Molecular Characterization Of Tumors Research Articles

Bringing Hope to Improve Treatment in Pancreatic Ductal Adenocarcinoma—A New Tool for Molecular Profiling of KRAS Mutations in Tumor and Plasma Samples

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) incidence is rising, and prognosis remains poor due to late diagnosis and limited effective therapies. Currently, patients are treated based on TNM staging, without molecular tumor characterization. This study aimed to validate a technique that combines the amplification refractory mutation system (ARMS) with high-resolution melting analysis (HRMA) for detecting mutations in codon 12 of KRAS in tumor and plasma, and to assess its prognostic value. Methods: Prospective study including patients with newly diagnosed PDAC with tumor and plasma samples collected before treatment. Mutations in codon 12 of KRAS (G12D, G12V, G12C, and G12R) were detected using ARMS–HRMA and compared to Sanger sequencing (SS). Univariate and multivariate analyses were used to evaluate the prognostic significance of these mutations. Results: A total of 88 patients, 93% with ECOG-PS 0–1, 57% with resectable disease. ARMS–HRMA technique showed a higher sensitivity than SS, both in tumor and plasma (77% vs. 51%; 25 vs. 0%, respectively). The most frequent mutation was G12D (n = 32, 36%), followed by G12V (n = 22, 25%). On multivariate analysis, patients with G12D and/or G12C mutations, either in tumor or plasma, had lower PFS (HR 1.792, 95% CI 1.061–3.028, p = 0.029; HR 2.081, 95% CI 1.014–4.272, p = 0.046, respectively) and lower OS (HR 1.757, 95% CI 1.013–3.049, p = 0.045; HR 2.229, 95% CI 1.082–4.594, p = 0.030, respectively). Conclusions: ARMS–HRMA is a rapid and cost-effective method for detecting KRAS mutations in PDAC patients, offering the potential for stratifying prognosis and guiding treatment decisions. The presence of G12D and G12C mutations in both tumor and plasma is associated with a poorer prognosis.

Clinical and molecular risk factors for repeat interventions due to symptomatic uterine leiomyomas

BackgroundRepeat leiomyoma occurrence or even reintervention is common after myomectomy. Little is known about the factors related to repeat interventions. ObjectivesThis study aimed to determine the frequency of leiomyoma-related reintervention after an initial laparoscopic or abdominal myomectomy and to analyze both clinical and molecular risk factors for reinterventions. Another objective was to define the frequency of clonally related tumors from repeat operations. Study DesignThis retrospective cohort study included 234 women who had undergone laparoscopic or abdominal myomectomy in 2009-2014. Information on repeat leiomyoma-related interventions as well as on other clinical factors was collected from medical records after a median follow-up time of 11,4 years (range 7,9-13,8 years) after the index procedure. The effect of clinical risk factors on the risk of reintervention was analyzed by the Kaplan-Meier estimator and the Cox proportional hazards model. For molecular analyses, we examined the mutation profiles of 133 formalin-fixed paraffin-embedded leiomyoma samples from 33 patients with repeat operations. We screened the tumors for the three primary leiomyoma driver alterations—MED12 mutations, HMGA2 overexpression, and FH-deficiency—utilizing Sanger sequencing and immunohistochemistry. To further assess the clonal relationship of the tumors, we executed whole-exome sequencing for 52 leiomyomas from 21 patients who exhibited the same driver alteration in tumors obtained from multiple procedures. ResultsReintervention rate at 11,4 years after myomectomy was 20% (46/234). Number of leiomyomas removed at the index myomectomy was a risk factor (hazard ratio 1.21; 95% confidence interval 1.09-1.34). Age at index myomectomy (hazard ratio 0.94; 95% confidence interval 0.89-0.99) and postoperative parity (hazard ratio 0.23; 95% confidence interval 0.09-0.60) were protective factors. Molecular characterization of tumors from index and non-index operations confirmed a clonal relationship of the tumors in 3/33 (9%) patients. None of the leiomyomas harboring a MED12 mutation —the most common leiomyoma driver— were confirmed clonally related. FH-deficiency was detected in repeat leiomyomas from 3/33 (9%) patients. All these patients harbored a germline FH mutation, which is distinctive for the hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome. Finally, we identified three (3/33; 9%) patients with two tumors each displaying somatic mutations in a recently identified novel leiomyoma driver gene, YEATS4. All YEATS4 mutations were different and thus the tumors were not clonally related. ConclusionOur study shows that reintervention is common after surgical myomectomy. Uterine leiomyomas typically develop independently, but some share a clonal origin. Repeat leiomyoma occurrence may be due to genetic predisposition, such as a germline FH mutation. Distinct somatic YEATS4 mutations identified in multiple leiomyomas from the same patient indicate a possible role for YEATS4 in repeat leiomyomas.

NURS-21. EXPLORATION OF CORRELATIVE STUDIES IN EARLY PHASE TRIALS FOR PEDIATRIC AND YOUNG ADULT CENTRAL NERVOUS SYSTEM (CNS) TUMORS AND THE POTENTIAL TRANSLATION TO CLINICAL CARE

Abstract BACKGROUND Correlative studies are common in early phase clinical trials. In addition to primary aims establishing maximum tolerated dose or efficacy, supplementary information from biospecimens is frequently collected with patient consent. The Pediatric Neuro-Oncology Consortium (PNOC) has included several correlative studies with implications for understanding patterns in the development of tumors, response to treatment, and prognosis. A needs assessment survey of PNOC institutions by the Advanced Practice Provider and Investigational Nurse Committee (APPNIC) highlighted that nurses and advanced practice providers (APPs) desire further education regarding correlative studies. METHODS Blood, stool, cerebrospinal fluid (CSF) and hair strands are examples of correlative biospecimens incorporated in PNOC protocols. We will share a review of the literature and implications for practice. RESULTS Blood, drawn in conjunction with clinical labs, is commonly analyzed for circulating tumor DNA to conduct molecular profiling in blood compared to tissue, explore less invasive means of molecular evolution of tumor somatic mutations, and identify early markers of tumor response or resistance. Stool is collected to utilize the gut microbiome as a lens into treatment response in CNS tumors via the gut-brain axis. Stool samples are compared to normal controls and longitudinally within patients during treatment. CSF sampling provides less invasive disease monitoring, tumor molecular characterization, markers of tumor response or resistance, and drug pharmacokinetics. Hair sampling can be used to further quantify drug levels for pharmacokinetics and assess treatment compliance. The robustness of these correlative samples collected at various timepoints (diagnosis, pre-surgery and post-surgery, post-radiation and/or with recurrence) informs on prognosis, response to treatment; and ultimately, interventions to improve outcomes for pediatric and young adult CNS tumors. CONCLUSION Our assessment identified a need for APP and nursing-focused education on biospecimen collection to inform on emerging clinical and research advances while improving protocol compliance.

A case series of non-small cell lung cancer patients with EGFR or HER2 exon 20 insertion in Li Fraumeni syndrome.

Germline pathogenic mutations in TP53 gene are associated with a cancer predisposition syndrome known as Li Fraumeni syndrome. Albeit infrequently, non-small cell lung cancer, especially as oncogene-addicted disease, may be diagnosed in young patients with Li Fraumeni syndrome. We report three cases of patients affected by Li Fraumeni syndrome who developed non-small cell lung cancer with EGFR or HER2 exon 20 insertions. The first patient suffered from liposarcoma and, then, brain metastases from HER2-mutated non-small cell lung cancer: after stereotactic radiotherapy, he benefited from enrollment in a clinical trial with a HER2-targeted therapy. The second young patient was a female with personal history of rhabdomyosarcoma, diagnosed with brain metastases from EGFR-mutated non-small cell lung cancer: enrollment in a clinical trial led to a temporary clinical benefit. The last case was a female diagnosed with breast carcinoma, ovarian granulosa cell tumor and advanced EGFR-mutated non-small cell lung cancer at a young age. Young patients affected by oncogene-addicted non-small cell lung cancer and with a positive familial cancer history should be referred for an accurate genetic counselling to look for Li Fraumeni syndrome. The underlying molecular connection between TP53 and HER family receptor tyrosine kinases remains unclear, but an extensive molecular characterization of tumors from patients with Li Fraumeni syndrome should always be performed, to offer patients a personalized therapeutic approach.

Molecular Landscape and Therapeutic Strategies against Colorectal Cancer.

Colorectal cancer (CRC) is the second leading cause of cancer deaths worldwide. Although the overall incidence of CRC is decreasing, the incidence of young-onset CRC, characterized by a diagnosis of CRC before age 50, is increasing. Outcomes for CRC patients are improving, partly due to comprehensive molecular characterization of tumors and novel therapeutic strategies. Advances in genomic and transcriptomic analyses using blood- and tumor-tissue-based sequencing have facilitated identification of distinct tumor subtypes harboring unique biological characteristics and therapeutic vulnerabilities. These insights have led to the development and incorporation of targeted therapies and immunotherapy in CRC treatment. In this review, we discuss the molecular landscape and key oncogenes/tumor suppressors contributing to CRC tumorigenesis, metastasis, and therapeutic resistance. We also discuss personalized therapeutic strategies for subsets of CRC patients and provide an overview of evolving novel treatments being evaluated in clinical trials.

Precision Immuno-Oncology in NSCLC through Gender Equity Lenses.

Precision immuno-oncology involves the development of personalized cancer treatments that are influenced by the unique nature of an individual's DNA, immune cells, and their tumor's molecular characterization. Biological sex influences immunity; females typically mount stronger innate and adaptive immune responses than males. Though more research is warranted, we continue to observe an enhanced benefit for females with lung cancer when treated with combination chemoimmunotherapy in contrast to the preferred approach of utilizing immunotherapy alone in men. Despite the observed sex differences in response to treatments, women remain underrepresented in oncology clinical trials, largely as a result of gender-biased misconceptions. Such exclusion has resulted in the development of less efficacious treatment guidelines and clinical recommendations and has created a knowledge gap in regard to immunotherapy-related survivorship issues such as fertility. To develop a more precise approach to care and overcome the exclusion of women from clinical trials, flexible trial schedules, multilingual communication strategies, financial, and transportation assistance for participants should be adopted. The impact of intersectionality and other determinants of health that affect the diagnosis, treatment, and outcomes in women must also be considered in order to develop a comprehensive understanding of the unique impact of immunotherapy in all women with lung cancer.

Tumor-host cell interaction in the microenvironment: new target points for treatment?

Primary brain tumors and metastases in the central nervous system (CNS) are characterized by their unique microenvironment, which interacts with neuronal structures and influences structural and adaptive immunity. How significant are various tumor-host interactions from aprognostic and therapeutic perspective? A literature search was carried out for relevant articles on the topic: microenvironment glioblastoma or metastasis through PubMed and Medline. Modern high-throughput methods, such as spatial and single-cell resolution molecular characterization of tumors and their microenvironment enable adetailed mapping of changes and adaptation of individual cells within the microenvironment of tumors; however, treatment approaches based on altered tumor-host cell interactions, such as immune modeling, cell-based treatment methods or checkpoint inhibition have so far not shown any significant advantages for survival. Adeeper understanding of the complex immune landscape and the microenvironment of metastases of the CNS and intracerebral tumors is essential to optimize future treatment strategies.

Molecular analysis of cancer genomes in children with Lynch syndrome: Exploring causal associations.

Lynch syndrome (LS) predisposes to cancer in adulthood and is caused by heterozygous germline variants in a mismatch repair (MMR) gene. Recent studies show an increased prevalence of LS among children with cancer, suggesting a causal relationship. For LS-spectrum (LSS) cancers, including high-grade gliomas and colorectal cancer, causality has been supported by typical MMR-related tumor characteristics, but for non-LSS cancers, causality is unclear. We characterized 20 malignant tumors of 18 children with LS, including 16 non-LSS tumors. We investigated second hits, tumor mutational load, mutational signatures and MMR protein expression. In all LSS tumors and three non-LSS tumors, we detected MMR deficiency caused by second hit somatic alterations. Furthermore, these MMR-deficient tumors carried driver variants that likely originated as a consequence of MMR deficiency. However, in 13 non-LSS tumors (81%), a second hit and MMR deficiency were absent, thus a causal link between LS and cancer development in these children is lacking. These findings demonstrate that causality of LS in children with cancer, which can be determined by molecular tumor characterization, seems to be restricted to specific tumor types. Large molecular and epidemiological studies are needed to further refine the tumor spectrum in children with LS.

The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma.

Low-grade gliomas (LGGs) represent children's most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples. We examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants. Our findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9ng). While CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.

Abstract C049: Copenhagen Prospective Personalized Oncology (CoPPO) – The utility of using genomic profiling for tailored therapy in a Phase 1 setting

Abstract Purpose: In recent years, targeted therapy based on the molecular characterization of tumors has been among the most remarkable advances in cancer medicine. Here, we report the impact of comprehensive genomic profiling in patients (pts) with advanced solid tumors at the Phase 1 unit, Department of Oncology, Rigshospitalet, Denmark. Materials and Methods: A prospective, single-center, single-arm open label study (NCT02290522) was conducted, enrolling pts with advanced cancer referred to a Phase I Unit. Fresh tumor tissue 18G core needle or equivalent preserved in RNAlater was obtained for whole genome or exome sequencing and RNA sequencing. In cases where fresh tumor tissue was unavailable, archived formalin-fixed paraffin-embedded tumor tissue or circulating tumor DNA extracted from plasma were obtained. Each individual genomic report was reviewed and discussed by a multidisciplinary tumor board dedicated to precision medicine. When possible, pts were treated with regimen matched to the genomic profile. Results: Between April 2013 and December 2022, a total of 2151 pts with advanced cancer and exhausted treatment options were enrolled. Median age of pts was 62 years (range: 17- 87) and most common tumor types included colorectal cancer (N=465, 22%), breast cancer (N=290, 13%), non-small cell lung cancer (N = 251, 12%) and prostate cancer (N = 174, 8%). Genomic profiles were obtained in 1870 pts (87%). At least one actionable target was identified in 1067 pts (57%). The most common actionable targets were expression profiles matched to monoclonal antibodies (N=559, 52%), alteration of the DNA damage repair response pathway (N=407, 38%) and tumor mutational burden-high (N=84, 8%). Overall, 261 pts (24%) with an actionable target were treated with targeted therapy. 11 pts were treated with more than one line of targeted therapy. In total 276 targeted treatment regimens were initiated. The treatments predominantly targeted; the DNA damage repair response pathway (N=54, 20%), BRAF V600E mutation (N= 47, 17%), expression profiles matched to monoclonal antibodies (N=35, 13%), ERBB2 family pathway alterations (N=34, 12%) and tumor mutational burden-high (N=34, 12%). Conclusion: This large-scale study demonstrates that genomic profiling is efficient to identify actionable targets and to match pts to targeted therapies. Outcomes of pts treated with matched therapy will be presented at the meeting. Citation Format: Laila Belcaid, Martin Hoejgaard, Ida Tuxen, Iben Spanggaard, Ulrik Lassen, Finn Cilius Nielsen, Christina Westmose Yde, Kristoffer Rohrberg. Copenhagen Prospective Personalized Oncology (CoPPO) – The utility of using genomic profiling for tailored therapy in a Phase 1 setting [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C049.

Molecular diagnostics tailoring personalized cancer therapy-an oncologist's view.

Medical oncology is rapidly evolving with the implementation of personalized, targeted therapies. Advances in molecular diagnostics and the biologic understanding of cancer pathophysiology led to the identification of specific genetic alterations as drivers of cancer progression. Further, improvements in drug development enable the direct interference with these pathways, which allow tailoring personalized treatments based on a distinct molecular characterization of tumors. Thereby, we are currently experiencing a paradigm-shift in the treatment of cancers towards cancer-type agnostic, molecularly targeted, personalized therapies. However, this concept has several important hurdles and limitations to overcome to ultimately increase the proportion of patients benefitting from the precision oncology approach. These include the assessment of clinical relevancy of identified alterations, capturing and interpreting levels of heterogeneity based on intra-tumoral or time-dependent molecular evolution, and challenges in the practical implementation of precision oncology in routine clinical care. In the present review, we summarize the current state of cancer-agnostic precision oncology, discuss the concept of molecular tumor boards, and consider current limitations of personalized cancer therapy. Further, we provide an outlook towards potential future developments including the implementation of functionality assessments of identified genetic alterations and the broader use of liquid biopsies in order to obtain more comprehensive and longitudinal genetic information that might guide personalized cancer therapy in the future.

Imaging-based characterization of tumoral heterogeneity for personalized cancer treatment.

With personalized tumor therapy, understanding and addressing the heterogeneity of malignant tumors is becoming increasingly important. Heterogeneity can be found within one lesion (intralesional) and between several tumor lesions emerging from one primary tumor (interlesional). The heterogeneous tumor cells may show a different response to treatment due to their biology, which in turn influences the outcome of the affected patients and the choice of therapeutic agents. Therefore, both intra- and interlesional heterogeneity should be addressed at the diagnostic stage. While genetic and biological heterogeneity are important parameters in molecular tumor characterization and in histopathology, they are not yet addressed routinely in medical imaging. This article summarizes the recently established markers for tumor heterogeneity in imaging as well as heterogeneous/mixed response to therapy. Furthermore, a look at emerging markers is given. The ultimate goal of this overview is to provide comprehensive understanding of tumor heterogeneity and its implications for radiology and for communication with interdisciplinary teams in oncology. KEY POINTS:: · Tumor heterogeneity can be described within one lesion (intralesional) or between several lesions (interlesional).. · The heterogeneous biology of tumor cells can lead to a mixed therapeutic response and should be addressed in diagnostics and the therapeutic regime.. · Quantitative image diagnostics can be enhanced using AI, improved histopathological methods, and liquid profiling in the future..

Comprehensive Genomic Profiling in Predictive Testing of Cancer.

Despite the rapid progress in the field of personalized medicine and the efforts to apply specific treatment strategies to patients based on the presence of pathogenic variants in one, two, or three genes, patient response to the treatment in terms of positive benefit and overall survival remains heterogeneous. However, advances in sequencing and bioinformatics technologies have facilitated the simultaneous examination of somatic variants in tens to thousands of genes in tumor tissue, enabling the determination of personalized management based on the patient's comprehensive genomic profile (CGP). CGP has the potential to enhance clinical decision-making and personalize innovative treatments for individual patients, by providing oncologists with a more comprehensive molecular characterization of tumors. This study aimed to highlight the utility of CGP in routine clinical practice. Here we present three patient cases with various advanced cancer indicated for CGP analysis using a combination of SOPHiA Solid Tumor Solution (STS, 42 genes) for DNA and SOPHiA RNAtarget Oncology Solution (ROS, 45 genes and 17 gene fusions with any random partners) for RNA. We were able to identify actionable genomic alterations in all three cases, thereby presenting valuable information for future management of these patients. This approach has the potential to transform clinical practice and greatly improve patient outcomes in the field of oncology.

State of the science and future directions for research on HIV and cancer: Summary of a joint workshop sponsored by IARC and NCI.

An estimated 38 million people live with human immunodeficiency virus (HIV) worldwide and are at excess risk for multiple cancer types. Elevated cancer risks in people living with HIV (PLWH) are driven primarily by increased exposure to carcinogens, most notably oncogenic viruses acquired through shared transmission routes, plus acceleration of viral carcinogenesis by HIV-related immunosuppression. In the era of widespread antiretroviral therapy (ART), life expectancy of PLWH has increased, with cancer now a leading cause of co-morbidity and death. Furthermore, the types of cancers occurring among PLWH are shifting over time and vary in their relative burden in different parts of the world. In this context, the International Agency for Research on Cancer (IARC) and the US National Cancer Institute (NCI) convened a meeting in September 2022 of multinational and multidisciplinary experts to focus on cancer in PLWH. This report summarizes the proceedings, including a review of the state of the science of cancer descriptive epidemiology, etiology, molecular tumor characterization, primary and secondary prevention, treatment disparities and survival in PLWH around the world. A consensus of key research priorities and recommendations in these domains is also presented.

CBD Inhibits In Vivo Development of Human Breast Cancer Tumors.

Inflammation is a critical component of cancer development. Previously, we showed in vitro that IL-1β treatment of non-invasive human breast cancer MCF-7 cells promoted their transition to a malignant phenotype (6D cells). This epithelial-mesenchymal transition was reverted by exposure to cannabidiol (CBD). We show in a murine model that subcutaneous inoculation of 6D cells induced formation and development of tumors, the cells of which keep traits of malignancy. These processes were interrupted by administration of CBD under two schemes: therapeutic and prophylactic. In the therapeutic scheme, 6D cells inoculated mice developed tumors that reached a mean volume of 540 mm3 at 45 days, while 50% of CBD-treated mice showed gradual resorption of tumors. In the prophylactic scheme, mice were pre-treated for 15 days with CBD before cells inoculation. The tumors formed remained small and were eliminated under continuous CBD treatment in 66% of the animals. Histological and molecular characterization of tumors, from both schemes, revealed that CBD-treated cells decreased the expression of malignancy markers and show traits related with apoptosis. These results confirm that in vivo CBD blocks development of breast cancer tumors formed by cells induced to malignancy by IL-1β, endorsing its therapeutic potential for cancer treatment.

Functional Impact of Protein–RNA Variation in Clinical Cancer Analyses

Comprehensive molecular characterization of tumors aims to uncover cancer vulnerabilities, drug resistance mechanisms, and biomarkers. Identification of cancer drivers was suggested as the basis for patient-tailored therapy, and transcriptomic analyses were proposed to reveal the phenotypic outcome of cancer mutations. With the maturation of the proteomic field, studies of protein–RNA discrepancies suggested that RNA analyses are insufficient to predict cellular functions. In this article we discuss the importance of direct mRNA–protein comparisons in clinical cancer studies. We make use of the large amount of data generated by the Clinical Proteomic Tumor Analysis Consortium, which includes protein and mRNA expression analyses from the exact same samples. Analysis of protein–RNA correlations showed marked differences among cancer types, and highlighted the protein–RNA similarities and discrepancies among functional pathways and drug targets. Additionally, unsupervised clustering of the data based on protein or RNA showed substantial differences in tumor classification and the cellular processes that differentiate between clusters. These analyses show the difficulty to predict protein levels from mRNAs, and the critical role of protein analyses for phenotypic tumor characterization.

Training oncologists (Oncs) to conduct better informed discussions with African American (AA) cancer (CA) patients (pts) about tumor genomic profiling (TGP): Results of a randomized pilot trial of gene pilot pro (GPP).

10552 Background: Molecular characterization of tumors to guide therapy choices using next-generation sequencing-based TGP has become standard practice for pts w/multiple CA types. AAs are more likely to have negative attitudes towards genetics, rooted in concerns about privacy, cost and discrimination, and higher mistrust of medical institutions. Oncs are poorly prepared for informed discussions w/CA pts about secondary hereditary risks of TGP and often fail to have these conversations despite 2015 ASCO guidelines benchmarking this standard, and further are poorly informed of the potential challenges of discussing TGP and germline risk w/their AA CA pts. Methods: Formative work included 1-on-1 interviews (n = 10) to assess oncs’ perceptions of TGP use and discussions w/AA CA pts, and a national survey (n = 50) to assess TGP practice patterns, communication of hereditary risk, and challenges encountered in AAs. Interviews/survey data and advisory board input informed development of GPP, a 12 min online training video to improve Oncs’ awareness of ASCO guidelines, confidence and preparation to have TGP discussions w/pts, and improve awareness of barriers to TGP unique to AA CA pts. The control consisted of 10 slides with information about TGP drawn from industry/academic websites and the 2015 ASCO guidelines. Participants (n = 63) completed baseline (100%), post-intervention (100%), and 1-month (95%) follow-up surveys. The study was approved by the Fox Chase Cancer Center IRB 18-8006. Results: Oncs were recruited by email and randomized to view GPP or control material. The majority were age 40-49 (38%), 71% male, 44% White, w/mean 15 yrs in practice; 85% reported none or only informal training to communicate TGP risks/results to pts. GPP produced a durable increase in recognition of 4 core ASCO guideline elements (20% baseline, 67% post, 63% 1 month). At 1-month follow-up, GPP significantly improved recognition of barriers specific to AA CA pts related to TGP and hereditary risk (p = 0.001) and promoted greater preparedness to support TGP discussions w/AA pts including preparedness to identify (p &lt; 0.01) and understand (p &lt; 0.01) issues that matter most to their AA pts. 1-month confidence to conduct difficult discussions related to genetic mistrust (p = 0.004) and TGP cost (p = 0.003) was better preserved after viewing GPP compared to control. Among Oncs viewing GPP, 90% agreed/strongly agreed that GPP helped them “better understand how to address concerns my AA pts may have about TGP” and 97% definitely/probably would recommend GPP to other Oncs. Conclusions: GPP significantly improved Oncs’ awareness of barriers related to TGP communication in AA CA pts, improved preparedness to facilitate informed decision-making, and supported sustained confidence to lead difficult discussions.

Novel computational biology modeling system can accurately forecast response to neoadjuvant therapy in early breast cancer

BackgroundGeneralizable population-based studies are unable to account for individual tumor heterogeneity that contributes to variability in a patient’s response to physician-chosen therapy. Although molecular characterization of tumors has advanced precision medicine, in early-stage and locally advanced breast cancer patients, predicting a patient’s response to neoadjuvant therapy (NAT) remains a gap in current clinical practice. Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously validated biophysical simulation platform.MethodsA single-blinded study was performed using a retrospective database from a single institution (9/2014–12/2020). Patients included: ≥ 18 years with breast cancer who completed NAT, with pre-treatment dynamic contrast enhanced magnetic resonance imaging. Demographics, chemotherapy, baseline (pre-treatment) MRI and pathologic data were input into the TumorScope Predict (TS) biophysical simulation platform to generate predictions. Primary outcomes included predictions of pathological complete response (pCR) versus residual disease (RD) and final volume for each tumor. For validation, post-NAT predicted pCR and tumor volumes were compared to actual pathological assessment and MRI-assessed volumes. Predicted pCR was pre-defined as residual tumor volume ≤ 0.01 cm3 (≥ 99.9% reduction).ResultsThe cohort consisted of eighty patients; 36 Caucasian and 40 African American. Most tumors were high-grade (54.4% grade 3) invasive ductal carcinomas (90.0%). Receptor subtypes included hormone receptor positive (HR+)/human epidermal growth factor receptor 2 positive (HER2+, 30%), HR+/HER2− (35%), HR−/HER2+ (12.5%) and triple negative breast cancer (TNBC, 22.5%). Simulated tumor volume was significantly correlated with post-treatment radiographic MRI calculated volumes (r = 0.53, p = 1.3 × 10–7, mean absolute error of 6.57%). TS prediction of pCR compared favorably to pathological assessment (pCR: TS n = 28; Path n = 27; RD: TS n = 52; Path n = 53), for an overall accuracy of 91.2% (95% CI: 82.8% – 96.4%; Clopper–Pearson interval). Five-year risk of recurrence demonstrated similar prognostic performance between TS predictions (Hazard ratio (HR): − 1.99; 95% CI [− 3.96, − 0.02]; p = 0.043) and clinically assessed pCR (HR: − 1.76; 95% CI [− 3.75, 0.23]; p = 0.054).ConclusionWe demonstrated TS ability to simulate and model tumor in vivo conditions in silico and forecast volume response to NAT across breast tumor subtypes.

Abstract 2852: Targeting NPEPPS overcomes cisplatin resistance in patient-derived bladder cancer tumoroids

Abstract Introduction and Objectives: Cisplatin-based neoadjuvant chemotherapy (NAC) is the recommended treatment for muscle-invasive bladder cancer (MIBC) patients. Patients with a pathological complete response after NAC (pCR), have a good 5-yr OS of 80%. However, due to NAC resistance, only 25% of patients achieve a pCR. Our aim is to increase the number of patients reaching a pCR by overcoming cisplatin resistance. Previously we identified NPEPPS as a key player in cisplatin resistance that prevents cisplatin uptake via volume-regulated anion channels (VRAC) in cisplatin-resistant cell lines. Studies have demonstrated that patient-derived bladder cancer tumoroids recapitulate the originating tumor at the molecular level, presenting a model system to study chemotherapy resistance ex vivo. Here, we used MIBC tumoroids to functionally interrogate NPEPPS’ role in cisplatin resistance. Material and Methods: Ex vivo interrogation of NPEPPS function in cisplatin resistance was performed in tumoroid cultures generated from MIBC patients (N=10). Tumor tissue was obtained either at transurethral resection of bladder tumor (TURBT, N=5) or RC (N=5), and clinical resistance to NAC was defined as ypT≥2, nodal positive disease at RC or progression during NAC. Molecular characterization of tumor specimens and corresponding tumoroids was performed by bladder cancer-specific SNaPshot mutation analysis, copy-number aberrations analysis, immunohistochemistry (IHC), and hematoxylin &amp; eosinophilic staining (HE). The effect of NPEPPS on cisplatin uptake was investigated using cisplatin treatment combined with the pharmacological NPEPPS-inhibitor tosedostat, shRNA-mediated NPEPPS knock-down or lentiviral NPEPPS over-e xpression followed by cytometry by time of flight (CyTOF) analysis. CellTiter-Glo cell viability assays and caspase 3/7 apoptosis assays were used to investigate whether NPEPPS inhibition overcomes cisplatin resistance ex vivo. Results: Five out of ten patients received NAC, all whom had tumors that were clinically resistant to NAC. Tumoroid cultures from MIBC patients unresponsive to NAC showed resistance to serum concentrations of cisplatin as well as increased NPEPPS mRNA expression. Meanwhile, molecular characterization of tumor and tumoroid pairs confirmed that patient-specific tumor traits were maintained in tumoroids. Pharmacological NPEPPS inhibition or NPEPPS depletion by shRNA-mediated knock-down increased cisplatin influx into the cell and resensitized NAC resistant tumoroids to serum concentrations of cisplatin. Furthermore, NPEPPS overexpression increased cisplatin resistance in cisplatin-sensitive tumoroids. Conclusion: We confirm that NPEPPS is associated with cisplatin-resistance in an ex vivo MIBC tumoroid model. These findings have potential for rapid translation into the clinic and invite trials investigating tosedostat to overcome chemoresistance. Citation Format: Mathijs P. Scholtes, Maryam Akbarzadeh, Shahla Romal, Miranda van Dijk, Tsung Wai Kan, Tokameh Mahmoudi, Tahlita C. Zuiverloon. Targeting NPEPPS overcomes cisplatin resistance in patient-derived bladder cancer tumoroids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2852.

Abstract 2304: Circulating tumor extracellular vesicles to monitor metastatic prostate cancer genomic and transcriptomic evolution

Abstract Background: Liquid biopsies enable minimally-invasive molecular characterization of tumors, allowing the study of tumor evolution, and are valuable in supporting clinical decisions in metastatic prostate cancer. Extracellular vesicles (EVs) secreted by tumor cells are abundant in the plasma of cancer patients, but their potential as a source of tumor material for multi-omic profiling remains widely unexplored. Design: We present a comprehensive analysis of plasma-derived tumor EV-DNA and EV-RNA by next-generation sequencing (NGS), in metastatic castration resistant prostate cancer (mCRPC). First, we used a range of in vitro (PC3, LnCap, 22Rv1 and C4-2) and in vivo models, including patient-derived tumor xenografts (PDXs), to optimize genomic and transcriptomic analysis of DNA and RNA contained in tumoral EVs. Next, we validated our findings in a cohort of 35 mCRPC patients with longitudinal plasma samples (n=92) collected before, 4-weeks after treatment and at progression to androgen receptor signaling inhibitor (ARSI) therapy. Tumor copy number alterations (CNAs) obtained by low-pass whole genome sequencing (lpWGS) were used to infer tumor fraction (TF). In addition, transcriptomic signatures were obtained from EV-RNA sequencing. Results: We demonstrate that circulating EV-DNA copy-number (CN) profiling matches tumor CN profiles in same-patient mCRPC biopsies (r: 0.47-0.85, p&amp;lt;0.001) and ctDNA, confirming its tumoral origin. EV-DNA tumor fraction (TF) was prognostic, identifying patients with shorter time to progression (HR 2.29, p=0.04). In addition, we developed a novel approach for the analysis of mRNA Expression in Circulating EVs (RExCuE), showing high correlation between EV-RNA and tumor biopsy RNA in vivo and in patient samples for the whole transcriptome, tumor-associated transcripts and the Hallmark androgen response gene set (all r&amp;gt;0.70, p&amp;lt;0.001). EV-RNAseq was able to detect and monitor transcriptomic signatures of response and resistance to ARSI in clinical samples as early as after 4 weeks of therapy. Last, we derived a specific signature of ARSI response in EV-RNA in vivo that predicts patient response to therapy. Conclusion: Our work represents the first evidence for circulating EVs as a biomarker to monitor evolution of tumor genomics and transcriptomics in mCRPC on therapy, allowing the study of drug response and resistance mechanisms and with a unique potential to be developed as clinical biomarker. Citation Format: Irene Casanova-Salas, Sarai Córdoba-Terreros, Daniel Aguilar, Laura Agúndez, Julián Brandariz, Nicolás Herranz, Alexandre Sierra, Pablo Cresta, Maria del Mar Suanes, Mario Soriano, Elena Castellano, Javier Hernández-Losa, Héctor Peinado, Joan Carles, Joaquin Mateo. Circulating tumor extracellular vesicles to monitor metastatic prostate cancer genomic and transcriptomic evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2304.