created mixed-cell models depicting heterogeneity in various clinical contexts, where multiple PC cell lines representative of distinct CRPC tumor variants were labeled and combined in co-cultures to mimic the complex molecular landscape of CRPC patient cohorts. Specifically, transcriptomic profiles of PC cell lines were clustered with patient tumor specimens to identify cell lines that are genetically similar to distinct patient clusters representing CRPC tumor subtypes. Since heterogeneity has been linked to the clinical efficacy of combinatorial therapies, we applied these models to evaluate drug combinations. A combination of docetaxel and dasatinib that was previously assessed in a PC trial, was tested in the mixed-cell model and experimental findings concurred with the published clinical results, demonstrating the utility and accuracy of the model. Additionally, a computational model, IDACombo, was employed to nominate novel potentially efficacious drug combinations using monotherapy response data of cancer cell lines, a number of which were successfully validated in the mixed-cell model. More importantly, we demonstrated that while individual cell line screens may result in erroneous conclusions, combination efficacy can be accurately measured in a heterogeneous cell pool emulating a diverse patient cohort. We further explored phenotypic heterogeneity in advanced disease states, by mixing parent and standard-of-care (SOC)-resistant CRPC clonal variants. Drugs with selective potency in the resistant (vs. the parent) clone were computational prioritized and when combined with the SOC and tested in the mixed-cell models, outperformed either monotherapy. Additionally, we investigated the effects of altering the relative proportion of the constituent clones to mimic different stages of acquired therapy resistance. Furthermore, we generated mixed-cell xenograft models by subcutaneously injecting the labeled cell-line mixtures in mice and characterized the harvested tumors to detect and quantify the individual subpopulations. Development of these preclinical models holds enormous promise not only for advancing novel therapeutic strategies for cancer, but also for providing insights into the mechanisms of resistance and recurrence. Citation Format: Sampreeti Jena, Daniel Kim, Adam M. Lee, Weijie Zhang, Scott Dehm, R. Stephanie Huang. Development of novel mixed-cell models to capture heterogeneity in castration-resistant prostate 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 6625.

Transferable AmpCs in Klebsiella pneumoniae: interplay with peptidoglycan recycling, mechanisms of hyperproduction, and virulence implications.

Chromosomal and transferable AmpC β-lactamases represent top resistance mechanisms in different gram-negatives, but knowledge regarding the latter, mostly concerning regulation and virulence-related implications, is far from being complete. To fill this gap, we used Klebsiella pneumoniae (KP) and two different plasmid-encoded AmpCs [DHA-1 (AmpR regulator linked, inducible) and CMY-2 (constitutive)] as models to perform a study in which we show that blockade of peptidoglycan recycling through AmpG permease inactivation abolished DHA-1 inducibility but did not affect CMY-2 production and neither did it alter KP pathogenic behavior. Moreover, whereas regular production of both AmpC-type enzymes did not attenuate KP virulence, when blaDHA-1 was expressed in an ampG-defective mutant, Galleria mellonella killing was significantly (but not drastically) attenuated. Spontaneous DHA-1 hyperproducer mutants were readily obtained in vitro, showing slight or insignificant virulence attenuations together with high-level resistance to β-lactams only mildly affected by basal production (e.g., ceftazidime, ceftolozane/tazobactam). By analyzing diverse DHA-1-harboring clinical KP strains, we demonstrate that the natural selection of these hyperproducers is not exceptional (>10% of the collection), whereas mutational inactivation of the typical AmpC hyperproduction-related gene mpl was the most frequent underlying mechanism. The potential silent dissemination of this kind of strains, for which an important fitness cost-related contention barrier does not seem to exist, is envisaged as a neglected threat for most β-lactams effectiveness, including recently introduced combinations. Analyzing whether this phenomenon is applicable to other transferable β-lactamases and species as well as determining the levels of conferred resistance poses an essential topic to be addressed.IMPORTANCEAlthough there is solid knowledge about the regulation of transferable and especially chromosomal AmpC β-lactamases in Enterobacterales, there are still gaps to fill, mainly related to regulatory mechanisms and virulence interplays of the former. This work addresses them using Klebsiella pneumoniae as model, delving into a barely explored conception: the acquisition of a plasmid-encoded inducible AmpC-type enzyme whose production can be increased through selection of chromosomal mutations, entailing dramatically increased resistance compared to basal expression but minor associated virulence costs. Accordingly, we demonstrate that clinical K. pneumoniae DHA-1 hyperproducer strains are not exceptional. Through this study, we warn for the first time that this phenomenon may be a neglected new threat for β-lactams effectiveness (including some recently introduced ones) silently spreading in the clinical context, not only in K. pneumoniae but potentially also in other pathogens. These facts must be carefully considered in order to design future resistance-preventive strategies.

Abstract 4006: IL12-secreting CAR-T cells eliminate the requirement for lymphodepletion and promote epitope spreading via local antigen presenting cells

Abstract Introduction: EGFRvIII is a commonly studied tumor-specific antigen in glioblastoma (GBM) and poses an enticing target for immunotherapy. Its varied expression, however, complicates its effectiveness as a Chimeric Antigen Receptor (CAR) T cell target. Given the increasing prominence of Interleukin-12 (IL12) in treating solid tumors, its synergy with EGFRvIII specific CARs in treating preclinical models of GBM is explored. Methods: To simulate tumor heterogeneity, mice were implanted with equal ratios of CT2A and CT2A EGFRvIII+ cells. We developed EGFRvIII-specific third-generation CAR T cells, both with and without IL12 using a MSGV retrovirus backbone and transduced them into murine T cells. Their antitumor effectiveness was gauged by evaluating survival rates, and their capability to enhance and modify the tumor environment was determined using single-cell sequencing. Results: Standalone EGFRvIII CARs were unsuccessful in curing mice with heterogeneous tumors. However, 60% of mice treated with EGFRvIII CARs combined with IL12 were long term survivors. IL12 secreting CARs exhibited prolonged persistence in vivo, and there was no need for prior lymphodepletion before ALT introduction. Our studies reveal that EGFRvIII CARs secreting IL12 can eliminate EGFRvIII negative tumor cells by drawing on the inherent CD8 T cell compartment. Moreover, IL12 prominently impacted microglia among all Antigen Presenting Cells in the tumor environment, amplifying antigen presentation processes and broadening epitope exposure. Conclusion: By leveraging IL12, EGFRvIII CARs can counteract antigen heterogeneity in tumors by recruiting endogenous CD8 T cells and polarizing microglia. These IL12-secreting CARs outlast their traditional counterparts without requiring lymphodepletion. Harnessing CAR-T cells that secrete IL12 represents a novel strategy for overcoming tumor heterogeneity and treating GBM in a clinical context. Citation Format: Aditya Mohan, Steven Shen, Kelly Hotchkiss, Sarah Quackenbush, John Sampson, Peter Fecci, Anoop Patel. IL12-secreting CAR-T cells eliminate the requirement for lymphodepletion and promote epitope spreading via local antigen presenting cells [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 4006.

"Therapeutic potential of licorice extract in a prenatal valproic acid model of autism spectrum disorder in Wistar rats: Neurobehavioral and neurobiochemical insights"

Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), impose significant burdens on society due to their genetic and clinical complexity. We explored the therapeutic potential of Glycyrrhiza glabra (licorice) extract in a prenatal valproic acid (VPA) model of ASD. Neurobehavioral parameters encompassing social interaction, locomotor activity, repetitive behaviour, anxiety-related behaviour, and learning and memory were assessed in Wistar rat offspring. Licorice extract administration at 150 mg/kg and 300 mg/kg was initiated from postnatal day 21, emulating the developmental stage of early childhood. The study incorporated a controlled group, a VPA-induced ASD group, and groups treated with two different doses of licorice extract and Risperidone.Results revealed that licorice extract, particularly at 300 mg/kg, exhibited remarkable potential in restoring social interaction deficits, enhancing locomotor activity, attenuating repetitive behaviour, and mitigating anxiety-related behaviour-like behaviours. Furthermore, licorice extract displayed cognitive benefits, as evidenced by the discrimination index enhancement in object recognition memory. Importantly, licorice extract demonstrated modulatory effects on neuroinflammation and oxidative stress, evident through suppressed interleukin-6 (IL-6) and tumour necrosis factor-α (TNF-α) levels, as well as reduced thiobarbaturic acid reactive substances (TBARS) in the brain.These findings underscore the promising neuroprotective properties of Glycyrrhiza glabra extract against prenatal VPA-induced ASD-like behaviours. The elucidation of licorice's multifaceted impact on behaviour, cognition, and neurobiochemical markers offers a potential avenue for future therapeutic interventions for ASD, meriting further investigation in clinical contexts. This study contributes to the expanding knowledge of natural compounds in ameliorating complex neurodevelopmental disorders and highlights the necessity of multi-faceted approaches to address their intricate etiology and manifestation.

Abstract 6653: Oncolytic virotherapy induces a long-term immune antitumoral response leading to glioma eradication

Abstract Oncolytic herpes simplex viruses (oHSVs) have shown promise as effective treatments against various cancers. Our study evaluated the efficacy of R-115, an oHSV retargeted to human Her2 (hHer2), fully virulent in its target cells and expressing murine interleukin 12 (mIL12), in a high-grade, immunocompetent murine glioma model. This model is based on orthotopically transplant of cells derived from PDGFB-induced primary gliomas in syngeneic mice, engineered to express hHer2. Our experimental design compared the impact of R-115 on gliomas where all cells expressed hHer2 against a setup where only about 50% of cells expressed hHer2. The latter aimed to replicate the heterogeneity of patient’s high-grade gliomas, where not all cells express the target molecule. Strikingly, results in terms of overall survival and tumor eradication were similar in both setups, with about a quarter of animals showing complete glioma eradication. This suggests that mIL12-armed oHSV's impact is less about direct viral-induced cell death and more about the immune response elicited by the mIL12-expressing virus. This response effectively targets cells lacking the viral-targeted protein but likely sharing other neoantigens with hHer2-positive cells. Mice cured in both experimental setups were rechallenged with purely hHer2-negative cells. Almost all did not develop gliomas, indicating a strong immune response capable of rejecting the tumor. Plasma analysis revealed that R-115-treated mice from both setups were more immunoreactive against both hHer2-positive and negative cells compared to untreated mice. Further, co-culturing long-surviving mice's splenocytes with glioma cells showed increased cell division in CD8, CD4 and CD19 populations, and elevated IFN-γ, granzyme B, and TNF-α production. These findings underscore R-115's profound anti-cancer potential, especially its capacity to elicit an immune response effective against glioma cells, irrespective of their expression of the target molecule. This outcome, coupled with the results of the rechallenge experiments, is pivotal. It suggests that in a clinical context, an interleukin-12-expressing oHSV could effectively target not only residual cells post-surgical resection but also infiltrating cells that are distant from the site of virus administration. Encouraged by these promising findings, we are currently advancing our research with a novel oHSV that expresses mIL12 and targets EGFRvIII, a mutation found exclusively in tumor cells. This is aimed at enhancing the safety and translatability of this therapeutic approach. Citation Format: Francesca Piaggio, Francesco Alessandrini, Chiara Riviera, Irene Appolloni, Davide Ceresa, Daniela Marubbi, Tatiana Gianni, Gabriella Campadelli-Fiume, Paolo Malatesta. Oncolytic virotherapy induces a long-term immune antitumoral response leading to glioma eradication [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 6653.

Abstract 6199: Defining and capturing progression in glioma by harnessing NLP in unstructured electronic health records

Abstract Gliomas exhibit nearly uniform recurrence and poor prognosis. Management of high-grade tumors is surgery followed by chemoirradiation (CRT). Radiographic progression is assessed using contrast-enhanced MRI with reporting captured in Electronic Health Records (EHR). The ability to harness large scale EHR data is limited by the Response Assessment in Neuro-Oncology (RANO) tumor progression criteria, which defines progression as an aggregate of clinical and/or radiographic parameters requiring clinician judgement. As a result, glioma progression is not captured systematically in large data sets, limiting Progression Free Survival (PFS) as an outcome endpoint in data analysis. We developed an AI-based method using natural language processing to capture PFS parameters for analysis of MRI radiology reports. 1088 available brain MRI radiology reports for 81 patients with a pathologically confirmed diagnosis of glioblastoma (GBM) were aggregated in the NIH Integrated Data Analysis Platform. MRI reports were systematically analyzed and PFS manually captured using RANO criteria as ground truth. Common report terms indicating progression were compiled and included in task prompts applied to Large Language Model (LLM) Extraction Tools. The words progression (n=1047) and stable (n=1133) did not necessarily indicate either overall progression or stability in a report. Yet, in the 24 (30%) patients who progressed within 3 months of CRT, recurrence and mass effect occurred in 3.7% and 53% of reports, respectively, which was comparable to the term frequencies of 5.8% and 54% in patients with stable disease. Thus, mass effect and recurrence could not necessarily be used alone as terms to signal overall progression. The analysis identified other commonly employed radiology report terms relevant to determining tumor progression including enhancement (n=2445), perfusion (n=2085), enhancing (n=1785), resection (n=1576), and increased (n=1331), which allowed for experimentation with more detailed LLM extraction task prompts. Our method flagged radiographic progression prior to clinician-coded progression in 43 (53%) patients. Future directions include handling further clinical context such as surgical features, radiation therapy dates, progress notes, and the coadministration of agents such as bevacizumab and steroids. These results indicate the feasibility of LLMs to identify tumor progression dates using EHR text with potential transferability to large glioma data sets pending further optimization and validation. Citation Format: Shreya Chappidi, Hawon Lee, Sarisha Jagasia, Casey Syal, George Zaki, Dylan Junkin, Nathan Golightly, Patrick Chitwood, Kevin Camphausen, Andra Krauze. Defining and capturing progression in glioma by harnessing NLP in unstructured electronic health records [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 6199.

Abstract 2532: Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia

Abstract The BCL2 protein family controls apoptosis by shifting the dynamic equilibrium state of complex formation. BH3 mimetics disrupt this balance by disturbing the interaction of a specific anti-apoptotic protein, leading to the initiation of apoptosis. However, relying solely on molecular data for the specific anti-apoptotic protein can be challenging due to the functional redundancy within the BCL2 protein family and their complex interaction network. Therefore, comprehensive profiling information considering protein complexes is essential to determine apoptotic dependencies, particularly in a clinical context. In this study, we adapted a Single-molecule Protein Interaction Detection (SPID) platform that can assess levels of protein complexes in a quantitative manner. Out of the 47 metrics included in our Apoptosis Signaling 47 panel, we utilized 22 assays to measure apoptosis dependencies in acute myeloid leukemia (AML) cells obtained from 32 patients. By combining these metrics, we developed a predictive model for the ex vivo response to ABT-199 treatment, focusing on three key biomarkers: BCL2-BAX complex, BCL2-BIM binding potential, and BCLxl-BAK level. From a receiver operating curve (ROC) analysis, the model exhibited high accuracy with a value of 0.94 area under the curve (AUC). We further validated our model by comparing the predicted response to the therapeutic outcomes in 10 AML patients according to the 2017 ELN guidelines, and achieved 100% sensitivity (4 out of 4 identified correctly) and 83.3% specificity (5 out of 6 identified correctly). Overall, our platform provides an effective method to explore apoptosis dependencies in clinical samples based on the information regarding protein complexes within the BCL2 protein family. Three key molecular biomarkers can be translated into a gauge for predicting therapeutic outcomes of BH3 mimetics, suggesting an improvement of precision medicine in AML treatment. Citation Format: Hongwon Lee, Changju Chun, Byungsan Choi, Saem Hong, Yunseo Lee, Youngil Koh, Tae-Young Yoon. Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia [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 2532.

Abstract 4560: Assessing cancer drug combination efficacy across 900+ PRISM cell lines in a multiplexed screening assay

Abstract Combination therapies are crucial in cancer care, yet identifying which combination will benefit a specific patient is challenging. The vast array of clinical, investigational, and tool anticancer agents and diverse cancer contexts makes investigating many drug combinations over a large number of cell lines infeasible. Here, we describe a multiplexed screening approach using the PRISM assay, where drug combinations are screened on >900 DNA-barcoded cancer cell lines. We analyze cell viability data in drug combinations and single agents using established metrics to describe the combined effects such as additivity, synergy, and antagonism. Quantifying and classifying combined effects will help prioritize specific combinations for follow-up investigations and provide biological and mechanistic insights, thus enabling rationally designed combination therapies. We illustrate our methodology through data from three drug combinations that exemplify synergy and antagonism. In the first combination, temozolomide+O6-benzylguanine (alkylating agent + MGMT inhibitor), we found that cell lines expressing MGMT were sensitized to temozolomide in the presence of O6-benzylguanine, thus illustrating synergy. In the second combination, we screened two anti-apoptosis compounds A-1331852+AZD5991 (BCL-xL + MCL1 inhibitor) and found that BCL-xL and MCL1 inhibition were also synergistic. In the third combination, ML210+ferrostatin-1 (GPX4 inhibitor inducing ferroptosis + ferroptosis inhibitor), we found that ferrostatin-1 antagonized the effects of ML210. Our analysis also reveals the importance of appropriate dose selection and analytical metrics for reliably measuring combined effects. In conclusion, the PRISM platform's multiplexed cell line screening is a robust method for characterizing rationally designed drug combinations, offering a systematic approach to enhance the precision of combination therapy development in cancer care. Citation Format: Ashish Bino George, Shiker Nair, Mustafa Kocak, Ellen Nguyen, Alvin Kalathungal, Anthony Fazio, Cole Ponsi, Aydin Golabi, Melissa A. Ronan, Matthew G. Rees, Jennifer A. Roth. Assessing cancer drug combination efficacy across 900+ PRISM cell lines in a multiplexed screening assay [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 4560.

Abstract 3834: Plasmablastic lymphoma provisional prognostic score

Abstract Background Plasmablastic Lymphoma (PBL) is a rare and aggressive subtype of non-Hodgkin's lymphoma. It tends to be associated with immunosuppressive clinical contexts, such as HIV infection and immunosuppressive therapies for autoimmune disorders and organ transplants. However, due to the rarity of the disease, which needs to be better understood, varied treatment approaches have been implemented, and no optimal data or guidelines for managing PBL are available. Therefore, we conducted this study to develop a provisional PBL prognostic score (PBLPS) for this rare disease. Methods We used our constructed PBL database, which contains retrospective data on 300 cases. Such data included demographics such as sex, age, and race. It also included disease presentation symptoms, duration of symptoms before diagnosis, site(s) of the disease, blood counts, coexisting comorbidities, disease immunohistochemical and molecular phenotype, types of treatment, and survival outcomes. Of the 300 cases, 291 had complete survival and outcomes data, the sample chosen for this study. Cox proportional-hazards model and Log-rank tests were used to assess the influence of clinicopathologic factors on overall survival (OS). We included factors that statistically impacted OS and scored them by the impact of their hazard ratios. Results The median OS of the cohort was 25 months. The following dichotomous variables were identified as impactful prognostic factors in this cohort: LDH>500 (p=0.04), CD4<100 (p=0.006), bone marrow (BM) involvement (p<0.0001), EBER-negative (p=0.01), HHV8+ (p=0.02), and involvement of liver (p=0.003), lungs/pleura (p<0.0001), and upper GI tract (p=0.001). A prognostic model was devised using these variables to identify different levels of risk. Involvement of BM and involvement of any of the worse prognosis organs (liver, lung/pleura, and/or upper GI tract) were each assigned a score of 2 when present. CD4<100, EBER-negative, and LDH>500 were assigned 1 point each as they had the lowest hazard ratios of all the other variables. In this exploratory cohort, we assigned low risk a score of 0, intermediate risk a score of 1-2, and high risk a score of 3-7. This prognostic score system led to our cohort's most optimal risk discriminatory model, where low, intermediate, and high risk had a median OS of NR, 15, and 4 months, respectively (p<0.0001). Conclusion This PBLPS is a promising new tool for risk-stratifying patients with PBL. However, it still requires prospective validation. Citation Format: Philip A. Haddad, Jaren Lerner. Plasmablastic lymphoma provisional prognostic score [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 3834.

Abstract 5673: Transposable element expression patterns in epigenetic mutational subtypes of clear cell renal cell carcinoma

Abstract Background: Clear cell renal cell carcinoma (ccRCC) is characterized by mutations in epigenetic modulators and by aberrant transposable element (TE) expression, each of which have been separately associated with immunotherapy (IO) benefit in specific clinical contexts. However, the relationship between mutations in epigenetic regulators and TE expression, and the potential effect of both somatic mutations and TE expression on clinical outcomes, has not been fully investigated. Methods: We utilized RNA sequencing from ccRCC patients’ tumors and cell lines to quantify TE subfamily expression with TEtranscripts (n=123 metastatic IO-treated; CheckMate-009, 010, 025, n=355 all stage TCGA untreated, n=8 CCLE). Locus-specific endogenous retrovirus (ERV) expression was quantified using hervQuant. Differential TE and ERV expression was determined using DESeq2. Samples were stratified by mutations in PBRM1, SETD2, BAP1 and KDM5C, four of the top five mutated genes in ccRCC. Multivariable CoxPH models and the log-rank test were used to compare overall (OS) and progression-free survival (PFS). Two validation metastatic ccRCC cohorts were employed: the everolimus arm of CheckMate-025 (n=78, CM025e) and IMmotion150 (n=146, IM150). Results: Global TE expression (LTR, LINE, SINE and DNA transposons) did not differ significantly across mutational and clinical subtypes. However, 29 of 795 TE subfamilies were differentially expressed in >1 mutational subtype across datasets, and 22 of 29 were ERVs. At locus-specific resolution, 52 of 3173 ERVs were differentially expressed in >1 mutational subtype across datasets. Additionally, 6 of the 52 ERVs nominally associated with PFS, and 4 nominally associated with OS, in the IO cohort. Among them, only ERVs 544 and 2014 associated with improved PFS (multivariable CoxPH p = 0.03 and 0.02, respectively) and were expressed across all datasets. Both ERVs also exhibited increased expression in PBRM1 mutant and decreased expression in BAP1 mutant vs. wildtype samples, in discovery (IO, TCGA, CCLE) and validation (CM025e, IM150) cohorts. Lastly, PBRM1 mutant patients with high ERV 544 or 2014 expression had improved PFS in the IO (log-rank p = 0.04 and 0.03, multivariable CoxPH p = 0.008 and 0.009, respectively, HR = 0.43 both), but not in the CM025e cohort, compared to other patients regardless of PBRM1 mutations. Conclusion: ERVs 544 and 2014 were upregulated in PBRM1 mutant and downregulated in BAP1 mutant samples. Coupled with PBRM1 inactivation, their expression served as a candidate biomarker of improved PFS in IO-treated ccRCC that may have additional biological relevance. Expanded functional and clinicogenomic studies of epigenetic mutational subtype-specific patterns of TE expression, and their relation to selective IO response, may guide additional discovery and therapeutic development strategies in ccRCC. Citation Format: Kevin Meli, Cora A. Ricker, Sabrina Y. Camp, Christof C. Smith, Chris Labaki, Eddy Saad, Hanna Soulati, Brendan Reardon, Jihye Park, Natalie I. Vokes, Benjamin G. Vincent, Toni K. Choueiri, David A. Braun, Eliezer M. Van Allen. Transposable element expression patterns in epigenetic mutational subtypes of clear cell renal cell 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 5673.