tbuckley/cabot-search huggingface dataset:
Single-cell transcriptome sequencing to explore the infiltration and disappearance of NK cells in liver cancer.
Authors: Hongyu Cang, Yingchun Qin, Yuting Shi, Tianliang Liu, Shaochen Cheng, Yingxiang Li, Run Liang
Journal: Journal of Clinical Oncology (2024)

e14520 Background: The emergence of tumor immunotherapy such as immune checkpoint blocking has greatly promoted the development of Hepatocellular carcinoma (HCC) treatment. However, the response rate of HCC patients to immunotherapy is not high, and the probability of adverse reactions is high. Natural killer (NK) cells play a crucial role in inhibiting the proliferation and metastasis of tumor cells and are expected to become a new hope for tumor therapy. Methods: The HCC single-cell transcriptome atlas was constructed by using the tumor tissues, adjacent tissues, peripheral blood of HCC patients. To emulate the hypoxic state within the tumor, NK cells were treated with rotenone, and the post-rotenone treatment changes of NK cells in transcriptome levels were evaluated using qPCR. The proliferation, apoptosis, and cytotoxicity of NK cells were assessed via flow cytometry. The study also investigated the role of c-Jun N-terminal protein kinase (JNK) in NK cell function by applying the JNK inhibitor tanzisertib (CC-930) in vitro. The impact of JNK inhibition on the tumor-killing potential of NK cells was examined in vivo using tumor-bearing mice NCG (NOD/ShiLtJ-Prkdc em26Cd52 Il2rg em26Cd22 /Gpt). Results: Analysis of the source of NK cell subsets found that the specific NK cells in tumor tissues were tissue-resident NK cells (trNK). Both RNA velocity analysis and pseudo-time sequence analysis suggested that trNK cells differentiated from PBMC-1 NK cells. Upon treatment of PBMC-1 NK cells with Tanzisertib, we observed inhibition of NK cell apoptosis. Through the subcutaneous tumor formation experiment of NCG mice, Tanzisertib-treated NK cells were transferred into tumor-bearing mice. Notably, we observed a significant reduction in tumor weight (Before treatment: 0.19g, 0.19g, 0.22g, 0.24g, 0.26g, 0.27g; After treatment: 0.16g, 0.17g, 0.17g, 0.19g, 0.21g, 0.23g; P value = 0.049). TUNEL assay confirmed a significant increase number of apoptotic cells within the tumor and an increased number of infiltrated NK cells. Conclusions: The NK cells in HCC tumors are likely derived from the infiltration of NK cells in peripheral blood. Importantly, the inhibition of JNK function can significantly inhibit the apoptosis of NK cells and enhance the killing ability of NK cells against tumor cells in vivo.
Intravenous infusion (IV) or intracavitary perfusion (IP) of T3011, an oncolytic HSV expressing IL-12 and PD-1 antibody: Analyses of two phase 1 studies.
Authors: Jiaxin Niu, Minal A. Barve, Alexander I. Spira, William Jeffery Edenfield, Kevin Wang, Gaiyun Liu, Meredith McKean, Wenmin Fu, Meng Qiu, Peng Cheng
Journal: Journal of Clinical Oncology (2024)

e14581 Background: T3011 is a recombinant HSV-1 oncolytic virus expressing both IL-12 and anti-human PD-1 antibody. Upon delivery, locally produced IL-12 and PD-1 induces IFN-γ production, enhances the oncolytic activity of NK cells and cytotoxic T lymphocytes, promotes anti-angiogenesis, and inhibits tumor growth. We present the results of T3011 monotherapy administered via IV in advanced solid tumors or IP for malignant pleural effusion/ascites. Methods: In a phase 1, dose-escalation and expansion study using a 3+3 design with 5 cohorts (1×10 6 , 1×10 7 , 1×10 8 , 5×10 8 , 1×10 9 PFU), T3011 was administered intravenously on Days 1, 4, 8, 11,15,18 of a 28-day cycle in pts with advanced solid tumors. The primary objective was to evaluate the safety and tolerability of IV T3011, characterize dose-limiting toxicities (DLTs), MTD or RP2D, pharmacokinetic and pharmacodynamic profiles. In another pilot study to evaluate the safety and efficacy of T3011 in pts with malignant pleural effusion or ascites, T3011 was infused into the pleural or peritoneal cavity through an indwelling catheter on Days 1, 4, 8, 11 with 2 cohorts (5×10 8 , 2×10 9 PFU). The response of malignant pleural effusion or ascites was assessed by WHO criteria. Results: As of 15 Dec 2023, 18 pts were enrolled and treated with IV T3011,4 pts received IV T3011 therapy at the highest dose level, 1×10 9 PFU. T3011 was well tolerated without ≥ Grade 3 TRAEs or DLTs. MTD was not reached. The most common TRAEs (≥ 10%) were nausea and infusion-related reactions, diarrhea, etc. Among 14 evaluable pts with advanced solid tumors, 3 pts had confirmed SD per RECIST1.1 and tumor burden reduced significantly. All the pts had detectable T3011 DNA in blood within 0.5-2 hours after administration, which was cleared subsequently within 3-7 days. As of 5 Jan 2024, 6 pts (pleural effusion 3, ascites 3) were dosed with IP T3011. 2 pts received 5×10 8 PFU and 4 pts received 2×10 9 PFU. Most TEAEs were grade 1 or 2. Only 1 pt developed grade 3 leukopenia, which resolved with G-CSF. No SAE occurred. 3 pts with pleural effusion showed 1 CR, 1 PR and 1 SD. 3 pts with malignant ascites secondary to advanced colorectal cancer, 1 was evaluable with PR. Conclusions: IV T3011 monotherapy has a very manageable safety profile and some encouraging activity in advanced solid tumors. IP T3011 monotherapy is also well tolerated and demonstrates promising activity against malignant pleural effusion and ascites. Clinical trial information: NCT04780217 .
In vitro cell killing proficiency of autologous immune cells educated with allogenic multi-cancer tumor cell lysate.
Authors: Rajan Datar, Raymond Page, Darshana Patil, Kirubakaran Shanmugam, Dadasaheb Akolkar
Journal: Journal of Clinical Oncology (2024)

e14675 Background: Allogenic tumor lysate therapies offer a novel approach in oncology, to initiate a measured immune system response to combat cancer. Loaded with tumor antigens, these lysates stimulate the patient's immune system for targeted cancer cell destruction. In vitro data suggesting efficacy is pivotal prior to clinical trials. Per-C-Vax is a novel, organ-agnostic, allogenic tumor lysate immuno-stimulant, and is intended to target solid organ malignancies via subcutaneous injection. It is derived from a multi-organ cell-line cocktail, which has been induced into apoptosis to capture diverse Tumor Associated Molecular Patterns (TAMPs) and Damage Associated Molecular Patterns (DAMPs). Our study assesses Per-C-Vax-educated patient-specific immunocytes' in-vitro cell-killing activity against their autologous tumor cells. Methods: We collected simultaneous blood and tumor tissue samples from 22 patients with solid organ tumors under approved protocols. The cohort included 10 head and neck (45%), 4 breast (18%), and 8 other cancers (36%) comprising colorectal, ovary, lung, gallbladder, prostate, uterine, cervix, and gastric cancers. Peripheral Blood Mononuclear Cells (PBMCs) from a 10 ml venous draw were split into control and Per-C-Vax incubated aliquots for each patient. Approximately 1,000 tumor cells, stained with Calcein AM, were co-cultured with about 20,000 cells from each of the Per-C-Vax and control PBMC aliquots (autologous). Imaging-based pre- and post-co-culture counts determined the cell-kill rate for each aliquot. Results: PBMCs not treated with Per C Vax showed a significantly reduced cancer cell killing activity against autologous tumor cells compared to Per-C-Vax -treated PBMCs, suggesting the tolerogenic characteristic of immunocytes to the malignancy (0%-32%, 95% CI 10.16 to 16.65). On the other hand, PBMCs treated with Per-C-Vax showed significant cell-kill activity ranging from 46% to 84% in head and neck (mean 62.1%, 95% CI 52.67 to 71.53), 51% to 73% in breast (mean 62%, 95% CI 44.33 to 79.67), 38% to 87% in other cancers (colorectal, ovary, lung, gallbladder, prostate, uterine, cervix, gastric) (mean 50.87%, 95% CI 37.71 to 64.04). A comparative analysis between the untreated group and the group treated with Per-C-Vax revealed a statistically significant result with a p-value &lt;0.005. Conclusions: Patient-specific PBMCs incubated with Per-C-Vax tumor lysate immuno-stimulant show significant autologous cancer cell killing activity against multiple cancers in vitro. Human trials to establish safety and efficacy are planned.
Low-dose radiation as a preconditioning regimen for dendritic cell vaccines.
Authors: Eric Kwon, Shelby Namen, Solomon Kang, Colin Willoughby, Kevin Zhang, Guarav Pandey, Joanna Chensi Yang, Carl DeSelm
Journal: Journal of Clinical Oncology (2024)

e14519 Background: Dendritic cells are potent antigen-presenting cells that induce the adaptive immune system to protect against cancer. While anti-tumor immunity can be improved with dendritic cell vaccines, it is not fully known what approved preconditioning agents, if any, improve dendritic cell vaccine-induced antitumor T-cell response and tumor elimination. We explored the effect of low-dose radiation (LDR), cyclophosphamide, and paclitaxel as preconditioning regiments for a dendritic cell vaccine. Methods: KP tumors were engineered with ovalbumin and orthotopically injected subcutaneously (SQ) into the flank of wild type B6 mice. Preconditioning regiments of a control, LDR (2 Gy), cyclophosphamide (20mg/kg), LDR (2 Gy) + cyclophosphamide (20mg/kg), and paclitaxel (20mg/kg) were given on day 4. Bone marrow dendritic cells (DCs) were electroporated with ovalbumin peptide SIINFEKL and then one million cells were injected i.v. on day 5 and 8. Blood collection was done and ovalbumin-specific T-cell populations were examined by tetramer staining for SIINFEKL-specific TCR over time. Tumor size was measured over time and survival data was analyzed accordingly. Results: LDR effectively produced a significant increase in CD8+ SIINFEKL tetramer+ T-cell count per uL of blood compared to the non-preconditioned group. In addition, this LDR preconditioning regiment produced a significantly improved tumor response over time. The overall survival rate of subjects receiving LDR was significantly improved compared to all other groups. Conclusions: Here, we find that LDR is most effective as a preconditioning regimen prior to dendritic cell vaccination for inducing an antitumor T-cell response and achieving tumor control over time. LDR provides a promising method to supplement dendritic cell vaccination and potentially improve patient outcomes. Further study is needed to confirm its efficacy.
Impact of the tumor proportion score (TPS) and the combined positive score (CPS) on the use of immunotherapy in patients with metastatic non-small cell lung cancer.
Authors: Duaa Kanan, Tarek Kanan, Serkan Celik, Ezgi Hacıhasanoğlu, Basak Bala Oven
Journal: Journal of Clinical Oncology (2024)

e14611 Background: Expression of programmed cell death ligand 1 (PD-L1) in non-small cell lung cancer (NSCLC) has often been measured by the Tumor Proportion Score (TPS) (1). Recently, the Combined Positive Score (CPS), which evaluates PD-L1 expression in tumor and inflammatory cells and applies to other types of cancer including gastric and head and neck cancers, was found to be equally predictive of the response to immunotherapy in NSCLC (1). In this study, we aimed to conduct a single center retrospective analysis to evaluate the clinical use and impact of using TPS and CPS data in patients with metastatic NSCLC. Methods: Patients with NSCLC who had TPS and CPS scores and received PD-1/PD-L1 inhibitors between 2021-2022 as a monotherapy or in combination with chemotherapy were included. Patients’ data was retrieved from the electronic medical record data and analysis included histopathological data, lung cancer surgical history, presence of EGFR mutation, ALK mutation, Ki67, use of adjuvant chemotherapy, type of immunotherapy used, and development of immune checkpoint inhibitor- related toxicity and treatment as applicable. TPS and CPS positivity was defined as &gt;1 % and &gt;1 respectively. Statistical methods employed included descriptive approaches such as calculated means as well as the Kaplan-Meier estimate. Results: 40 patients with NSCLC were included. Patients’ age ranged from 19 to 82 years old with an average age of 64.3 years old. Most patients had adenocarcinoma (65 %) and were at stage IV (72.5 %). TPS positivity was identified in 29 patients (72.5 %) and CPS positivity was identified in 35 patients (87.5 %). Patients received immunotherapy mostly as first or second line of treatment (90 %). Immune checkpoint inhibitors received by patients were pembrolizumab (50 %), nivolumab (35 %), atezolizumab (12.5 %), and durvalumab (2.5 %). The median overall survival was 16, 12, and 17 months in the &lt;1 %, 1-49 % and &gt; 49 % TPS groups respectively (p= 0.354); while the median overall survival was 11, 16 and 17 months in the &lt;1, 1-49, and &gt; 49 CPS groups respectively (p= 0.417). It is critical to highlight that there were 7 patients (17.5 %) with TPS of zero who had CPS positivity (score range: 1-10). Most of these patients had adenocarcinoma (71.4 %), received pembrolizumab or atezolizumab (85.7 %) and had a median survival of 16 months. Conclusions: The Combined Positive Score (CPS) has proven to be an effective method in evaluating the level of expression of PD-L1 in NSCLC (1,2). Similar to TPS, CPS provides critical information that can be applied to guide the use of immunotherapy, and which can greatly impact patients with NSCLC. 1. De Marchi et al., 2021. 2. Ulas et al., 2023.
Effect of a novel anti-PD-1-proIL-2 bifunctional fusion protein on potent anti-tumor activity via PD-1 checkpoint inhibition and conditional IL-2R agonism.
Authors: Harry Zhou, Zijuan Li, Feifei Zhang, Ze Zhang
Journal: Journal of Clinical Oncology (2024)

e14697 Background: HD IL-2 was approved by FDA for metastatic melanoma (mM) and renal cell carcinoma (mRCC) but the treatment is associated with severe toxicities. PD-1 blockade has improved the overall survival, but only in 20-30% of cancer patients and many of them experience frequent relapses. Interestingly, HD IL-2 therapy displayed durable anti-tumor activity in mM and mRCC patients who progressed on anti-PD-1. Furthermore, combination therapy of IL-2 and pembrolizumab in mRCC has shown durable 70% response rate, while the ORR of monotherapy is 20% and 33% for IL-2 and pembrolizumab, respectively. Thus, combining IL-2 receptor activation and PD-1 blockade may represent a promising strategy in the post PD-1 era to overcome the resistance and improve the clinical efficacy. PTX-912 is a novel bifunctional PD-1-proIL-2v fusion protein designed to simultaneously harness PD-1 blockade and PD-1-cis directed IL-2R agonism conditionally in TME without the peripheral toxicities associated with IL-2. Methods: The biological functions were demonstrated in human PBMC assays. Anti-tumor efficacy and biomarker studies were evaluated in mouse / human PBMC xenograft models. Tox studies were performed in NHP. Results: PTX-912 shows dose-dependent inhibition of PD-1 pathway measured by GM-CSF and IFNgamma production in an MLR assay. Protease activated PTX-912, but not the intact drug, stimulates the phosphorylation of STAT5 of NK and T cells, the proliferation of CD8 T cells as well as the cytokine production in human whole blood. The potency of pSTAT5 by protease activated product is enhanced by &gt; 10 folds on PD-1 + T cells than T cells without PD-1. When tested in mouse tumor models resistant to PD-1 blockade, PTX-912 demonstrated high potency of tumor inhibition at as low as 0.1 mg/kg dose. In contrast, non-targeted proIL-2v at molar equivalent or higher dose showed minimal antitumor effect in either monotherapy or combination with anti-PD-1. Analysis of PTX-912 treated mice showed increased tumor infiltrating CD4 + and CD8 + T cells, including PD-1 + Tcf-1 + and PD-1 + IL-18Ra + TIM3 - CD8 + T cells, referred to “stem-like” progenitor effector cells and “better” effector cells, respectively. Activation of the IL-2v in PTX-912 was observed in mouse tumor tissues but not in the plasma. In monkey GLP-compliant 4-week repeat-dose toxicity study, PTX-912 demonstrated excellent safety profiles without overt irAEs that are characteristic of IL-2. Conclusions: Our preclinical data demonstrated that PTX-912 effectively stimulated the expansion and reinvigoration of antigen specific T cells in the tumor tissue resulting in strong anti-tumor efficacy while it did not cause significant peripheral toxicity. Phase 1 clinical trial of PD-1-proIL-2v is planned to start in early 2024 to evaluate the safety, pharmacokinetics and anti-tumor activity in patients with advanced solid tumors.
CRPA1A2: A novel TCR-based T-cell engager targeting MAGEA1-positive solid tumors.
Authors: Xingwang Xie, Dong J, Jinglei Bi, Jiahui Zhai, Baoqi Yan, Yonghong Li, Jianghua Wang, Yaping Zhu
Journal: Journal of Clinical Oncology (2024)

e14589 Background: MAGEA1, identified as a cancer/testis antigen, is highly expression in various solid tumors, including hepatocellular carcinoma, non-small cell lung cancer, but absent in normal tissues except male germ cells and placenta, both of which lacking HLA class molecules. This selective expression of HLA-MAGEA1 epitope makes it a promising target for cancer therapy. However, its intracellular localization poses a challenge for conventional antibodies designed to target surface-expressed antigens. TCR-based T-cell engagers, such as Tebentafusp, overcome this hurdle by targeting intracellular protein-derived peptides presented on cancer cell surfaces via HLA, enabling precise cytotoxic T cell attacks. Notably, Tebentafusp has shown significant clinical benefits by improving survival rates in metastatic uveal melanoma, underscoring the efficacy of TCR-based T-cell engagers in treating MAGEA1-positive tumors. Methods: We have developed an advanced structural format, CR62, consisting of a anti-CD3 single chain fragment, a soluble modified TCR, and an Fc region. Additionally, the use of CorreGene's SMART-TCR system has facilitated the acquisition of TCRs with high affinities in the pico-molar range. By leveraging CR62 and a high-affinity TCR, we have conceptualized the TCR-based T-cell engager, CRPA1A2. Comprehensive preclinical assessments have been conducted to evaluate CRPA1A2's safety and efficacy. Results: CRPA1A2 is designed to specifically target the HLA-A*02:01-restricted MAGEA1 epitope, effectively inhibiting tumor growth. CRPA1A2 is characterized by its exceptional soluble expression in CHO cells, minimal homodimer miss-assembly and simplifying purification. It is strategically engineered with a high-affinity TCR and a low-affinity anti-CD3 scFv to optimize the efficacy and safety. In vitro studies, CRPA1A2 showed strong ability to eliminate tumor cells and induce IFN-γ release, effective even at low MAGEA1 epitope densities, with a therapeutic window that spans over three orders of magnitude, suggesting a 1000-fold greater activity against antigen-positive cancer cells compared to antigen-negative cells. In vivo, using a tumor-bearing mouse model, CRPA1A2 has been shown to recruit T cells into subcutaneous solid tumors, expand CD8+ T cell populations, and significantly reduce tumor mass. Notably, CRPA1A2 has an extended half-life of 120 hours and demonstrates preferential accumulation in tumor tissues, thereby enhancing its therapeutic potential. Moreover, the safety assessments for CRPA1A2 highlight its exceptional specificity, with in vitro studies showing no evidence of off-target toxicity, on-target off-tumor toxicity, or alloreactivity and favorable tolerance in mice during in vivo studies. Conclusions: CRPA1A2 has emerged as a superior TCR-based T-cell engager with exceptional antitumor efficacy and promising safety profile.
Tumor purity as confounder for the determination of tumor mutational burden (TMB).
Authors: Susanne Beck, Michael Menzel, Daniel Kazdal, Peter Schirmacher, Albrecht Stenzinger, Jan Budczies
Journal: Journal of Clinical Oncology (2024)

e14656 Background: TMB determination is a prerequisite to stratify advanced cancer patients for pembrolizumab based on the histology-agnostic FDA approval. The accuracy of TMB measurement is challenged by low tumor purity resulting in a lower number of detected somatic variants for a fixed threshold of variant allele frequency (VAF) and a lower measured TMB level as a consequence. Methods: We derived a mathematical formula describing the influence of tumor purity on the VAF of somatic variants, in which the DNA copy number of the corresponding region of the tumor genome is a parameter. We simulated the effect of tumor purity in a cohort of 4,900 tumors from the TCGA project with tumor purity of at least 80%. TMB was calculated as the number of missense mutations with VAF greater or equal than 5%. Tumors were classified as TMB-high when harboring at least 199 missense mutations. This cutpoint corresponds to 10 mut/Mb as derived in the TMB bridging study. We compared tumors with a simulated tumor purity of 70%, 60%, ..., and 10% with tumors with a tumor purity of 80%, which served as reference. Results: The median of TMB in the pan-cancer cohort was reduced by 2%, 10%, and 32% for tumor purity of 60%, 40%, and 20% compared to the reference of 80%. For the 10% tumors with the worst estimation, TMB was reduced even by 12%, 35%, and 77% or more, respectively. In the pan-cancer cohort, the sensitivity to detect high TMB was 98%, 90%, and 62% for tumor purity of 60%, 40%, and 20%, respectively. For head and neck cancer, lung adenocarcinoma, lung squamous cell carcinoma, and cutaneous melanoma, the sensitivity to detect high TMB was 80%, 89%, 92%, and 91%, respectively, for tumors of tumor purity 40%. Conclusions: High tumor purity is critical for accurate determination of the TMB and to reach a high sensitivity concerning the selection of patients for immunotherapy. As shown by the simulations, the sensitivity to detect high TMB is close to 100% for tumor purity of at least 60%, while a substantial proportion of patients that could receive immunotherapy is missed for tumors with purity of 40% or less. Potential ways out of the TMB underestimation include increasing the sequencing coverage and lowering the VAF threshold for mutation calling or using clonal TMB with an adapted cutpoint instead of total TMB as biomarker for immunotherapy guidance.