Tumor Biopsies Research Articles

A Phase III Randomized Trial of Integrated Genomics and Avatar Models for Personalized Treatment of Pancreatic Cancer: the AVATAR Trial

Abstract Purpose: Pancreatic adenocarcinoma (PDAC) has limited treatment options. We compared the efficacy of comprehensive precision medicine against the conventional treatment in PDAC. Methods: Phase III trial of advanced PDAC where patients were randomized (1:2) to a conventional treatment treated at physician’s discretion (arm A), or to precision medicine (arm B). Subjects randomized to arm B underwent a tumor biopsy for whole exome sequencing (WES) and to generate avatar mouse models and patient derived organoids for phenotypic drug screening, with final treatment recommended by molecular tumor board. The primary objective was median overall survival (OS). Results: 137 patients were enrolled with 125 randomized, 44 to arm A and 81 to Arm B. WES was performed in 80.3% (65/81) patients of arm B, with potentially actionable mutations detected in 21.5% (14/65). Experimental models were generated in 16/81 patients (19.8%). Second-line treatment was administered to 39 patients in the experimental arm, but only 4 (10.2%) received personalized treatment, while 35 could not be receive matched therapy due to rapid clinical deterioration, delays in obtaining study results or absence of actionable targets. Median OS was 8.7 and 8.6 months (p=0.849) and median progression-free survival was 3.8 and 4.3 months (p=0.563) for the conventional and experimental arms, respectively. Notably, the four patients who received personalized treatment had median OS of 19.3 months. Conclusions: Personalized medicine was challenging to implement in most patients with PDAC, limiting the interpretation of intention to treat analysis. Survival was improved in the subset of patients who did receive matched therapy.

Abstract B071: Identifying the clinical utility of CSF as a source of liquid biopsy in pediatric brain tumors

Abstract Pediatric tumors of the central nervous system (CNS) are a leading cause of cancer-related childhood mortality. Along with imaging, it is essential to molecularly characterize tumor tissue for the diagnosis, treatment, and prognosis of these cancers. Biopsies of deeply-seeded lesions may not be possible or may carry significant risks. On the other hand, liquid biopsy, using cerebral spinal fluid (CSF), provides a minimally invasive alternative to identify and monitor tumor DNA at crucial time points, from diagnosis to follow-up. This allows for molecular diagnosis, identification of therapeutic targets, monitoring response to therapy, and early detection of recurrence or progression. The aim of our study was to assess the practicality and usefulness of liquid biopsies in a diverse group of CNS tumor patients. We used a combination of methods, including a targeted hybridization capture panel and low-pass whole genome sequencing (LP-WGS) based on the sample characteristics. We analyzed a total of 243 CSF samples from patients with CNS tumors including: low-grade glioma (LGG; N=57), high-grade glioma (HGG; N=53), medulloblastoma (MB; N=40), germinoma (CNS-GCT; N=29), and no prior biopsy (N=42). We found somatic mutations in 88% of CSF samples from HGG and 67% from LGG with known tumor DNA variants and sufficient sequencing quality. It's important to note that in LGG patients, samples collected from lumbar puncture were positive only in disseminated cases, while a higher positivity rate was found in cases where CSF was collected from ventricular spaces. Moreover, we observed positive copy number alterations (CNA) in CSF samples collected from HGG, embryonal tumors, and CNS-GCT patients at the time of diagnosis and follow-up with a sensitivity of 64%. Within our sample cohort that had an unknown or query tumor due to no prior biopsy, we were able to detect diagnostic, targetable mutations and/or a positive CNA profile in 30% of cases. This supports the utility of liquid biopsy as a diagnostic tool in in CNS lesions. This tool may also assist in monitoring for relapse in high-grade tumors. For example, in a case study, we were able to detect recurrent MB by indication of a positive CNA profile in keeping with the primary tumor CNV, six years post-surgical resection. In CNS- GCT patients, we found that LP-WGS was highly sensitive at diagnosis as we have observed similar CNV in both CSF and tumor DNA. In summary, the utility of our liquid biopsy platform in the context of CNS cancers is an impactful tool that can aid clinicians in diagnosis, treatment and monitoring disease in a minimally invasive manner. Citation Format: Liana Nobre, Mansuba Rana, Yoshiko Nakano, Ian Burns, Robert Siddaway, Richard Yuditskiy, Cyril Li, Andrew Bondoc, Anthony Liu, Uri Taboori, Cynthia Hawkins. Identifying the clinical utility of CSF as a source of liquid biopsy in pediatric brain tumors [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B071.

Abstract A038: Investigating PD-L1 status in circulating tumor cells isolated from blood samples of lung cancer patients

Abstract Background: This research study aimed to assess the performance of a research use only (RUO) immunofluorescence (IF) assay targeting programmed death-ligand 1 (PD-L1) evolution in epithelial and/or mesenchymal circulating tumor cells (CTCs) isolated from blood using Parsortix® microfluidic technology. Upregulation of PD-L1 enables cancer cells to evade the host immune response. Assessment of PD-L1 status in the tumor, as determined by traditional tissue biopsy, can indicate if immunotherapy has the potential to be an effective treatment. However, PD-L1 expression in tumor biopsies may not reflect metastatic sites in their entirety and can become outdated during tumor evolution, as the process cannot be repeated due its invasive nature. Liquid biopsy offers a minimally invasive option for dynamic testing of PD-L1 in CTCs as patients undergo treatment. Methods: Analytical linearity, and specificity and sensitivity were assessed by spiking HCC1954 and Hs 578T cancer cell lines into the blood samples of 34 healthy volunteers. The assay was then evaluated in samples from 47 metastatic lung cancer patients, among which 32 had a known PD-L1 tissue status (19 positive, 13 negative). Up to six successive draws were taken for each patient, collected into Streck Cell-Free DNA blood collection tubes. ANGLE’s Parsortix® instruments were used to isolate spiked cancer cells or CTCs from blood samples based on their size and deformability. The CTC- enriched harvests were processed onto ANGLE’s CellKeepTM slides and IF stained with ANGLE’s Portrait® PD-L1 RUO assay for PD-L1 identification on CTCs. Slides were imaged on a BioView automated imaging system. Results: Analytical specificity of PD-L1 was 98% and analytical sensitivity was 81%. Analytical linearity (R2=0.91) was shown over a 0–500 cells range. In metastatic lung cancer patients, ≥1 CTC was identified in at least one draw for 91% of donors, with 55% of those donors exhibiting ≥1 PD-L1 positive CTC. A majority (81%) of donors exhibited a positive correlation between PD-L1 tissue status and CTC expression. However, the remaining 19% of donors exhibited discordance with a PD-L1 negative tissue status but PD-L1 positivity identified in ≥1 CTC. Of the PD-L1 positive CTCs identified, 98% expressed mesenchymal markers. Dynamic change was shown in all but one donor, with PD-L1 status of the CTCs changing over time. Conclusions: This study demonstrated the ability to determine PD-L1 status in CTCs from the blood of metastatic lung cancer patients and, subject to further study, the future potential to develop dynamic PD-L1 testing for advancement of more personalized cancer treatments. Patients with a PD-L1 negative tissue status exhibited PD-L1 positive CTCs, demonstrating the feasibility of a more repeatable and accurate assessment of PD-L1 status than can be achieved through a traditional tissue biopsy. Citation Format: Morgan Spode, Chloe Goodwin, Aarabhi Varatharajah, Aaron Cottingham, Elisha Duhig, Laura Kaja, David Greaves, Mariacristina Ciccioli, Anne-Sophie Pailhes-Jimenez. Investigating PD-L1 status in circulating tumor cells isolated from blood samples of lung cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A038.

Abstract IA021: Plasma-only ultrasensitive liquid biopsy to monitor tumor burden and clonal evolution

Abstract Individual bulk tumor biopsies are invasive and may fail to capture clonal heterogeneity within primary tumors and metastatic sites of disease. Further, analyses of subclonal variants are often hindered by background error rates related to tissue preservation methods (e.g. FFPE) and sequencing artifact. Use of plasma-only ultrasensitive liquid biopsy approaches may allow for noninvasive inference of clonality and dynamically track changes in tumor burden. We previously developed MRD-EDGE, a tumor-informed machine learning classifier for ultrasensitive liquid biopsy monitoring of single nucleotide variants (SNVs) and copy number variants (CNVs) using standard plasma whole genome sequencing. For SNVs, MRD- EDGE uses a novel machine learning framework to classify individual cell free DNA (cfDNA) fragments as circulating tumor DNA or cfDNA sequencing artifact. We demonstrated the potential of plasma-only MRD-EDGE to identify SNVs in advanced melanoma and monitor tumor burden throughout treatment with immune checkpoint inhibiton. In tumor-informed settings, MRD-EDGE was used to identify minimal residual disease at tumor fractions (TFs) of 1:100,000 and below. Accurate SNV classification is a function of classifier performance and background error rate. To reduce error rates, we combined MRD-EDGE SNV with paired plus- minus sequencing (ppmSeq) from Ultima Genomics. ppmSeq is a PCR-free approach that leverages the hydrogen bonds of complementary DNA to carry matched native strands directly into sequencing, enabling scalable duplex sequencing. Use of MRD-EDGE SNV together with ppmSeq enables ultrasensitive tracking of early-stage non-small cell lung cancer throughout neoadjuvant immunotherapy. Plasma-only MRD-EDGE is therefore poised to enable dynamic monitoring of tumor burden and clonal composition outside the scope of tumor-informed approaches, including the comparison of SNV composition in cancer recurrence with preoperative disease. Citation Format: Adam Widman, Alexandre P. Cheng, John Zinno, Srinivas Rajagopalan, Ashish Saxena, Nasser Altorki, Dan A. Landau. Plasma-only ultrasensitive liquid biopsy to monitor tumor burden and clonal evolution [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr IA021.

Abstract B065: FabricaTM: A large-scale data simulation platform isolates tumor signal from cell-free DNA and improves tissue of origin prediction accuracy

Abstract Cell-free DNA (cfDNA) liquid biopsy is a promising non-invasive method for disease detection, but data availability and the complexity of cfDNA composition pose barriers to model development. Cancer prediction models trained on cfDNA data from clinically collected blood samples often struggle to isolate tumor-derived signals from confounding factors, and tissue of origin (TOO) models suffer from small sample sizes of rarer tumor types. To address these challenges, we developed FabricaTM, a platform to generate diverse, large-scale, high-fidelity simulated cfDNA datasets for robust and accurate machine learning (ML) model training. A key advantage of FabricaTM is its ability to enhance ML models by matching confounding variables between non-cancer and cancer samples. We first synthesized age-balanced non-cancer samples, then simulated tumor DNA shedding into circulation from 502 reference biopsy samples across 16 indications, optimizing for final tumor content distributions ranging from 0.001 to 14.2%. All reference non-cancer and biopsy samples consisted of aligned bisulfite sequencing reads from a custom target hybrid capture panel. This approach expanded a non-cancer dataset of 177 samples to 1,212 simulated samples and generated 6,400 simulated cancer cfDNA samples matching the non-cancers in age distribution. We then assessed this dataset for equivalence with clinical data and ability to improve cancer prediction. Non-linear dimensionality reduction and clustering of methylation signal showed simulated samples cluster indistinguishably from 2,290 samples (1,149 non-cancer, 1,141 treatment-naïve cancer) from the CORE-HH clinical study (NCT05435066). A binary cancer prediction model trained on the FabricaTM-generated dataset and evaluated on the CORE-HH dataset showed reduced reliance on age-associated signal (R2=0.15) and increased tuning towards tumor content, with minor cost to sensitivity (<4% at 95% specificity), relative to a model trained and cross-validated on the CORE-HH data (R2=0.60). To evaluate the benefit of these data for TOO prediction, we trained multiclass TOO models using FabricaTM's tumor biopsy reference data with and without the addition of our simulated data for 10 target indication groupings and benchmarked their performance on our clinical dataset. Training with both data types yielded a 10% increase in balanced accuracy. Moreover, peak performance was achieved at different training sample numbers per indication, illustrating FabricaTM's potential to estimate sample size requirements during study design. Our findings suggest FabricaTM-generated data can augment limited datasets to train ML models to identify tumor-specific biomarkers obscured by technical and demographic biases in real-world data. The age-balancing approach is readily applied to other confounders to help models learn true disease signatures. The platform is also adaptable to other diseases and biofluids (e.g., Alzheimer's disease, urine), allowing for extension to diagnostic and screening development beyond cancer and blood across the care spectrum. Citation Format: Kade Pettie, Shiva Farashahi, Jackson Killian, Dorna Kashef, Josh Hubbell, Feras Hantash, Jocelyn Charlton, Kieran Chacko. FabricaTM: A large-scale data simulation platform isolates tumor signal from cell-free DNA and improves tissue of origin prediction accuracy [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B065.

Abstract A019: Analytical and clinical validation of HPV-SEQ, an NGS-based liquid biopsy platform for detection and quantification of human papilloma virus circulating tumor DNA

Abstract Human papillomavirus (HPV) infection is the primary causative factor driving the rising incidence of oropharyngeal squamous cell carcinoma (OPSCC). High-risk HPV16 and HPV18 strains are responsible for the majority of HPV related OPSCC cases, with ∼90% and 3-5% respectively. As HPV positivity is associated with improved treatment response and prognosis, correct determination of HPV status is critical for risk stratification and treatment management. While diagnostic tumor biopsy remains a useful tool for HPV profiling, the drawbacks of this approach include pain and discomfort caused by its invasive nature, as well as inability to repeat multiple serial biopsies over time. Noninvasive detection of circulating tumor (ct)HPV-DNA in plasma has emerged as an attractive investigative strategy for early disease diagnosis, real-time response monitoring, and cancer surveillance. However, to date, there is no standard or routine liquid biopsy-based HPV testing for patients with OPSCC. The accuracy of HPV detection in plasma depends on the metrics of the specific method used. Comparison of the most common approaches for detection of ctHPV-DNA shows that next-generation sequencing (NGS)-based assays are superior to that of qPCR and ddPCR, especially in patients with low disease burden. Furthermore, as the majority of current liquid biopsy tests are designed to detect viral E6 and E7 genes, it may comprise a potential challenge for detection of patient-derived ctHPV-DNA among individuals treated with therapeutic vaccines expressing non-oncogenic E6/E7 constructs, actively evaluated in clinical trial settings. To this end, we have developed HPV-SEQ, a novel NGS method designed to achieve maximum sensitivity for HPV16/18 L1 gene in DNA libraries prepared from plasma of OPSCC patients. Here we describe the thorough analytical characterization and clinical validation studies of this lab-developed test conducted and certified under clinical laboratory improvement amendments regulations. HPV-SEQ assay were assessed using both contrived samples and biological specimens by measuring a set of performance attributes including limits of blank, limits of detection, limits of quantitation, accuracy and precision. The assay has demonstrated a robust quantitative detection across a wide ctHPV-DNA range, with low level of background signal (<0.05 copies/sample) in healthy donors and qualitative cut-off of >1.39 copies for both HPV strains (ensuring sufficient differentiation between negative and low positive samples), as well as outstanding sensitivity and specificity, approaching 100%. Given the rapid decrease in sequencing cost and effective integration of sequencing data in clinical care, NGS is likely to displace other HPV detection tests over the next few years. As such, our well-validated, ultra-sensitive, plasma-based HPV profiling method with optimal analytical performance may represent a significant advancement in risk stratification, treatment management, and surveillance for patients with OCSCC and other HPV- driven malignancies. Citation Format: Samaneh Eickelschulte, Anna Starus, David H Murray, Anja K Keyser, Oliver Schauer, Johannes Fredebohm, Frederick Jones, Alexander T Pearson, Everett E Vokes, Ari J Rosenberg, Nishant Agrawal, Evgeny Izumchenko. Analytical and clinical validation of HPV-SEQ, an NGS-based liquid biopsy platform for detection and quantification of human papilloma virus circulating tumor DNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A019.

PATH-49. INTRA-OPERATIVE GENETIC ANALYSES FOR DECISION-MAKING DURING TUMOR REMOVAL OF ADULT-TYPE DIFFUSE GLIOMA USING RAPID QUANTITATIVE PCR DEVICE

Abstract BACKGROUND Recent comprehensive molecular analyses of central nervous system (CNS) tumors identified several diagnostic or prognostic markers. Especially, for adult-type diffuse glioma, IDH mutation, TERT promoter (pTERT) mutation and CDKN2A homozygous deletion are quite important markers for diagnosis and prognosis of this type of glioma. Intra-operative identification of these molecular alterations could be effective for decision-making of tumor removal strategy. METHODS In this study, we established intra-operative gene analysis method using rapid quantitative PCR device, GeneSoC, by which we could obtain genotype of these important genes for 20 minutes in an operating room. Using GeneSoC, we could perform 50 cycles of quantitative PCR for approximately 12 minutes. Results; We established rapid gene analyses of mutations of IDH1 R132H, pTERT C225T, pTERT C250T and homozygous deletion of CDKN2A for adult-type diffuse gliomas. For elution of DNA, we incubated at least 1mg of tumor tissue at 95°for 5 minutes. Combined this boiling method with GeneSoC, we could obtain those genetic alterations for 20 minutes after collection of tumor tissue. In analyses of 111 adult-type diffuse glioma cases, sensitivity and specificity for detection of IDH1 p.R132H are 98% and 98%, respectively, and those of pTERT (C225T or C250T) are 100% and 100%, respectively. In analyses of 50 cases, sensitivity and specificity for detection of CDKN2A homozygous deletion are 100% and 83%, respectively. Conclusion; In this study, we could obtain the genotype of important molecular markers intra-operatively, not only during tumor removal but even during tumor biopsy, using GeneSoC device. This rapid genetic analysis might be effective not only for intra-operative diagnosis but also for detection of boundary between tumor and normal tissue.

PATH-61. GENOMIC SIGNATURE IN NON-SMALL CELL LUNG CANCER PATIENTS METASTATIC TO BRAIN-A SINGLE INSTITUTION EXPERIENCE

Abstract BACKGROUND Lung cancer is leading cause of cancer-related death in US, with 10-30 % of NSCLC patients developing brain metastasis, which challenges curative treatment and life expectancy. Somatic mutations in KRAS and EGFR genes have been commonly implicated with brain metastasis. Other studies have shown higher amplification frequencies in MYC, YAP1, and MMP13 and deletions in CDKN2A/B. METHODS We conducted a retrospective study on observational cohort of NSCLC patients from January 2022 to July 2023, using IRB-approved data in patients with confirmed brain metastasis (CBS). Beyond demographic information, data on genomic signatures was obtained from maximum parallel/next-generation sequencing on tumor biopsy samples. Comparative analysis was conducted to predict commonalities in brain metastasis gene signatures. RESULTS The study involved 143 newly diagnosed lung cancer patients, with 29 having CBS. Genomic data was available in 24 patients. Most common abnormality was noted in TP53 gene in about 47% of patients, followed by LRP1B (12%). Mutations in KRAS, EGFR, NF1, MET, SMARCA4, KEAP1, and STK11 genes were seen in two patients each. Interestingly, 3 of 4 patients with LRP1B had brain metastasis. Actionable mutations/rearrangements were significantly lower compared to general prevalence of these mutations (KRAS gene 8% and EGFR gene 5%). CONCLUSIONS Lung cancer with brain metastasis has an abysmal prognosis due to poor CNS penetration of chemotherapeutic agents. Surgical resection and RT remain cornerstones of treatment, but certain TKI has shown some potential. Our study uncovered a notably higher prevalence of TP53 mutation among patients with brain metastasis. While patient cohort was small, those harboring an LRP1B mutation exhibited significantly higher incidence of brain metastasis. Contrary to prevalent epidemiological data, our patient population demonstrated a lower frequency of targetable mutations (specifically in EGFR and KRAS genes). We hypothesize that this observation is due to a markedly higher smoking prevalence in our region.

IMMU-31. DAMAGE RESPONSE FROM SYSTEMIC RNA VACCINATION RESTORES HUMORAL IMMUNITY IN GLIOBLASTOMA

Abstract Therapies against glioblastoma (GBM) remain stymied by poor penetration across the blood-brain barrier (BBB) and systemic immunotolerance. These outcomes necessitate development of therapies simultaneously targeted to tumors while engineering peripheral immunity to co-localize for synergistic responses. We developed RNA loaded lipid particles (LPs) to simultaneously function as inducers of cytotoxic responses in the GBM tumor microenvironment (TME) and as systemic activators of peripheral immunity. RNA-LP mediated response was studied in mice bearing KR158b tumors and in canines and humans with spontaneous glioma and glioblastoma respectively. We found that RNA-LPs could localize to the brain TME of animals bearing murine gliomas and rapidly upregulate damage associated signaling pathways including p53-CDKN2A. This correlates with increased gene signatures for complement and proteosome processing. Simultaneously, in the periphery, RNA-LPs increase integrin expression on activated T cells and ICAM expression in brain tumors helping steer T cell translocation across the BBB. In canines with malignant gliomas, response to RNA-LPs correlated with increasing tumor size suggesting pseudoprogression. Similar to murine glioma, canine gliomas harvested within 48h of vaccine administration demonstrated rapid increases in complement and p53 pathway activation. In one human patient treated with RNA-LPs per NCT04573140 (PNOC020 trial), we demonstrate biopsy confirmed pseudoprogression with increases in p53 pathway signaling and complement activation. In post-treatment tumor biopsy samples, there was increased hyperexpanded post-infusion intratumoral IgH clones. Systemic administration of RNA-LP elicits damage response in the TME that predisposes complement activation and humoral immunity. Coupled with peripheral recruitment of T cells that can translocate across the BBB, RNA-LPs elicit potent bi-directional adaptive immunotherapy against GBM.

An Atypical Case of Pancreatic Cancer with Mesenchymal Differentiation in a Patient with Primary Lung Adenocarcinoma: Insights into Tumor Biology and Novel Therapeutic Pathways

Background: Pancreatic cancer is among the malignancies with the poorest prognosis, largely due to its aggressive nature and resistance to conventional therapies. Case Summary: This report describes the case of a 69-year-old male patient with stage IV primary lung adenocarcinoma presenting with high levels of programmed death-ligand 1 (PD-L1). Simultaneously, abdominal computed tomography (CT) showed a dilated pancreatic duct at the level of the pancreatic head and a hypodense lesion in the uncinate process involving the superior mesenteric artery. Fine-needle aspiration (FNA) of the pancreatic lesions was negative. After three cycles of chemoimmunotherapy, positron emission tomography–computed tomography (PET-CT) showed complete remission of the lung nodules, lymphadenopathy, and pleural thickening, as well as a decrease in the size of the pancreatic lesion. After another six months, a PET-CT scan showed a focal increased uptake in the pancreatic mass in the same location, indicating disease progression. A core biopsy of the pancreatic tumor showed atypical spindle cell morphology with positive staining for vimentin, characteristic of mesenchymal differentiation with no apparent epithelial features. Comprehensive molecular profiling through Caris Molecular Intelligence® revealed four genes with actionable mutations in the pancreatic tissue, including KRAS (p.G12D) and TP53 (p.R175H). These molecular findings suggested the diagnoses of sarcomatoid carcinoma and conventional pancreatic ductal adenocarcinoma with epithelial–mesenchymal transition. Primary mesenchymal tumors and neuroendocrine neoplasms were excluded because immunohistochemistry was negative for anaplastic lymphoma kinase (ALK), smooth muscle actin (SMA), desmin, CD34, signal transducer and activator of transcription 6 (STAT6), S100, HMB45, CD117, discovered on GIST-1 (DOG1), CD56, progesterone, and synaptophysin. However, despite multiple rounds of systemic chemotherapy, immunotherapy, and radiation, his pancreatic disease rapidly deteriorated and metastasized to the liver and bone. Conclusions: Despite multiple lines of treatment, the patient’s condition worsened and he succumbed to his pancreatic malignancy. This study highlights the clinical characteristics, diagnosis, and treatment of rare pancreatic cancer, emphasizing the importance of molecular testing and histopathological biomarkers in personalizing treatment. It also provides insights into promising therapeutic approaches for similar cases with an unusual presentation.

Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies

A comprehensive endoscopic small and large intestinal untargeted step biopsy procedure was conducted to compare gene expression between the normal intestinal mucosa of healthy individuals and that of patients with colorectal tumors. From 78 participants (healthy individuals [n = 17], patients with colorectal conventional adenomas [n = 6], patients with Tis–T1 colorectal cancer [n = 41], patients with T2–4 colorectal cancer [n = 14]), biopsies of normal mucosa of the terminal ileum, right-sided colon (cecum and ascending colon), and left-sided colorectum (descending colon, sigmoid colon, and rectum) were obtained using a lower gastrointestinal endoscope. RNA was extracted from all samples, and total transcriptome sequencing was performed. Transcriptome data from 388 samples was analyzed. DNA was also extracted from tumor biopsy tissues and analyzed for whole-exome sequencing. In healthy individuals, gene expression differed significantly among the terminal ileum, right-sided colon, and left-sided colorectum, presumably linked to embryological factors. There were differences in gene expression in the normal mucosa in colorectal cancer patients, compared to healthy controls. Patients with tumors, especially T2–4 colorectal cancer, showed considerable variation in gene expression in non-tumor tissues, even in the terminal ileum distant from the tumor site. Based on endoscopic biopsies, the results imply cancer-predisposing conditions in seemingly normal tissues. The present study points to the importance of small intestine and cancer-predisposing conditions in the colon of colorectal cancer patients, with possible implications for developing novel immunotherapy and other therapeutic modalities.

Single intravenous administration of oncolytic adenovirus TILT-123 results in systemic tumor transduction and immune response in patients with advanced solid tumors

BackgroundA limitation of approved oncolytic viruses is their requirement for intratumoral (i.t.) injection. TILT-123 (igrelimogene litadenorepvec, Ad5/3-E2F-D24-hTNFα-IRES-hIL-2) is a chimeric oncolytic adenovirus suitable for intravenous (i.v.) delivery due to its capsid modification and dual selectivity devices. It is armed with tumor necrosis alpha and interleukin-2 for promoting T-cell activation and lymphocyte trafficking to tumors, thereby enhancing the antitumor immune response. Here, we present the findings after a single i.v. administration of TILT-123 in three phase I dose escalation clinical trials.MethodsPatients with advanced solid tumors initially received a single i.v. dose of TILT-123 ranging from 3 × 109 to 4 × 1012 viral particles (VP). Blood was collected at baseline, 1, 16, and 192 h (7 days) post-treatment for bioavailability and serum analysis. Tumor biopsies were collected prior to treatment and 7 days post-treatment for analysis of viral presence and immunological effects. Patients did not receive any other cancer therapies during this period.ResultsAcross all three trials (TUNIMO, TUNINTIL, and PROTA), 52 total patients were treated with i.v. TILT-123. Overall, TILT-123 was found to be well-tolerated, with no dose-limiting toxicities observed. Post-treatment tumor biopsies showed expression of viral genes, presence of TILT-123 adenovirus proteins or DNA, and changes in immune cell infiltration from baseline. Increased virus dose did not lead to increased virus detection in tumors. Median overall survival was longer in patients with confirmed presence of TILT-123 in post-treatment biopsies (280 versus 190 days, p = 0.0405).ConclusionTILT-123 demonstrated safety and significant intratumoral immunomodulation following a single i.v. administration, warranting further investigation.Trial registrationsTUNIMO—NCT04695327. Registered 4 January 2021, https://clinicaltrials.gov/study/NCT04695327. TUNINTIL—NCT04217473. Registered 19 December 2019, https://clinicaltrials.gov/study/NCT04217473. PROTA—NCT05271318. Registered 4 February 2022, https://clinicaltrials.gov/study/NCT05271318.

Small renal mass: which criteria are decisive for a tumor board?

Small renal masses (SRM) are aheterogeneous group of tumors with varying metastatic potential. The increasing use and improvement in the quality of abdominal imaging have led to an increasingly earlier diagnosis of incidental SRM, which are asymptomatic and confined to the organ. Despite these advances in imaging and the growing use of renal tumor biopsies, preoperative diagnosis of malignancy remains difficult. The treatment of SRM has shifted away from radical nephrectomy and now primarily includes organ-sparing surgery or active surveillance. The optimal strategy for treating SRM is continuously evolving as studies from prospective data registries can identify factors that influence both short- and long-term patient outcomes. Recent research on biomarkers, imaging techniques, and machine learning offer promising approaches to adeeper understanding of tumor biology and treatment options for this patient population.

Increased levels of versican and insulin-like growth factor 1 in peritumoral mammary adipose tissue are related to aggressiveness in estrogen receptor-positive breast cancer

The adipose tissue (AT) surrounding breast cancer (BC) plays a pivotal role in cancer progression and represents an optimal source for new biomarker discovery. The aim of this work was to investigate whether specific AT factors may have prognostic value in estrogen receptor-positive (ER+) BC. Proteoglycan Versican (VCAN), Insulin-like Growth Factor 1 (IGF1), Reticulon 4B (RTN4), chemokines CCL5 (also known as RANTES) and interleukin 8 (IL-8) are expressed in AT and may play important roles in BC progression. Peritumoral AT and tumoral biopsies were obtained from patients with ER+ BC (N = 23). AT specimens were collected also from healthy women (N = 17; CTRL-AT). The analysis of gene expression by qPCR revealed significantly higher mRNA levels of VCAN, IGF1, RTN4, and CCL5 in BC-AT compared to the CTRL-AT, and no difference in IL-8 mRNA levels. VCAN positively correlated with patient Body Mass Index (BMI) in BC-AT, while not in CTRL-AT. Moreover, VCAN and IGF1 positively correlated with RTN4 and negatively with CCL5. Interestingly, VCAN correlated with tumoral Ki67, while IGF1 with tumoral OCT4 that, in turn, correlated with tumoral Ki67 and patient BMI. Thus, peritumoral AT content of VCAN, and IGF1 are related to BC proliferation and aggressiveness.

Comparison of the Predictive and Prognostic Capacities of Neutrophil, Lymphocyte and Platelet Counts and Tumor-infiltrating Lymphocytes in Triple-negative Breast Cancer: Preliminary Results of the PERCEPTION Study.

Triple-negative breast cancer (TNBC) is the most heterogeneous breast cancer subtype, posing numerous challenges in clinical decision-making. Biomarkers are essential to personalize management of TNBC patients. While tumor infiltrating lymphocytes (TILs) are validated prognostic biomarkers, the requirement for tumor biopsy limits their routine use. Therefore, more accessible and reliable quantitative biomarkers are needed. Given the significant role of systemic inflammatory response in tumor onset and progression, assessing inflammatory cells via liquid biopsies emerges as a promising alternative. The PERCEPTION study, conducted at Centre Jean Perrin in France, aims to determine the correlation between TILs and peripheral blood components at diagnosis. An interim analysis was conducted after enrolling 50% of the estimated population, to evaluate study feasibility and preliminary correlations between blood cell counts and TILs. Sixty-one patients were enrolled over 4.5 years, demonstrating a good inclusion rate with minimal missing data. Preliminary results for 36 analyzable patients showed no correlation between the neutrophil-to-lymphocyte ratio (NLR) and TILs (rs=-0.19, 95%CI=-0.49-0.16, p=0.3). However, a moderate, positive, statistically significant correlation was found between NLR and the CD8/FoxP3 TILs ratio (rs=0.36, 95%CI=0.03-0.64, p=0.043). The probabilistic index of 0.7 (p=0.06) between NLR-high and NLR-low groups for this ratio supports the correlation. The interim analysis of the PERCEPTION study confirms the feasibility of correlating blood cell counts with TILs in TNBC. Although no significant correlation was observed between NLR and TILs, the moderate positive correlation between the CD8/FoxP3 ratio and TILs suggests a potential link between systemic inflammation and local immune response. These findings underscore the potential of blood-based markers as non-invasive surrogates for TILs, encouraging further research to enhance prognosis and guide treatment strategies in TNBC.

Rapid Intraoperative Amplicon Sequencing of CNS Tumor Markers

Currently, central nervous system tumors are diagnosed with an integrated diagnostic approach that combines histopathological examination with molecular genetic profiling, which requires days to weeks to achieve a precise and informative classification of CNS tumors. This study demonstrated the feasibility of rapid multiplexed amplicon nanopore sequencing for identifying critical mutations relevant to molecular stratification of brain tumors within the timeframe of standard resection surgery. Utilizing live analysis of nanopore sequencing data, we evaluated the brain tumor-associated molecular markers IDH1 R132, IDH2 R172, pTERT C228 and C250, H3F3A K27 and G34, Hist1H3B K27, and BRAF V600. Our method achieved a turnaround time of 105minutes at the point-of-care from receipt of a tumor biopsy to result with the potential to impact surgical strategy. Our approach can be integrated with recently developed DNA methylation-based diagnostic classification systems, corroborating diagnoses and even further specifying tumor grades, thus enabling a multimodal diagnostic intraoperative assessment of CNS malignancies.

Mitochondrial double-stranded RNA homeostasis depends on cell-cycle progression.

Mitochondrial gene expression is a compartmentalised process essential for metabolic function. The replication and transcription of mitochondrial DNA (mtDNA) take place at nucleoids, whereas the subsequent processing and maturation of mitochondrial RNA (mtRNA) and mitoribosome assembly are localised to mitochondrial RNA granules. The bidirectional transcription of circular mtDNA can lead to the hybridisation of polycistronic transcripts and the formation of immunogenic mitochondrial double-stranded RNA (mt-dsRNA). However, the mechanisms that regulate mt-dsRNA localisation and homeostasis are largely unknown. With super-resolution microscopy, we show that mt-dsRNA overlaps with the RNA core and associated proteins of mitochondrial RNA granules but not nucleoids. Mt-dsRNA foci accumulate upon the stimulation of cell proliferation and their abundance depends on mitochondrial ribonucleotide supply by the nucleoside diphosphate kinase, NME6. Consequently, mt-dsRNA foci are profuse in cultured cancer cells and malignant cells of human tumour biopsies. Our results establish a new link between cell proliferation and mitochondrial nucleic acid homeostasis.

Multicenter validation of an RNA-based assay to predict anti-PD-1 disease control in patients with recurrent or metastatic head and neck squamous cell carcinoma: the PREDAPT study.

Despite advances in cancer care and detection, >65% of patients with squamous cell cancer of the head and neck (HNSCC) will develop recurrent and/or metastatic disease. The prognosis for these patients is poor with a 5-year overall survival of 39%. Recent treatment advances in immunotherapy, including immune checkpoint inhibitors like pembrolizumab and nivolumab, have resulted in clinical benefit in a subset of patients. There is a critical clinical need to identify patients who benefit from these antiprogrammed cell death protein 1 (anti-PD-1) immune checkpoint inhibitors. Here, we report findings from a multicenter observational study, PREDicting immunotherapy efficacy from Analysis of Pre-treatment Tumor biopsies (PREDAPT), conducted across 17 US healthcare systems. PREDAPT aimed to validate OncoPrism-HNSCC, a clinical biomarker assay predictive of disease control in patients with recurrent or metastatic HNSCC treated with anti-PD-1 immune checkpoint inhibitors as a single agent (monotherapy) and in combination with chemotherapy (chemo-immunotherapy). The test used RNA-sequencing data and machine learning models to score each patient and place them into groups of low, medium, or high. The OncoPrism-HNSCC prediction significantly correlated with disease control in both the monotherapy cohort (n=62, p=0.004) and the chemo-immunotherapy cohort (n=50, p=0.01). OncoPrism-HNSCC also significantly predicted progression-free survival in both cohorts (p=0.015 and p=0.037, respectively). OncoPrism-HNSCC had more than threefold higher specificity than programmed death-ligand 1 combined positive score and nearly fourfold higher sensitivity than tumor mutational burden for predicting disease control. Here, we demonstrate the clinical validity of the OncoPrism-HNSCC assay in identifying patients with disease control in response to anti-PD-1 immune checkpoint inhibitors. NCT04510129.

A machine learning-based analysis for the definition of an optimal renal biopsy for kidney cancer

ObjectiveRenal Tumor biopsy (RTB) can assist clinicians in determining the most suitable approach for treatment of renal cancer. However, RTB's limitations in accurately determining histology and grading have hindered its broader adoption and data on the concordance rate between RTB results and final pathology after surgery are unavailable. Therefore, we aimed to develop a machine learning algorithm to optimize RTB technique and to investigate the degree of concordance between RTB and surgical pathology reports. Materials and methodsWithin a prospectively maintained database, patients with indeterminate renal masses who underwent RTB at a single tertiary center were identified. We recorded and analyzed the approach (US vs. CT), the number of biopsy cores (NoC), and total core tissue length (LoC) to evaluate their impact on diagnostic outcomes. The K-Nearest Neighbors (KNN), a non-parametric supervised machine learning model, predicted the probability of obtaining pathological characterization and grading. In surgical patients, final pathology reports were compared with RTB results. ResultsOverall, 197 patients underwent RTB. Overall, 89.8% (n=177) and 44.7% (n=88) of biopsies were informative in terms of histology and grading, respectively. The discrepancy rate between the pathology results from renal tissue biopsy (RTB) and the final pathology report following surgery was 3.6% (n=7) for histology and 5.0% (n=10) for grading. According to the machine learning model, a minimum of 2 cores providing at least 0.8 cm of total tissue should be obtained to achieve the best accuracy in characterizing the cancer. Alternatively, in cases of RTB with more than two cores, no specific minimum tissue threshold is required. ConclusionsThe discordance rates between RTB pathology and final surgical pathology are notably minimal. We defined an optimal renal biopsy strategy based on at least 2 cores and at least 0.8 cm of tissue or at least 3 cores and no minimum tissue threshold. Patients summaryRTB is a useful test for kidney cancer, but it's not always perfect. Our study shows that it usually matches up well with what doctors find during surgery. Using machine learning can make RTB even better by helping doctors know how many samples to take. This helps doctors treat kidney cancer more accurately.

Endoscopic Treatment of Neurosurgical Pathologies: Experience and Future Prospects in the Neurosurgery Department at Mohammed 6 University Hospital, Marrakech

Endoscopy is a new procedure in neurosurgery that uses optical magnification and video-assisted endoscopes to guide the hand to hard-to-reach locations. Despite extensive trials and meta-analyses, no definitive results have been published on its benefits. Neuroendoscopy has expanded beyond ventricular operations to treat various neurosurgical conditions, including cyst fenestration, tumor biopsy, tumor excision, and metastatic disease evaluation. It is beneficial for patients with hydrocephalus, intraventricular cysts, and concurrent hydrocephalus. Intracranial cysts are ideal for neuro-endoscopic therapy, and it can treat cystic craniopharyngiomas, dysontogenic tumors, gliomas, and metastases. Endoscopic tumor biopsy is a reliable technique for ventricle brain tumors. our study treated 480 hydrocephalus patients using endoscopic third ventriculostomy, accounting for 50.5% of cases. The most common cause was Sylvius aqueduct stenosis. Endoscopy was beneficial for treating colloidal cysts, arachnoid cysts, pituitary adenoma, and craniopharyngioma. It also served as a complement to microsurgery in 55 cases. Neuroendoscopy improved sciatic pain in 15 patients who underwent lumbar discectomy, with only minor issues due to the surgical scar. Neuroendoscopic surgery is expected to advance significantly in the future, with advancements in camera and optical technology, surgical instrument design, navigation systems, multiport surgery, and improved microsurgery.