Multiple Tumor Types Research Articles

Pan-canceranalysis reveals the prognostic and immunomodulatory potential of super-enhancer-induced ANGPT2 and experimental validation in colorectal cancer.

ANGPT2 plays important roles in cancer development. However, there is still no systematic analysis of ANGPT2 in pan-cancer. In this paper, we conducted a pan-cancer analysis to investigate the characteristics of ANGPT2. Furthermore, we investigated the impact of genetic and epigenetic factors on ANGPT2 expression by bioinformatics and assays. By several TCGA and GEO databases, we identified elevated expression of ANGPT2 in various tumor types. Besides, high expression of ANGPT2 induced poor prognosis of patients in multiple tumors. Through enrichment analysis, we found that ANGPT2 participated in various biological processes, including angiogenesis and immunity. Various immune analyses indicated that high expression of ANGPT2 might suggest a propensity towards a hot tumor microenvironment, but its impact on immunotherapy was negative. Bioinformatics analysis and experiments confirmed that genetic and epigenetic factors explained part of the mechanism behind ANGPT2 abnormal expression. Finally, we screened candidate drugs targeting the ANGPT2 protein by molecular docking and molecular dynamics simulation. ANGPT2 has diagnostic and prognostic values in multiple tumor types. Though with a hot tumor microenvironment, ANGPT2 high expression patients are not suitable for immunotherapy because of its proangiogenic function, contributing to selecting the exact patients for immunotherapy. Both genetic and epigenetic factors influenced ANGPT2 expression, with the influence of super-enhancer being more pronounced. This paper for the first time did the systematic analysis of ANGPT2 and showed its characteristic in pan-cancer. We summarized the biomarker role of ANGPT2 on tumor diagnosis and prognosis, as well as its target role on tumor immunotherapy.

Abstract IA018: Pan-RAF-MEK molecular glue NST-628 is a potent and brain-penetrant inhibitor of the RAS-MAPK pathway

Abstract Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and is a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analysis of RAF-MEK complexes show that NST-628 engages all isoforms of RAF, including ARAF, and prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given a mechanism differentiated from previous therapies targeting RAF or MEK catalytic activity, NST-628 is positioned to make an impact clinically in an areas of unmet patient need. Citation Format: Klaus P. Hoeflich. Pan-RAF-MEK molecular glue NST-628 is a potent and brain-penetrant inhibitor of the RAS-MAPK pathway [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr IA018.

Abstract IA008: Leveraging conformational dynamics for improved selectivity

Abstract Maximizing the clinical activity and combinability of oncogene inhibitors requires the development of molecules that can achieve necessary levels of target inhibition at a tolerated and feasible human dose. This is enabled by improving selectivity against off-targets and/or for the mutant form of the target over wild-type. While conventional structural insights can inform the design of selective drug candidates, there are often cases where clear selectivity hypotheses are not readily identifiable. Here, we present two examples illustrating how conformational dynamics can be leveraged to obtain improved selectivity for validated oncogene targets. The first example focuses on the selective inhibition of FGFR2, a well-established target in various cancers harboring FGFR2 fusions or rearrangements. Although clinical efficacy of pan-FGFR inhibitors has been demonstrated, their benefit is limited by FGFR1- and FGFR4- mediated toxicities. We leveraged differences in conformational dynamics between FGFR2 and other FGFRs observed through molecular dynamics simulations to enable the development of Lirafugratinib, the first FGFR2 selective inhibitor. Lirafugratinib inhibits FGFR2 with a high degree of selectivity in pre-clinical models. In cancer patients, Lirafugratinib achieves >95% FGFR2 occupancy at a dose of 70mg once daily, with minimal evidence of inhibition of other FGFR isoforms. This improved selectivity translates to higher objective response rates compared to pan-FGFR inhibitors across multiple tumor types harboring FGFR2 fusions or rearrangements. The second example illustrates mutant-selective targeting of PI3Kα, the most frequently mutated kinase in cancer. While non-mutant selective inhibitors have shown clinical efficacy, their benefit is limited by hyperglycemia caused by inhibition of wild-type PI3Kα. Conformational differences between mutant and wild-type PI3Kα were identified using structural insights combined with molecular dynamics simulations, leading to the discovery of RLY-2608- the first mutant-selective inhibitor of PI3Kα. RLY-2608 binds to a novel allosteric pocket and demonstrates mutant selective inhibition in pre-clinical models. RLY-2608 has a favorable pharmacokinetic profile in cancer patients, with dose-dependent increases in exposure and low peak to trough fluctuations, resulting in high levels of target coverage throughout the dosing interval. When combined with fulvestrant, this translates into a higher objective response rate and lower rate of hyperglycemia in patients with hormone-receptor positive, PI3Kα-mutant breast cancer compared to non-mutant selective PI3Kα inhibitors. These examples demonstrate the power of leveraging conformational dynamics to obtain selective target inhibition, ultimately translating into improved patient outcomes. Citation Format: James Watters. Leveraging conformational dynamics for improved selectivity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr IA008.

Prognostic value of preoperative D-dimer to albumin ratio in patients with locally advanced rectal cancer after neoadjuvant chemoradiotherapy

BackgroundThe prognostic value of Albumin and D-dimer has been established for multiple tumor types, indicating their potential for predicting tumor development. Nevertheless, the predictive capability of the DDI-to-albumin ratio (DAR) in locally advanced rectal cancer (LARC) remains uncertain.PurposeThe objective of this study was to investigate the prognostic significance of the DAR in LARC.MethodsA total of 513 patients who underwent neoadjuvant chemoradiotherapy (nCRT) prior to total mesorectal excision (TME) between March 2013 to October 2019 were included in this study. Patients were divided into high-level DAR (> 0.016) or low-level DAR (≤ 0.016) groups based on ROC curve analysis optimum cut-off value. The prognostic value of the DAR in LARC was analyzed.ResultsThe study enrolled 513 patients. Patients were stratified into high-level DAR (> 0.016) and low-level DAR (≤ 0.016) cohorts according to the optimal cut-off value determined by ROC curve analysis. The 5-year overall survival (OS) rates for patients in the low DAR group (≤ 0.016) and the high DAR group (> 0.016) were 89.4% and 80.9%, respectively (p = 0.013). The 5-year disease-free survival (DFS) rates were 85.7% and 77.4% (p = 0.027). Multivariate analyses demonstrated that DAR were independent prognostic factors for OS (p = 0.02) and DFS (0.025). Predictive nomograms that included the DAR score group (C-index: OS-0.743, DFS-0.705) were superior to those without DAR scores (C-index: OS-0.721, DFS-0.697).ConclusionThe DAR demonstrates high usability and prognostic value in predicting OS and DFS outcomes among patients diagnosed with LARC who undergo nCRT.

HO-1 impairs the efficacy of radiotherapy by redistributing cGAS and STING in tumors.

Type I IFNs (IFN-Is) induced by radiotherapy (RT) are critical for its efficacy, while the mechanism by which tumor cells inhibit IFN-I production remains largely unsolved. By an unbiased CRISPR screen, we identified hemeoxygenase 1 (HO-1) as an RT-related regulator of IFN-I production. Mechanistically, the ER-anchored, full-length HO-1 disrupted stimulator of IFN genes (STING) polymerization and subsequent coat protein complex II-mediated (COPII-mediated) ER-Golgi transportation, leading to hampered activation of downstream signaling. This process was exacerbated by the upregulation of HO-1 expression under RT. Importantly, RT also induced HO-1 cleavage. Cleaved HO-1 underwent nuclear translocation, interacted with cyclic GMP-AMP synthase (cGAS), and inhibited its nuclear export upon irradiation, leading to suppressed 2'3'-cyclic GMP-AMP (cGAMP) production. Furthermore, we revealed that HO-1 inhibitors could enhance local and distant tumor control of RT in vivo. Clinically, higher HO-1 expression was associated with a poorer prognosis and earlier tumor relapse after RT in multiple types of patient tumors. Collectively, through comprehensive inhibition of the cGAS/STING pathway, HO-1 strongly inhibited RT-induced IFN-I production, and targeting HO-1 was shown to be a promising RT-sensitizing therapeutic strategy.

EEF2K as an important kinase associated with cancer survival and prognosis

Eukaryotic Elongation Factor 2 Kinase (eEF2K), a member of the α-kinase family, services as a crucial negative regulator of protein synthesis, particularly under conditions of cellular stress. A pan-cancer analysis of eEF2K expression, genetic variants, and clinical relevance across multiple tumor types was performed using data from the Cancer Genome Atlas (TCGA) and GEO. Our findings suggest that eEF2K has dual roles in cancer progression, with its expression correlating with patient prognosis. Significant phosphorylation of eEF2 at T57, Y434, and T59 was observed, which may regulate protein synthesis during stress. The elevated T59 phosphorylation in COAD, despite the low eEF2K expression, indicates that this may be regulated by alternative kinases, such as AMPK or mTOR. This suggests that compensatory mechanisms may be involved. In addition to modulating eEF2 phosphorylation, eEF2K is involved in a number of other processes, including peptidyl-serine phosphorylation, the G2/M transition, and the MAPK cascade. The protein products of eEF2K are capable of localizing to the nucleus, cytoplasm, and cytosol, where they bind to a range of proteins, including ATP and calcium ions. These findings provide novel insights into the role of eEF2K in cancer biology and suggest that the targeting of eEF2K and eEF2 phosphorylation may offer promising therapeutic strategies.

Abstract I004: Systematic Discovery and Annotation of Cancer Emergent Orphan non-coding RNAs in human Cancers

Abstract We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-specific small RNAs with the potential to play functional roles in breast cancer progression1. Here, we report a systematic search to annotate and characterize cancer-emergent oncRNAs across 32 tumor types. We also leverage large-scale in vivo genetic screens in xenografted mice to functionally identify driver oncRNAs in multiple tumor types. We have not only discovered a large repertoire of oncRNAs, but also found that their presence and absence represent a digital molecular barcode that faithfully captures the types and subtypes of cancer. Importantly, we discovered that this molecular barcode is partially accessible from the cell-free space as some oncRNAs are secreted by cancer cells. In a large retrospective study across 192 breast cancer patients, we showed that oncRNAs can be reliably detected in the blood and that changes in the cell-free oncRNA burden captures both short-term and long-term clinical outcomes upon completion of a neoadjuvant chemotherapy regimen. Citation Format: Hani Goodarzi. Systematic Discovery and Annotation of Cancer Emergent Orphan non-coding RNAs in human Cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr I004.

Pan-cancer analysis of STAT3 indicates its potential prognostic value and correlation with immune cell infiltration in prostate cancer

BackgroundTargeting the STAT3 signaling pathway is a promising therapeutic approach for cancer patients. However, the association between STAT3 expression, the tumor immune microenvironment, and genetic variation remains unclear across human cancers, especially prostate cancer.MethodsWe used R software and other tools to analyze pan-cancer and mutation data from publicly available databases statistically. A comprehensive investigation was performed to assess the genetic heterogeneity and clinical relevance of STAT3 in various malignancies, with a specific focus on its role in the immune landscape and prognostic significance in prostate cancer. The findings were validated through immunohistochemistry (IHC) and multiplex immunofluorescence (mIF).ResultsSTAT3 expression is abnormal in the majority of cancer tissues, which is strongly correlated with these patients' prognosis. Eight measures of tumor heterogeneity and six measures of tumor stemness of multiple tumor types showed a strong correlation with STAT3 expression. Furthermore, in individuals with prostate cancer, STAT3 expression indicated the degree of immune cell infiltration and the advancement of the disease. IHC analysis revealed that STAT3 was down-regulated in prostate tumor tissues, while mIF analysis demonstrated that STAT3 signaling (p-STAT3) was extensively active in tumor tissues and positive lymph node tissues.ConclusionSTAT3 may serve as a valuable prognostic biomarker and therapeutic target across various cancers, with particular relevance to prostate cancer.

Adipose Tissues Have Been Overlooked as Players in Prostate Cancer Progression.

Obesity is a common risk factor in multiple tumor types, including prostate cancer. Obesity has been associated with driving metastasis, therapeutic resistance, and increased mortality. The effect of adipose tissue on the tumor microenvironment is still poorly understood. This review aims to highlight the work conducted in the field of obesity and prostate cancer and bring attention to areas where more research is needed. In this review, we have described key differences between healthy adipose tissues and obese adipose tissues, as they relate to the tumor microenvironment, focusing on mechanisms related to metabolic changes, abnormal adipokine secretion, altered immune cell presence, and heightened oxidative stress as drivers of prostate cancer formation and progression. Interestingly, common treatment options for prostate cancer ignore the adipose tissue located near the site of the tumor. Because of this, we have outlined how excess adipose tissue potentially affects therapeutics' efficacy, such as androgen deprivation, chemotherapy, and radiation treatment, and identified possible drug targets to increase prostate cancer responsiveness to clinical treatments. Understanding how obesity affects the tumor microenvironment will pave the way for understanding why some prostate cancers become metastatic or treatment-resistant, and why patients experience recurrence.

Immuno-PET Imaging of CD93 Expression with 64Cu-Radiolabeled NOTA-mCD93 ([64Cu]Cu-NOTA-mCD93) and Insulin-Like Growth Factor Binding Protein 7 ([64Cu]Cu-NOTA-IGFBP7).

CD93 is overexpressed in multiple solid tumor types, serving as a novel target for antiangiogenic therapy. The goal of this study was to develop a 64Cu-based positron emission tomography (PET) tracer for noninvasive imaging of CD93 expression. Antimouse-CD93 mAb (mCD93) and the CD93 ligand IGFBP7 were conjugated to a bifunctional chelator, p-isothiocyanatobenzyl-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-SCN-NOTA) and labeled with 64Cu. To evaluate the pharmacokinetic properties and tumor-targeting efficacy of [64Cu]Cu-NOTA-mCD93 and [64Cu]Cu-NOTA-IGFBP7, PET imaging and biodistribution were performed on both 4T1 murine breast tumor-bearing mice and MDA-MB-231 human breast tumor-bearing mice. The tumor model HT1080-FAP, which does not overexpress CD93, was used as a negative control. Fluorescent immunostaining was conducted on different tissues to correlate radiotracer uptake with CD93 expression. 64Cu-labeling was achieved with high yield and specific activity. Serial PET imaging revealed that the in vivo performance of [64Cu]Cu-NOTA-IGFBP7 was superior to that of [64Cu]Cu-NOTA-mCD93, and that the tracer [64Cu]Cu-NOTA-IGFBP7 exhibited elevated tumor uptake values and excellent tumor retention in MDA-MB-231 mice, rather than in 4T1 murine mice. The MDA-MB-231 tumor uptake of [64Cu]Cu-NOTA-IGFBP7 was 2.85 ± 0.15, 3.69 ± 0.60, 6.91 ± 0.88, and 6.35 ± 0.55%ID/g at 1, 4, 24, and 48 h p.i., respectively, which were significantly higher than that in the CD93-negative HT1080-FAP tumor (0.73 ± 0.15, 0.97 ± 0.31, 1.00 ± 0.07, and 1.02 ± 0.11%ID/g, respectively). The significant difference between positive and negative tumors indicated [64Cu]Cu-NOTA-IGFBP7 was specifically binding to CD93. Biodistribution data as measured by gamma counting were consistent with the PET analysis. Ex vivo histology further confirmed the high CD93 expression on MDA-MB-231 tumor tissues. Herein, we prepared two novel radiotracers, [64Cu]Cu-NOTA-mCD93 and [64Cu]Cu-NOTA-IGFBP7, for the first immune-PET imaging of CD93 expression. Our results suggest that [64Cu]Cu-NOTA-IGFBP7 is a more potential radiotracer for visualizing angiogenesis due to its sensitive, persistent, and CD93-specific characteristics.

CNSC-10. WHEN GOOD THINGS GO OFF TRK: THE INTERSECTION OF NEUROSCIENCE & ONCOLOGY

Abstract How and why do processes and molecular players that were once an integral part of normal neurodevelopment go awry in pathological conditions, such as cancer? Embryogenesis, and neurodevelopment in particular, comprise an elegant and well-orchestrated series of tightly regulated events, culminating in an organized and highly functioning organism. Cancer, on the other hand, can often be viewed as an uncontrolled, unrestrained, genetically chaotic disease, lacking the precise spatial and temporal rigidity associated with normal development. While appearing to be on opposite sides of the organizational spectrum, the similarities between early neurodevelopment and oncogenesis are numerous. The link between developmental signaling and cancer initiation, maintenance, and metastasis has long been known for several members of the Wnt, Hedgehog, and Notch pathways and years of gene-level analyses have provided a wealth of knowledge and mechanistic insight. As advances in next generation sequencing allow for deeper characterization of genetic programs, it is increasingly possible to explore various isoforms of cancer associated genes. It is widely known that neurotrophins and their receptors (TrkA, TrkB, TrkC) are instrumental for neurodevelopment and that they remain critical for proper neuronal functioning throughout life. Our work highlights a previously unidentified role for an alternatively spliced neurotrophin receptor in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in humans and mice. This specific isoform, TrkB.T1, is the predominant NTRK2 isoform across embryonic organogenesis, and forced overexpression of this embryonic pattern causes multiple solid and nonsolid tumors in mice. TrkB.T1 also emerges as the predominant NTRK isoform expressed in a wide range of adult and pediatric tumors, including those harboring various NTRK fusions. This work hopes to address the fundamental question of how neurodevelopmental processes can go awry in cancer, while seeking to better characterize the role of TRKs, in normal developmental processes and oncogenesis.

Genomic Alterations in DNA Mismatch Repair Genes Across Different Cancer Types.

PD-1 inhibition is effective in patients with mismatch repair deficient (dMMR) solid tumors in a tumor-agnostic fashion. However, dMMR testing by immunohistochemistry (IHC) is not routinely performed across tumor types. By contrast, next-generation sequencing (NGS) for somatic genomic alterations is frequently performed across tumor types. We hypothesized that NGS would identify patients with alterations in mismatch repair (MMR) genes and that these patients would have higher rates of MMR protein loss by IHC. This would support the utility of IHC reflex testing after NGS and potential matching to approved therapeutic options. From January 2016 to December 2021, 15,701 patients with solid tumors received NGS covering the MMR genes, and 4,994 patients had both IHC and NGS. Sequencing results were analyzed for mutations in MMR genes, tumor type distribution, and concordance with IHC results when available. Six hundred and ninety-eight (4.4%) of 15,701 patients had mutations in one of the MMR genes. Mutations were found across tumor types. Three hundred and seventeen (6.3%) of 4,994 patients displayed IHC loss for at least one MMR protein. 33.8% patients (110/325) patients with MMR mutations had dMMR, compared with just 4.4% (207/4,669) patients without mutations (P < .001); dMMR rate varied by mutation type. Mutations in MMR genes are found in multiple tumor types where IHC testing is not routine. Reflex IHC testing of patients carrying MMR gene mutations, especially those known or inferred to be inactivating, may identify more patients with dMMR and matched treatment options. However, dedicated IHC screening is needed to capture majority of the patients.

LINC01929 Is a Prognostic Biomarker for Multiple Tumours and Promotes Cell Proliferation in Breast Cancer Through the TNF/STAT3 Axis.

The aim of this study was to investigate whether long intergenic non-coding RNA 1929 (LINC01929), a novel long non-coding RNA, could serve as a prognostic biomarker for various tumours and explore its function. The expression and prognosis of LINC01929 across 33 different tumour types in patients in the Cancer Genome Atlas (TCGA) database were analysed. Also, the correlation between LINC01929 expression, tumour mutational burden (TMB), microsatellite instability (MSI), immune checkpoint status and immune cell infiltration was examined. Moreover, the function of LINC01929 in the breast cancer cell lines was explored via CCK-8, colony formation and cell cycle assays. In addition, the downstream mechanisms of LINC01929 were analysed via transcriptome sequencing, RT-qPCR, and western blotting. Our analysis revealed that LINC01929 was weakly expressed in 3 tumour types and highly expressed in 14 tumour types, and low expression of LINC01929 was correlated with better clinical outcomes in 15 tumour types. Furthermore, LINC01929 expression was correlated significantly with the TMB, MSI, immune checkpoint and immune cell infiltration across multiple tumour types. The knockdown of LINC01929 inhibited cell cycle progression, cell proliferation, and tumorigenesis and downregulated the TNF pathway and STAT3 expression. The treatment with exogenous TNF-α partially reversed the cell cycle progression and proliferation inhibition caused by LINC01929 knockdown, and these effects were accompanied by changes in STAT3 expression. LINC01929 may serve as an effective biomarker affecting the TMB, MSI, immune cell infiltration and immune checkpoint status. Mechanistically, LINC01929 affects cell cycle progression and cell proliferation through the TNF/STAT3 axis. These findings offer valuable insights into the potential applications of LINC01929 in tumour therapy, which may yield novel targets and strategies for the diagnosis and treatment of patients.

Leveraging Neural Crest-Derived Tumors to Identify NF1 Cancer Stem Cell Signatures.

Neurofibromatosis type 1 (NF1) is a genetic disorder that predisposes individuals to develop benign and malignant tumors of the nerve sheath. Understanding the signatures of cancer stem cells (CSCs) for NF1-associated tumors may facilitate the early detection of tumor progression. Background: Neural crest cells, the cell of origin of NF1-associated tumors, can initiate multiple tumor types, including melanoma, neuroblastoma, and schwannoma. CSCs within these tumors have been reported; however, identifying and targeting CSC populations remains a challenge. Results: This study aims to leverage existing studies on neural crest-derived CSCs to explore markers pertinent to NF1 tumorigenesis. By focusing on the molecular and cellular dynamics within these tumors, we summarize CSC signatures in tumor maintenance, progression, and treatment resistance. Conclusion: A review of these signatures in the context of NF1 will provide insights into NF1 tumor biology and pave the way for developing targeted therapies and improving treatment outcomes for NF1 patients.

Risk and Benefit for Basket Trials in Oncology: A Systematic Review and Meta-Analysis.

Oncology research is increasingly adopting new clinical trial models that implement the concept of precision medicine. One of these is the basket clinical trial design. Basket clinical trials allow new treatments to be evaluated across multiple tumor types. Patients recruited to basket clinical trials share certain molecular characteristics of their cancer that are predictive of clinical benefit from the experimental treatment. Our aim was to describe the risks and benefits of basket clinical trials in oncology. Our study was prospectively registered in PROSPERO (CRD42023406401). We systematically searched PubMed, Embase, and ClinicalTrials.gov for reports of basket clinical trials in oncology published between 1 January, 2001, and 14 June, 2023. We measured the risk by treatment-related adverse events (grades 3, 4, and 5), and the benefit by objective response rate. We also extracted and analyzed data on progression-free survival and overall survival. When possible, data were meta-analyzed. We included 126 arms of 75 basket clinical trials accounting for 7659 patients. The pooled objective response rate was 18.0% (95% confidence interval [CI] 14.8-21.1). The rate of treatment-related death was 0.7% (95% CI 0.4-1.0), while 30.4% (95% CI 24.2-36.7) of patients experienced grade 3/4 drug-related toxicity. The median progression-free survival was 3.1 months (95% CI 2.6-3.9), and the median overall survival was 8.9 months (95% CI 6.7-10.2). Our results provide an empirical basis for communicating about the risks and benefits of basket clinical trials and for refining new models of clinical trials applied in precision medicine.

Abstract A033: Pro-inflammatory tumor cells drive CD4+ T cell localization within heterogeneous tumors

Abstract Immunotherapies such as immune checkpoint inhibitors (ICIs) have greatly improved patient outcomes in multiple tumor types, but ICIs have failed to achieve responses in many patients. Meta-analyses of patient cohorts treated with ICIs have observed that worse clinical outcomes are strongly correlated with high levels of intratumoral genetic heterogeneity (ITH). ITH occurs when tumor cells mutate as they divide, typically due to oxidative stress or DNA damage from rapid proliferation and continued carcinogenic insults, generating tumor subclones. However, the mechanisms by which ITH impairs the anti-tumor immune response are not fully understood. We propose a novel mechanism for how ITH in highly T cell-infiltrated inflamed tumors can adversely affect T cell behavior. We hypothesize that strongly pro-inflammatory tumor subclones secreting robust pro-inflammatory chemokine profiles can dominate T cell trafficking within the tumor, resulting in a weakened immune response against other tumor subclones. Using a murine squamous cell skin carcinoma (SCC) model, we have demonstrated that in immune-inflamed tumors, the spatial distribution and behavior of tumor-infiltrating T cells is influenced by ITH. A strongly pro-inflammatory tumor line expressing an endogenous RFP fluorophore was mixed with a weakly pro-inflammatory tumor line expressing an endogenous YFP fluorophore at a 1:1 ratio. The resulting tumors contained distinct RFP+ and YFP+ regions. These were analyzed by immunofluorescence (IF) and by manually dissecting the tumors and analyzing each region by flow cytometry. Flow cytometry analysis determined that the strongly pro-inflammatory RFP+ regions contained significantly more total T cells and CD4+ T cells than YFP+ regions. Furthermore, FoxP3- “conventional” CD4+ T cells were significantly more likely to be “terminal effector-like” CD44+CD62L- in RFP+ regions, and significantly more likely to be “naïve-like” CD62L+CD44- in YFP+ regions. IF analysis confirmed the preferential distribution of CD4+ T cells in RFP+ regions, and observed that this spatial pattern was evident as early as 11 days after subcutaneous injection. Notably, this localization trend did not occur with CD8+ T cells, which were evenly dispersed throughout the tumors. ELISA analysis of lysates of both tumor cell lines determined that the pro-inflammatory RFP+ cell line secretes significantly higher levels of the chemokine CCL5, which has been observed by other studies to selectively mediate CD4+ T cell chemotaxis. These results demonstrate that intratumoral CD4+ trafficking is shaped by the spatial distribution of specific tumor subclones, and suggest tumor cell chemokine signaling may directly mediate T cell spatial localization and behavior within tumors. Citation Format: Robert Letchworth, Savannah Hughes, Abigail Keku, Melissa Reeves. Pro-inflammatory tumor cells drive CD4+ T cell localization within heterogeneous tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2024 Oct 18-21; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2024;12(10 Suppl):Abstract nr A033.

Melittin treatment suppressed malignant NSCLC progression through enhancing CTSB-mediated hyperautophagy

Melittin is preclinically investigated as anticancer agent in multiple tumor types. But its regulation role and regulatory mechanism regarding NSCLC is unknown. In our investigation, Proteomic test was employed to identify proteins that expressed abnormally in cancer cells and that with Melittin treatmented. The results showed CTSB was one of the Top proteins with different expression levels in the lysosomes of Melittin-treatmented cancer cells and showed an up-regulation trend. CTSB expression was increased in NSCLC cancer tissues compared to adjacent normal tissues, as demonstrated in lung cancer tissue chips experiment. However, Melittin treatment increased the CTSB level in lysosomes, which inhibited the malignant progression of NSCLC. We hypothesized that the relative homeostasis of CTSB in cancer cells was destroyed, and CTSB exerts its hydrolytic effect excessively, resulting in excessive autophagy of cancer cells, thus inhibiting the malignant progression of cancer cells. The direct combination of Melittin and CTSB was proposed by molecular docking technique, LiP-SMap was used to analyze the target genes and active components extracted from high-throughput sequencing proteomic data, and successfully verified that melittin was successfully demonstrated to directly target CTSB-binding. In vivo and in vitro studies have shown that Melittin treatment inhibits the malignant progression of A549 and HCC1833 cells and animal tumors, namely non-small cell lung cancer, by promoting CTSB-mediated hyperautophagy. CTSB-specific inhibitor CA-074 Me and autophagy inhibitor 3-MA treatment reversed the inhibit effect of Melittin to the malignant progression of NSCLC. Taken together, Melittin treatment inhibited malignant progression regarding NSCLC through enhancing CTSB-mediated hyperautophagy.

EBNA1BP2 identified as potential prognostic biomarker for multiple tumor types in pan-cancer analysis

BackgroundEpstein-Barr virus (EBV) infection has been closely linked to the development of various types of cancer. EB nuclear antigen 1 binding protein 2 (EBNA1BP2) is a crucial molecule for stable isolation of EBV in latent infection. However, the role of EBNA1BP2 in multiple tumor types is remains unclear. In this study, we comprehensively analyzed the functional characteristics of EBNA1BP2 and investigate its potential as a prognostic biomarker in pan-cancer.MethodsWe utilized data from TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) databases and employed various bioinformatics analysis tools, including TIMER2.0, HPA, GEPIA2.0, PrognoScan, cBioPortal, CancerSEA, and BioGRID to explore the expression pattern, prognostic value, immune infiltration, and methylation level of EBNA1BP2 in pan-cancer. Additionally, we conducted enrichment analysis of genes associated with EBNA1BP2 to identify potential biological functions and pathways.ResultsOur analysis revealed that EBNA1BP2 expression was significantly higher in tumor tissues compared to tumor-adjacent tissues. We observed that lower expression of EBNA1BP2 in adrenocortical carcinoma (ACC), brain lower grade glioma (LGG), sarcoma (SARC), and uterine carcinosarcoma (UCS) was significantly associated with improved overall survival (OS) and disease-free survival (DFS). Furthermore, the promoter methylation level of EBNA1BP2 was downregulated in the majority of cancer types. At the single-cell level, EBNA1BP2 was found to be positively correlated with cell cycle and DNA repair processes, while negatively correlated with hypoxia. Additionally, EBNA1BP2 was associated with the infiltration of immune cells such as B cells, cancer-associated fibroblast cells, and CD8+ T cells. Gene enrichment analysis indicated that EBNA1BP2 was mainly involved in nucleoplasm and RNA binding pathways.ConclusionOur findings suggest that EBNA1BP2 may serve as a potential prognostic biomarker for survival in pan-cancer. Further experimental studies are needed to validate these findings and explore the underlying mechanisms by which EBNA1BP2 contributes to tumorigenesis.

Clinical trial design for novel targeted agents in neuro-oncology.

Biomarker-based clinical trials investigating targeted treatments for brain tumors have surged due to better access to biomarker testing and a deeper grasp of the molecular basis of tumor development. The design of clinical trials is crucial for evaluating safety, confirming effectiveness, and affirming the clinical advantage of novel agents, with the goal of approval by regulatory authorities to expand patient treatment options. Given some challenges unique to brain tumors, early-stage clinical trials for novel targeted agents must integrate pharmacokinetics and tissue-based pharmacodynamic assessments to establish timely go-no-go decisions for larger studies. Surgical window-of-opportunity trials can allow for the comparison of treated and untreated tumor samples, verifying target engagement and its modulatory effects for evidence of biological activity. Due to the challenges of achieving the required sample sizes to power efficacy analyses, later-stage trials of targeted therapies can include basket trials which test one drug on multiple tumor types, while umbrella trials evaluate several biomarkers within a single histology. Platform trials can also be leveraged to investigate multiple biomarker-driven hypotheses within a unified protocol and can incorporate Bayesian algorithms for adaptive randomization. Selecting appropriate endpoints, such as progression-free survival or overall response rate, is crucial and novel response assessment criteria need to be considered in the context of the tumor and therapy being investigated. Lastly, inclusivity in trials is essential to address health disparities and engage diverse patient populations to ensure real-world impact. Future trials should build upon the knowledge gained from both initial achievements and past setbacks in the field.

The pan-cancer landscape presented ITGA7 as a prognostic determinant, tumor suppressor, and oncogene in multiple tumor types.

Integrin α7 (ITGA7) is an extracellular matrix-binding protein. Integrins are the main type of cell adhesive molecules in mammals, playing a role in many biological pathways. Although various studies have shown correlations between ITGA7 and various types of cancer, a comprehensive study at a pan-cancer level has not yet been conducted. In this study, we investigated the function of ITGA7 in distinct tumor types using the multi-omics relevant information, then two CeRNA regulatory network was drawn to identify the ITGA7 hub regulatory RNAs. The results indicated that the expression of ITGA7 varies in different tumors. Overexpression of ITGA7 was correlated with a worse OS in BLCA, LGG, and UVM, and the downregulation of ITGA7 was related to a worse OS in PAAD. In addition, BLCA, and UVM showed poor PFS in association with ITGA7 overexpression, and PAAD, SARC, and THCA indicated poor PFS in correlation with ITGA7 under expression. Further analyses of ITGA7 gene alteration data showed that ITGA7 amplifications may have an impact on Kidney Chromophobe prognosis. In 20 types of tumors, ITGA7 expression was linked to cancer-associated fibroblast infiltration. ITGA7 expression was linked to cancer-associated fibroblast infiltration. ITGA7-Related Gene Enrichment Analysis indicated that ITGA7 expression-correlated and functional binding genes were enriched in homotypic cell-cell adhesion, focal adhesion, and ECM-receptor interaction. This pan-cancer study found that abnormal expression of ITGA7 was correlated with poor prognosis and metastasis in different types of tumors. Thus, the ITGA7 gene may prove to be a promising biomarker for the prognosis and complication prevention of different cancers.