Oncolytic viruses offer promising immunotherapy for cancer but face challenges such as delivery, targeting, and immune clearance. Our prior work showed that vaccinia virus (VACV) displaying the complement regulator CD55 evaded complement-mediated clearance, enhancing delivery and targeting in xenograft models. Importantly, this modified VACV also escaped neutralizing antibodies (NAbs) in vitro, a finding with significant implications. To improve translational relevance, we independently evaluated NAb evasion in immunocompetent in vivo models and against human-derived NAbs. Our novel platform virus, SJ-650-a CD55-displaying VACV expressing murine GM-CSF-retained superior antitumor efficacy despite the presence of NAbs in syngeneic breast cancer models. Additionally, SJ-650 effectively evaded NAbs derived from the serum of a clinical VACV trial (REN026). NAb evasion was CD55 dependent, occurred independently of complement activity, and was mediated by steric hindrance via the extracellular CD55 motif. NAb pretreatment masked binding of the key viral entry proteins A27, L1, and H3 in control viruses lacking CD55, but these interactions remained intact in SJ-650. By circumventing both complement and antibody responses, SJ-650 significantly inhibited tumor growth in two metastasis models, inducing immunogenic cell death and reprogramming the tumor microenvironment. These findings support SJ-650's potential as a robust oncolytic platform with broad translational applicability.

Chimeric antigen receptor macrophages (CAR-M) are emerging as a next-generation cellular modality for therapies ranging from viral infection to solid tumors, leveraging innate phagocytic and antigen-presenting functions. Here, we compared CAR constructs incorporating intracellular signaling domains (ICDs) derived from CD3ζ, Fc gamma receptor IIa (CD32a), complement receptor 3 (CR3), and Toll-like receptor 4 (TLR4) in THP-1-derived monocytes and macrophages. Using an anti-viral SARS-CoV-2 model as a screening platform, we subsequently validated key findings in an anti-tumor mesothelin (MSLN) model. Results indicated that CARCD32a exhibited superior phagocytic capacity compared with CARCD3ζ in both monocytes and macrophages. While combining CR3 (CD11b and CD18) and CD32a domains did not enhance phagocytosis, it significantly increased the expression of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α). The incorporation of TLR4 signaling domain reduced surface CAR expression and phagocytic capacity but markedly increased inflammatory cytokine induction, suggesting that TLR4-driven cytokine production can be enhanced despite diminished phagocytosis in this setting. Furthermore, following phagocytosis, CAR-monocytes induced antigen-specific CD8+ T cell activation via antigen presentation. Collectively, these findings highlight CD32a-based and combinatorial ICD designs as a framework for functionally tuned CAR-M platform for solid tumor immunotherapy and anti-viral applications.

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies due to its highly immunosuppressive tumor microenvironment (TME), which limits effective therapeutic interventions. Here, we demonstrate that V-domain immunoglobulin suppressor of T cell activation (VISTA) plays a crucial role in orchestrating macrophage polarity within the PDAC TME. Using murine PDAC models, we show that VISTA deficiency markedly impairs tumor growth, leading to prolonged survival. Functionally, VISTA deficiency is linked to a shift in tumor-associated macrophages (TAMs) from an immunosuppressive phenotype marked by secreted phosphoprotein 1 (SPP1), to one enriched for C-X-C motif chemokine ligand 9 (CXCL9), indicative of a pro-inflammatory state. This shift is accompanied by enhanced recruitment of CXCR3⁺ CD8⁺ T cells with sustained cytotoxic potential, among which terminal exhaustion-like CD8+ T cell states are less prevalent. Additionally, VISTA-deficient TAMs exhibit increased antigen cross-presentation, further amplifying CD8+ T cell response against tumors. These findings are corroborated by human PDAC data, which reflect similar immune reprogramming trends. By defining the role of VISTA in controlling Cxcl9:Spp1 ratio and modulating CD8⁺ T cell dynamics, this study positions VISTA inhibition as a promising strategy to reshape the TME and potentiate anti-tumor immunity in PDAC.

Diffuse-type gastric cancer (DGC), characterized by poorly cohesive cells within fibrotic stroma, is associated with advanced disease and poor prognosis. Here, to identify distinct biomarkers for DGC compared with intestinal-type gastric cancer, we constructed a comprehensive large-scale signaling network using RNA-sequencing data from three genomic databases (The Cancer Genome Atlas, GSE62254 and GSE26253), developed a mathematical model and conducted simulation analyses. For validation, we used tissue microarray blocks of gastric cancers with immunohistochemical staining, single-cell RNA sequencing, primary cultures of cancer-associated fibroblasts (CAFs) and organoids, and a co-culture system involving CAFs and cancer cells. Signaling network analysis identified six differentially activated signaling components across the database, including BIRC5, TTK, NEK2, FHL1, NR2F1 and FBLN5. Among the differentially activated signaling components, high tumoral expression of fibulin-5 protein encoded by FBLN5 correlated with poor overall and disease-specific survival rates in patients with DGC, even after adjusting for the tumor, node, metastases (TNM) stage. Fibulin-5, derived from CAFs within DGC stroma, promoted organoid growth and epithelial-mesenchymal transition (EMT) in DGC cell lines via the cAMP response element-binding protein (CREB) pathway in a CAF co-culture system. FBLN5 knockdown in CAFs reduced the aggressive phenotype of co-cultured DGC cells, while CREB inhibitors reversed EMT. Furthermore, levels of secreted FBLN5 in patient blood samples correlated with its expression in primary tumors. In summary, fibulin-5 secreted by CAFs and interacted with DGC cells promotes EMT and is clinically associated with poor patient outcomes. These findings suggest fibulin-5 as a potential prognostic marker and therapeutic target in patients with DGC.

Immunoglobulin A (IgA) nephropathy (IgAN) is a prevalent primary glomerulonephritis with progressive potential. Early identification of high-risk patients is critical; however, current clinical and pathological markers are limited. This study aimed to identify epigenetic biomarkers in circulating CD8⁺ T cells that discriminate IgAN patients with different disease severity. Seventeen patients with biopsy-proven IgAN were stratified into early- and late-stage groups based on kidney function. CD8⁺ T cells were isolated and analyzed using transposase-accessible chromatin sequencing (ATAC-Seq) to assess chromatin accessibility. Differentially accessible regions (DARs) were identified and selected biomarkers were additionally analyzed with ATAC-qPCR. In total, 279 DARs were identified, of which 122 were selected as stage-specific biomarkers. CD8⁺ T cells from the early-stage group exhibited higher chromatin accessibility, and t-SNE showed a clear separation between the stages. Deconvolution analysis revealed the enrichment of naïve CD8⁺ T cells in the early-stage group and terminally differentiated effector memory CD8⁺ T cells in the late-stage group. Motif analysis uncovered distinct regulatory signatures: ETS1, LEF1, and RUNX2 in the early-stage, EOMES, TBX21, and IRF4 in the late stage. Receiver operating characteristic (ROC) analysis showed strong discriminatory power of the top biomarkers, enhanced by a composite weighted score. ATAC-qPCR confirmed the chromatin accessibility patterns observed using ATAC-Seq. This study defined stage-specific chromatin landscapes in the circulating CD8⁺ T cells of patients with IgAN and identified non-invasive epigenetic biomarkers associated with different disease severity, which may be utilized in early risk stratification and personalized management.

Deep learning presents a promising approach to complex biological classifications, contingent upon the availability of well-curated datasets. This study addresses the challenge of analyzing three-dimensional protein structures by introducing a novel pipeline that utilizes open-source tools to convert protein structures into a format amenable to computational analysis. Applying a two-dimensional convolutional neural network (CNN) to a dataset of 12,143 avian influenza virus genomes from 64 countries, encompassing 119 hemagglutinin (HA) and neuraminidase (NA) types, we achieved significant classification accuracy. The pathogenicity was determined based on the presence of H5 or H7 subtypes, and our models, ranging from zero to six mid-layers, indicated that a four-layer model most effectively identified highly pathogenic strains, with accuracies over 0.9. To enhance our approach, we incorporated Principal Component Analysis (PCA) for dimensionality reduction and one-class SVM for abnormality detection, improving model robustness through bootstrapping. Furthermore, the K-nearest neighbor (K-NN) algorithm was fine-tuned via hyperparameter optimization to corroborate the findings. The PCA identified distinct clustering for pathogenic HA, yielding an AUC of up to 0.85. The optimized K-NN model demonstrated an impressive accuracy between 0.96 and 0.97. These combined methodologies underscore our deep learning framework's capacity for rapid and precise identification of pathogenic avian influenza strains, thus providing a critical tool for managing global avian influenza threats.

Abstract Oncolytic viruses (OVs) are potent cancer therapeutics that can selectively kill tumor cells and promote anti-tumor immunity. mSJ-650 (Wyeth, K2L-, TK-, murine GM-CSF, human CD55) is the Wyeth strain of vaccinia virus with human complement regulatory protein CD55 incorporated on the intracellular mature virion membrane to evade complement-mediated attack during circulation. The virus also expresses mGM-CSF in replace of thymidine kinase to increase tumor selectivity and enhance immunogenicity. We previously reported that a single dose of mSJ-650 effectively evades complement and shows prominent anti-tumor efficacy in A549 and HCT116 xenograft model. Here, we further investigated the capability of mSJ-650 in promoting anti-tumor response after multiple systemic administration in immunocompetent breast cancer mouse model. In an orthotopic EMT6 breast cancer model, mSJ-650 or control mSJ-612 devoid of CD55 was intravenously injected at low dose (1x106 pfu) and high dose (3x106 pfu), twice weekly. mSJ-650 treatment dose-dependently suppressed tumor growth, showing superior antitumor efficacy compared to treatment of control mSJ-612. Moreover, multiple systemic administration of mSJ-650 was well-tolerated with no apparent signs of toxicity in serum tested via AST and ALT assay. To further elucidate whether mSJ-650 can evade neutralization by antibody and maintain its antitumor potency in vivo, we designed two experimental models. Firstly, endogenous vaccinia virus specific neutralizing antibody was generated by intravenous injection of mSJ-650 prior to tumor cell inoculation in tumor-bearing mouse, followed by systemic administration of mSJ-650 twice weekly. Second, serum containing vaccinia virus specific neutralizing antibody was intravenously injected 24 hours prior to mSJ-650 administration in tumor-bearing mouse. In both experimental models, mSJ-650 treated group significantly inhibited tumor growth despite the presence of neutralizing antibody, while control mSJ-612 treated group failed to suppress tumor growth. These results imply that mSJ-650 is capable of evading neutralization and maintaining its antitumor efficacy. Moreover, we performed multi-color flow cytometry analysis of tumor-infiltrating leukocytes to evaluate immunogenicity of mSJ-650. As a result, we observed a significant increase in recruitment of activated CD4+ and CD8+ T cells by 2-fold and high expression level of cytotoxic molecules (perforin, TNF-α, IFN-γ) in tumor-infiltrating T cells. In summary, multiple systemic administration of mSJ-650 markedly evaded neutralization and suppressed tumor growth by promoting anti-tumor response in immunocompetent breast cancer mouse model, thus implying that mSJ-650 is a promising candidate for cancer immunotherapy. Citation Format: Yeonsoo Yang, Solchan Won, Namhee Lee, Eunhye Kim, Songyi Lee, Mi-Ju Park, Byung-Jin Jung, Yun-Kyoung Hong, Hang-Rae Kim, Dong-Sup Lee, Keunhee Oh. A novel oncolytic vaccinia virus with intravenous compatibility evaded complement- and neutralizing antibody-mediated inhibition and provided superior anti-tumor activity to intra-tumoral administration in immunocompetent mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB354.

Chimeric antigen receptor (CAR)-T cell therapy has revolutionized cancer treatment. CARs are activated at the immunological synapse (IS) when their single-chain variable fragment (scFv) domain engages with an antigen, allowing them to directly eliminate cancer cells. Here, an innovative IS biosensor based on fluorescence resonance energy transfer (FRET) for the real-time assessment of CAR-IS architecture and signaling competence is presented. Using this biosensor, scFv variants for mesothelin-targeting CARs and identified as a novel scFv with enhanced CAR-T cell functionality despite its lower affinity than the original screened. The original CAR promoted internalization and trogocytosis, disrupting stable IS formation and impairing functionality are further observed. These findings emphasize the importance of enhancing IS quality rather than maximizing scFv affinity for superior CAR-T cell responses. Therefore, the FRET-based IS biosensor is a powerful tool for predicting CAR-T cell function, enabling the efficient engineering of next-generation CARs with enhanced antitumor potency.

Abstract Colorectal cancer (CRC) is the third most common cancer worldwide and nearly 50% of CRC patients develop liver metastasis during the course of their disease. Treatment of colorectal cancer liver metastasis (CRLM) has been particularly challenging due to tolerogenic nature of liver immune microenvironment as well as an eventual development of therapy resistance to standard chemotherapy regimen. One promising area of cancer immunotherapy is oncolytic virotherapy that can selectively destroy tumor cells and stimulate anti-tumor immune response. In this study, we systemically administered mSJ-650, an intravenous compatible oncolytic Wyeth strain vaccinia virus that expresses human complement regulatory protein CD55 and murine GM-CSF in place of viral thymidine kinase gene and has a deletion of the viral K2L gene, and evaluated its anti-tumor efficacy in CRLM. Mouse CRLM was induced by intrasplenic injection of 5×105 MC38-OVA cancer cells. Following tumor nodules formation in the liver, low dose (1×106 pfu) or high dose (3×106 pfu) of mSJ-650 was administered multiple times via tail vein and liver was harvested for evaluation of anti-tumor efficacy. Flow cytometry analysis was performed to investigate changes in hepatic and tumor immune microenvironment upon mSJ-650 treatment. Liver and tumor tissue were stained for immunofluorescence imaging of viral replication within the tumor cells and subsequent oncolysis by the virus. Systemic administration of mSJ-650 showed potent anti-tumor efficacy and led to significant reduction in metastatic nodule formation in liver even at low dose. The anti-tumor efficacy was mediated by tumor cell-specific viral distribution and replication, followed by lytic egress of mSJ-650 from infected tumor cells. Anti-tumor efficacy of mSJ-650 also accompanied a dramatic shift in immunologically tolerant hepatic microenvironment to immune-stimulatory one by decreasing proportion of myeloid-derived suppressor cells, Kupffer cells, and monocyte-derived macrophages (MDMs) in the liver while increasing CD8+ T cell infiltration by 2~3 folds. Moreover, mSJ-650 treatment was associated with phenotypic change in hepatic immune cells, as evidenced by Kupffer cell and MDM polarization to M1 phenotype and elevated expression of activation markers and cytotoxic molecules in CD8+ T cells. Changes in hepatic immune microenvironment were also observed in tumor nodules, especially in those completely surrounded by adjacent liver tissue, suggesting that anti-tumor immune response in tumor bed is potentiated by reprogramming of tumor-adjacent hepatic immune microenvironment. Systemic administration of mSJ-650 demonstrated superior anti-tumor efficacy in CRLM which was mediated by direct tumor cell killing and tumor-adjacent hepatic immune microenvironment reprogramming by the virus. Citation Format: Eunhye Kim, Yeonsoo Yang, Solchan Won, Namhee Lee, Songyi Lee, Mi-Ju Park, Byung-Jin Jung, Yun-Kyoung Hong, Hang-Rae Kim, Dong-Sup Lee, Keunhee Oh. An intravenous compatible oncolytic vaccinia virus treated hepatic metastasis of colon cancer through extensive cancer cell killing and activation of cytotoxic effector differentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB441.

The fourth vaccination dose confers additional protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in individuals with no prior coronavirus disease-19 (COVID-19). However, its immunological benefit against currently circulating BA.4/5 is unclear in individuals who have received a booster shot and been infected with Omicron variant BA.1/2. We analyzed immune responses in whom had been boosted once and did not have COVID-19 (n = 16), boosted once and had COVID-19 when BA.1/2 was dominant in Korea (Hybrid-6M group, n = 27), and boosted twice and did not have COVID-19 (Vx4 group, n = 15). Antibody binding activities against RBDo BA.1 and RBDo BA.4/5 , antigen-specific memory CD4+ and CD8+ T-cell responses against BA.4/5, and B-cell responses against SARS-CoV-2 wild-type did not differ statistically between the Hybrid-6M and Vx4 groups. The humoral and cellular immune responses of the Hybrid-6M group against BA.4/5 were comparable to those of the Vx4 group. Individuals who had been boosted and had an Omicron infection in early 2022 may not have high priority for an additional vaccination.

Adipose tissues are central in controlling metabolic homeostasis and failure in their preservation is associated with age-related metabolic disorders. The exact role of mature adipocytes in this phenomenon remains elusive. Here we describe the role of adipose branched-chain amino acid (BCAA) catabolism in this process. We found that adipocyte-specific Crtc2 knockout protected mice from age-associated metabolic decline. Multiomics analysis revealed that BCAA catabolism was impaired in aged visceral adipose tissues, leading to the activation of mechanistic target of rapamycin complex (mTORC1) signaling and the resultant cellular senescence, which was restored by Crtc2 knockout in adipocytes. Using single-cell RNA sequencing analysis, we found that age-associated decline in adipogenic potential of visceral adipose tissues was reinstated by Crtc2 knockout, via the reduction of BCAA-mTORC1 senescence-associated secretory phenotype axis. Collectively, we propose that perturbation of BCAA catabolism by CRTC2 is critical in instigating age-associated remodeling of adipose tissue and the resultant metabolic decline in vivo.

Introduction Tocilizumab, a humanized anti-interleukin-6 receptor (IL-6R) antibody, is recommended for the treatment of severe to critical coronavirus diseases 2019 (COVID-19). However, there were conflicting results on the efficacy of tocilizumab. Therefore, we hypothesized that the differences in tocilizumab efficacy may stem from the different immune responses of critical COVID-19 patients. In this study, we described two groups of immunologically distinct COVID-19 patients, based on their IL-6 response. Methods We prospectively enrolled critical COVID-19 patients, requiring oxygen support with a high flow nasal cannula or a mechanical ventilator, and analyzed their serial samples. An enzyme-linked immunosorbent assay and flow cytometry were used to evaluate the cytokine kinetics and cellular immune responses, respectively. Results A total of nine patients with critical COVID-19 were included. The high ( n = 5) and low IL-6 ( n = 4) groups were distinguished by their peak serum IL-6 levels, using 400 pg/mL as the cut-off value. Although the difference of flow cytometric data did not reach the level of statistical significance, the levels of pro-inflammatory cytokines and the frequencies of intermediate monocytes (CD14 + CD16 + ), IFN-γ + CD4 + or CD8 + T cells, and HLA-DR + PD-1 + CD4 + T cells were higher in the high IL-6 group than in the low IL-6 group. Conclusion There were distinctive two groups of critical COVID-19 according to serum IL-6 levels having different degrees of cytokinemia and T-cell responses. Our results indicate that the use of immune modulators should be more tailored in patients with critical COVID-19.

Background: The clinical outcomes and immunological features of coronavirus disease 2019 (COVID-19) patients receiving B-cell depletion therapy (BCDT), especially in Omicron variant era, have not been fully elucidated. We aimed to investigate the outcomes and immune responses of COVID-19 patients receiving BCDT during the Omicron period.Methods: We retrospectively compared clinical outcomes between COVID-19 patients treated with BCDT (the BCDT group) and those with the same underlying diseases not treated with BCDT (the non-BCDT group). For immunological analyses, we prospectively enrolled COVID-19 patients receiving BCDT and immunocompetent COVID-19 patients as controls. We measured humoral and cellular immune responses using the enzyme-linked immunosorbent assay and flow cytometry.Results: Severe to critical COVID-19 was more frequent in the BCDT group than in the non-BCDT group (41.9% vs. 28.3%, p = .030). BCDT was an independent risk factor for severe to critical COVID-19 (adjusted odds ratio [aOR] 2.21, 95% confidence interval [CI] 1.21-4.04, p = .010) as well as for COVID-19-related mortality (aOR 4.03, 95% CI 1.17-13.86, p = .027). Immunological analyses revealed that patients receiving BCDT had lower anti-S1 IgG titres and a tendency to higher proportions of activated CD4+ T-cells than the controls.Conclusions: BCDT was associated with worse COVID-19 outcomes in the Omicron period. Humoral immune response impairment and T-cell hyperactivation were the main immunological features of COVID-19 patients treated with BCDT, which may have contributed to the worse outcomes of COVID-19 in this population.

Background:Little is known about the immune determinants for severe coronavirus disease 2019 (COVID-19) in individuals vaccinated against severe acute respiratory syndrome coronavirus 2. We therefore attempted to identify differences in humoral and cellular immune responses between patients with non-severe and severe breakthrough COVID-19.Methods:We prospectively enrolled hospitalized patients with breakthrough COVID-19 (severe and non-severe groups) and uninfected individuals who were vaccinated at a similar time (control group). Severe cases were defined as those who required oxygen therapy while hospitalized. Enzyme-linked immunosorbent assays and flow cytometry were used to evaluate humoral and cellular immune responses, respectively.Results:Anti-S1 IgG titers were significantly lower in the severe group than in the non-severe group within 1 week of symptom onset and higher in the non-severe group than in the control group. Compared with the control group, the cellular immune response tended to be diminished in breakthrough cases, particularly in the severe group. In multivariate analysis, advanced age and low anti-S1 IgG titer were associated with severe breakthrough COVID-19.Conclusions:Severe breakthrough COVID-19 might be attributed by low humoral and cellular immune responses early after infection. In the vaccinated population, delayed humoral and cellular immune responses may contribute to severe breakthrough COVID-19.

Despite the importance of antigen-specific T cells in infectious disease, characterizing and tracking clonally amplified T cells during the progression of a patient's symptoms remain unclear. Here, we performed a longitudinal, in-depth single-cell multiomics analysis of samples from asymptomatic, mild, usual severe, and delayed severe patients of SARS-CoV-2 infection. Our in-depth analysis revealed that hyperactive or improper T-cell responses were more aggressive in delayed severe patients. Interestingly, tracking of antigen-specific T-cell receptor (TCR) clonotypes along the developmental trajectory indicated an attenuation in functional T cells upon severity. In addition, increased glycolysis and interleukin-6 signaling in the cytotoxic T cells were markedly distinct in delayed severe patients compared to usual severe patients, particularly in the middle and late stages of infection. Tracking B-cell receptor clonotypes also revealed distinct transitions and somatic hypermutations within B cells across different levels of disease severity. Our results suggest that single-cell TCR clonotype tracking can distinguish the severity of patients through immunological hallmarks, leading to a better understanding of the severity differences in and improving the management of infectious diseases by analyzing the dynamics of immune responses over time.