bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S3 from Antitumor Immune Responses in B2M-Deficient Cancers
Authors: Torrejon Davis Y. , Galvez Mildred , Abril-Rodriguez Gabriel , Campbell Katie M. , Medina Egmidio , Vega-Crespo Agustin , Kalbasi Anusha , Comin-Anduix Begoña , Ribas Antoni
Published: December 2023

CIBERSORTx p-value versus tumor purity. Scatterplot of the samples (n=100) analyzed through CIBERSORTx with p-value readout on the x-axis and tumor purity (WES) on the y-axis; Pearson correlation R2= 0.11, p<2.2 x 10-16.
Data from Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma
Authors: Yao Tengteng , Zhang Zhe , Li Qian , Huang Rui , Hong Yanhong , Li Chen , Zhang Feng , Huang Yingying , Fang Yan , Cao Qin , Jin Xiaoliang , Li Chunliang , Wang Zefeng , Lin Xinhua (James) , Li Lingjie , Wei Wu , Wang Zhaoyang , Shen Jianfeng
Published: December 2023

Abstract
Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, the identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source, single-nucleotide variants (SNV), alternative splicing (AS) represents another rich source of neoepitopes and can be utilized in cancers with low SNVs such as uveal melanoma (UM). UM, the most prevalent adult ocular malignancy, has poor clinical outcomes due to a lack of effective therapies. Recent studies have revealed the promise of harnessing tumor neoepitopes to treat UM. Previous studies have focused on neoepitope targets associated with mutations in splicing factor 3b subunit 1 (SF3B1), a key splicing factor; however, little is known about the neoepitopes that are commonly shared by patients independent of SF3B1 status. To identify the AS-derived neoepitopes regardless of SF3B1 status, we herein used a comprehensive nanopore long-read-sequencing approach to elucidate the landscape of AS and novel isoforms in UM. We also performed high-resolution mass spectrometry to further validate the presence of neoepitope candidates and analyzed their structures using the AlphaFold2 algorithm. We experimentally evaluated the antitumor effects of these neoepitopes and found they induced robust immune responses by stimulating interferon (IFN)γ production and activating T cell–based UM tumor killing. These results provide novel insights into UM-specific neoepitopes independent of SF3B1 and lay the foundation for developing therapies by targeting these actionable neoepitopes.
Data from Effective Antitumor Immunity Can Be Triggered by Targeting VISTA in Combination with a TLR3-Specific Adjuvant
Authors: Wang Bo , Ou Ziwei , Zhong Wenlong , Huang Lin , Liao Wenjian , Sheng Yiyu , Guo Zhixing , Chen Junyu , Yang Wenjuan , Chen Ke , Huang Xiaodong , Yang Tenghao , Lin Tianxin , Huang Jian
Published: December 2023

Abstract
Resistance to anti–PD-1/PD-L1 treatment is often associated with accumulation of intratumoral inhibitory macrophages. V-domain immunoglobulin suppressor of T-cell activation (VISTA) is a nonredundant immune checkpoint that can induce both T-cell and myeloid-cell immunosuppression. In this study, we found that high levels of VISTA+ immune cells were associated with advanced stage bladder cancer and predicted poor survival in patients. A combination of high infiltration of VISTA+ immune cells and PD-L1+ immune cells or PD-1+ T cells predicted the worst survival. Flow cytometry and multiplex immunofluorescence analyses confirmed that VISTA expression was higher in macrophages than in T cells or neutrophils, and only VISTA+CD163+ macrophage density predicted poor prognosis in patients with bladder cancer. Toll-like receptor (TLR) agonists are known to trigger the innate immune response in macrophages. We found that the VISTA-specific mAb 13F3 augmented the ability of a TLR3-specific adjuvant to induce macrophage activation in vitro. In the MB49 syngeneic mouse model of bladder cancer, treatment with 13F3 curbed tumor growth and prolonged survival when combined with a TLR3-specific adjuvant. The combination treatment reduced the intratumoral frequency of CD206+ anti-inflammatory macrophages and levels of the immunosuppressive molecule TGFβ1, but it upregulated expression of immunostimulatory molecules (Ifna, Ifnb, and Trail) and increased the CD8+ T cell/regulatory T-cell ratio. These findings indicate that elevated VISTA expression in immune cells, particularly macrophages, is associated with an unfavorable prognosis in patients with bladder cancer and suggest that targeting VISTA in combination with a TLR3-specific adjuvant has translational potential.
Data from Tumor-Reactive CD8+ T Cells Enter a TCF1+PD-1− Dysfunctional State
Authors: Roetman Jessica J. , Erwin Megan M. , Rudloff Michael W. , Favret Natalie R. , Detrés Román Carlos R. , Apostolova Minna K.I. , Murray Kristen A. , Lee Ting-Fang , Lee Youngmin A. , Philip Mary
Published: December 2023

Abstract
T cells recognize several types of antigens in tumors, including aberrantly expressed, nonmutated proteins, which are therefore shared with normal tissue and referred to as self/shared-antigens (SSA), and mutated proteins or oncogenic viral proteins, which are referred to as tumor-specific antigens (TSA). Immunotherapies such as immune checkpoint blockade (ICB) can activate T-cell responses against TSA, leading to tumor control, and also against SSA, causing immune-related adverse events (irAE). To improve anti-TSA immunity while limiting anti-SSA autoreactivity, we need to understand how tumor-specific CD8+ T cells (TST) and SSA-specific CD8+ T (SST) cells differentiate in response to cognate antigens during tumorigenesis. Therefore, we developed a genetic cancer mouse model in which we can track TST and SST differentiation longitudinally as liver cancers develop. We found that both TST and SST lost effector function over time, but while TST persisted long term and had a dysfunctional/exhausted phenotype (including expression of PD1, CD39, and TOX), SST exited cell cycle prematurely and disappeared from liver lesions. However, SST persisted in spleens in a dysfunctional TCF1+PD-1– state: unable to produce effector cytokines or proliferate in response to ICB targeting PD-1 or PD-L1. Thus, our studies identify a dysfunctional T-cell state occupied by T cells reactive to SSA: a TCF1+PD-1– state lacking in effector function, demonstrating that the type/specificity of tumor antigen may determine tumor-reactive T-cell differentiation.
Abstract A027: Exploring autoantibody response to proteins encoded by prostate cancer driver genes
Authors: Zhang Jian-Ying , Qiu Cuipeng , Wang Xiao , Wang Bofei
Published: December 2023

Prostate cancer (PCa) is a complex disease driven by genomic alterations, and understanding the immune response to these alterations can provide valuable insights into the pathogenesis. This study aimed to explore the immunogenicity of proteins encoded by PCa driver genes and to further identify corresponding autoantibodies as potential biomarkers. Through a comprehensive screening process involving bioinformatics analysis based on published studies, a set of PCa driver genes was identified for further investigation. Three strategies were employed to identify candidate driver genes: (1) utilizing the IntOGen database (Martínez-Jiménez et.al, Nature Reviews Cancer 2020), nine cohorts comprising 1503 primary PCa patient samples were analyzed, resulting in the identification of 63 PCa driver genes, with the top 20 genes exhibiting high mutation rates and frequencies in these cohorts; (2) employing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 16 driver genes that were enriched in prostate cancer pathways were identified from the initial 63 genes; (3) referring to a published article (Dietlein et.al, Nature Genetics 2020), the top 17 driver genes specific to prostate cancer across 28 tumor types were selected. A final set of 15 PCa driver genes, which appeared in at least two of the screening strategies, were included in subsequent analyses. To assess the presence of autoantibodies targeting proteins encoded by these 15 PCa driver genes, an enzyme-linked immunosorbent assay (ELISA) was performed. Autoantibodies to proteins encoded by the selected PCa driver genes were evaluated using serum samples from PCa patients and normal controls. The results revealed that seven out of the 15 autoantibodies showed significantly elevated levels in the sera of PCa patients compared to normal controls. Notably, the autoantibody targeting SPOP (speckle-type POZ protein) exhibited the highest frequency of 42.4%, followed by the autoantibody to PTEN (phosphatase and tensin homolog) at 37.4% in the PCa group. These findings suggest that proteins encoded by PCa driver genes may possess immunogenic properties, leading to the production of corresponding autoantibodies. The identification of specific autoantibodies associated with PCa driver genes could offer novel opportunities for the discovery of autoantibody-based biomarkers in prostate cancer. Further validation and characterization of these autoantibodies are warranted to evaluate their diagnostic or prognostic potential and elucidate their functional roles in PCa pathogenesis.

Citation Format: Jian-Ying Zhang, Cuipeng Qiu, Xiao Wang, Bofei Wang. Exploring autoantibody response to proteins encoded by prostate cancer driver genes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A027.
Abstract PR02: Lyn kinase regulates myeloid-cell responses to mammary tumors
Authors: Greene Joseph T , Brian Ben F , Bapat Aditi , Freedman Tanya S
Published: December 2023

Myeloid-cell enrichment in tumors is correlated with increased metastasis, reduced survival times, and poor treatment outcomes in multiple cancers, including breast cancer. Many signals (CSF, Il-6, chemokine) to myeloid cells in the tumor microenvironment are transduced through the Src-family kinase Lyn. Expression of both isoforms of Lyn (LynA and LynB) is regulated by cytokine signaling and cell type, and total Lyn expression is negatively correlated with breast cancer patient survival. Lyn expression in macrophages contributes to leukemogenesis, but the functional contributions of LynA and LynB in solid tumors have not been studied. We are examining the contributions of Lyn in trafficking of myeloid cells to mammary tumors, pro-tumor polarization of tumor-associated macrophages, and growth and metastasis of mammary tumors. In an E0771 orthotopic transplant model in hosts expressing or lacking LynA or LynB expression, we have discovered that Lyn expression in the mammary tumor microenvironment promotes the early recruitment of monocytes, macrophages, neutrophils, and dendritic cells, as determined by flow cytometry analysis of tumors early in development. Furthermore, Lyn promotes pro-tumor polarization of tumor-associated macrophages. Tumors from Lyn knockout animals contained populations of inflammatory, anti-tumor macrophages that were not significantly different in size from WT, but the CD206+, anti-inflammatory population was reduced. Finally, we have observed that expression of either Lyn isoform in the tumor microenvironment can promote tumor growth and decrease survival in orthotopically transplanted mice. In contrast, our studies suggest that only LynB promotes metastasis to the lungs of transplanted mice, as determined by in vivo imaging of a hyper-metastatic, luciferase-expressing variant of E0771. Together, our findings suggest that Lyn kinase plays a role in the signaling response of myeloid cells, which are major factors in disease course and treatment response, to tumor-associated stimuli. Modulation of Lyn activity, specifically the LynB isoform, or the activity of its downstream signaling partners, is thus a potential strategy for influencing the trafficking and polarization of myeloid cells within breast tumors to benefit patients.

Citation Format: Joseph T Greene, Ben F Brian, Aditi Bapat, Tanya S Freedman. Lyn kinase regulates myeloid-cell responses to mammary tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr PR02.
Abstract PR04: Temporal single cell profiling identifies B-cell specific checkpoint molecules that regulate anti-tumor immunity
Authors: Bod Lloyd
Published: December 2023

B cells play key roles in both innate and adaptive immunity. Distinct specialized B cell subsets engage a range of responses from antigen presentation to antibody production and B cells are one of the most abundant cell types of tumor infiltrating leukocytes (TILs), especially in melanoma. However, their role in anti-tumor immunity remains unclear. Here, we examined the B cell repertoire at single cell resolution from tumor-infiltrating B cells and tumor-draining lymph nodes (dLN) and identify and characterize a subset of B cells expressing the checkpoint molecule TIM-1 and a unique transcriptional signature, including multiple co-inhibitory molecules such as PD-1, TIM-3, TIGIT and LAG-3. While conditional deletion of these co-inhibitory molecules on B cells had little or no effect on tumor burden, selective deletion of Havcr1 (the gene encoding TIM-1) in B cells both dramatically inhibited tumor growth and enhanced effector T cell responses. Mechanistically, loss of TIM-1 enhanced the type 1 interferon response in B cells, which augmented B cell activation and increased antigen presentation and co-stimulation, resulting in increased expansion of tumor-specific effector T cells. Our results demonstrate that manipulation of TIM-1-expressing B cells enables engagement of the second arm of adaptive immunity to promote anti-tumor immunity and inhibit tumor growth.

Citation Format: Lloyd Bod. Temporal single cell profiling identifies B-cell specific checkpoint molecules that regulate anti-tumor immunity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr PR04.
Supplementary Table S2 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Table S2
Supplementary Figure 9 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S9 shows cluster frequency per treatment group for each cluster.
Supplementary Figure 8 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S8 provides cluster identities.
Supplementary Figure 4 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S4 shows phenotype and cytotoxicity of murine B7-H3 CAR T cells.
Supplementary Figure 3 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S3 shows expression of murine B7-H3 CARs in producer cells and T cells.
Supplementary Figure 2 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S2 shows schematic of mB7-H3-CAR constructs.
Supplementary Figure 17 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S17 shows testing of BLZ945 effect on CAR T cell in vitro.
Supplementary Figure 15 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S15 shows GSEA of hallmark pathways in macrophage subclusters.
Supplementary Figure 13 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S13 shows cell-cell communication analysis within the TIME from our scRNAseq dataset.
Supplementary Figure 12 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S12 shows CAR presence in each cluster and GSEA analysis in specific clusters.
Supplementary Figure 10 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Supplementary Figure S10 shows diversity of T cell clusters per treatment group.
FIGURE 6 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Comprehensive flow cytometry analysis of the TIME from tumors at endpoint. Unsupervised clustering analysis of flow data from tumors at endpoint was done using algorithmic analysis with FlowJo software for phenotyping heterogenous populations based on multi-parameter marker expression. A, Experimental scheme. B, Representative cluster plot showing diversity of CD45+ cells from tumors with bar graph depicting quantitative analysis in each treatment group (Microglia CD45low; Activated microglia CD45low, F4/80low, MHCIIhigh, CD11blow; Immune cells CD45high). C, Graphical representation of the frequencies of major immune cell subsets per treatment group as defined by canonical cell surface markers. D and E, Quantitative plot of the CD4 and CD8 cell subsets after supervised subclustering analysis of lymphoid populations. F, Quantitative plot of myeloid cell populations per treatment group after supervised subclustering analysis. (cDC, conventional dendritic cells; pDC, plasmacytoid dendritic cells; TipDCs, TNF/iNOS-producing dendritic cells; PMN-MDSC, polymorphonuclear myeloid-derived suppressor cells; M-MDSC, monocytic myeloid-derived suppressor cells; MO-TAMs, monocyte-derived tumor associated macrophages; MG-TAMs, microglia-derived tumor associated macrophages).
FIGURE 5 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Successful responses with 28.mζ CAR T-cells are associated with balanced proinflammatory and anti-inflammatory myeloid cell responses. Seurat clusters 0, 7, 10, 14 were reclustered into 10 Mac/MG subclusters to further define the diversity of myeloid responses after CAR T-cell treatment. A, UMAP plots of the Mac/MG subclusters visualized by treatment group. B, Summary plot of Mac/MG subcluster 2 and 7 frequencies per treatment. Volcano plots showing differentially upregulated and downregulated genes in macrophage subclusters C2 in C, C7 in D as compared with all other myeloid subclusters. E, Dot plot depicting expression of myeloid lineage markers, genes associated with protumorigenic responses, antitumorigenic, and differentiation genes. Dot size represents the percentage of cells expressing each gene and dot color represents mean expression level with a gradient of lowest expression in blue to highest expression in red. F, Dot plot depicting differentially expressed genes associated with immunosuppression, invasion, recruitment, M1-like and M2-like macrophage responses per treatment group.
FIGURE 4 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

TIME heterogeneity after CAR T-cell treatment. A, Experimental scheme. Albino C57BL/6 mice were transplanted with 1 × 105 GL261 cells orthotopically, followed 25 days later by intratumoral injection of 3 × 106 mB7-H3-CAR T-cells (28.mζ, BBL-28.mζ,CD8tmBB.ζ, or Ctrl). Tumors were collected at 4 days after treatment and processed for scRNA-seq. Scheme created with BioRender.com. B, UMAP with major cell subsets in all tumor samples. C, Bar graph showing the percentage of each major cell type per treatment group. D, UMAP dimensionality reduction of single-cell data from all tumors clustered into 21 Seurat clusters annotated by number. E, UMAP visualization of the 21 Seurat clusters by treatment group from the best to the worst functioning CARs. Mac, macrophages; Mono, monocytes; MG, microglia; DC, dendritic cells.
FIGURE 3 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

CAR structural design significantly impacts anti-glioma efficacy of mB7-H3 CAR T-cells in the GL261 immunocompetent model. Albino C57BL/6 mice were transplanted with 1 × 105 GL261 cells orthotopically, followed 7 days later by intratumoral injection of 3 × 106 mB7-H3-CAR T-cells transduced with different constructs and adjusted to 40% CAR expression. A, Axial brain MRI images from 3 representative mice per treatment group at days 16 and 29 after tumor implantation. B, Summary plots showing percentage of survival and deceased mice within each treatment group at days 16, 29, and 45 after tumor implantation. C, Kaplan–Meier survival curve (n = 11, log-rank Mantel–Cox test with Bonferroni correction for multiple comparisons, *, P < 0.05; ***, P < 0.001). Experiments were repeated twice with CAR T-cells generated from 2 different T-cell donors. D, Summary table for performance of different mB7-H3 CAR designs from in vitro and in vivo data [(−) means no response, increasing number of (+) signs mean better response].
FIGURE 2 from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Surface expression of 41BBL on CD28-based mB7-H3-CAR T-cells enhances effector cytokines release in repeat stimulation assay. Culture supernatants were collected at 24 hours after repeated stimulation with GL261 tumor cells at 2:1 ratio and analyzed using Multiplex assay. Summary plots of cytokines and chemokines produced by CAR T-cells after first stimulation (A) and fourth stimulation (B) against GL261 tumor cells (n = 4, mean ± SEM, two-way ANOVA with Tukey test for multiple comparisons). C–E, CAR T-cell production of IFNγ, IL2, and GMCSF at 24 hours’ after stimulations one and four (n = 4, mean ± SEM, two-way ANOVA with Tukey test for multiple comparisons).
Data from CAR T-cell Design-dependent Remodeling of the Brain Tumor Immune Microenvironment Modulates Tumor-associated Macrophages and Anti-glioma Activity
Authors: Haydar Dalia , Ibañez-Vega Jorge , Crawford Jeremy Chase , Chou Ching-Heng , Guy Clifford S. , Meehl Michaela , Yi Zhongzhen , Perry Scott , Laxton Jonathan , Cunningham Trevor , Langfitt Deanna , Vogel Peter , DeRenzo Christopher , Gottschalk Stephen , Roussel Martine F. , Thomas Paul G. , Krenciute Giedre
Published: December 2023

Abstract
Understanding the intricate dynamics between adoptively transferred immune cells and the brain tumor immune microenvironment (TIME) is crucial for the development of effective T cell–based immunotherapies. In this study, we investigated the influence of the TIME and chimeric antigen receptor (CAR) design on the anti-glioma activity of B7-H3–specific CAR T-cells. Using an immunocompetent glioma model, we evaluated a panel of seven fully murine B7-H3 CARs with variations in transmembrane, costimulatory, and activation domains. We then investigated changes in the TIME following CAR T-cell therapy using high-dimensional flow cytometry and single-cell RNA sequencing. Our results show that five out of six B7-H3 CARs with single costimulatory domains demonstrated robust functionality in vitro. However, these CARs had significantly varied levels of antitumor activity in vivo. To enhance therapeutic effectiveness and persistence, we incorporated 41BB and CD28 costimulation through transgenic expression of 41BBL on CD28-based CAR T-cells. This CAR design was associated with significantly improved anti-glioma efficacy in vitro but did not result in similar improvements in vivo. Analysis of the TIME revealed that CAR T-cell therapy influenced the composition of the TIME, with the recruitment and activation of distinct macrophage and endogenous T-cell subsets crucial for successful antitumor responses. Indeed, complete brain macrophage depletion using a CSF1R inhibitor abrogated CAR T-cell antitumor activity. In sum, our study highlights the critical role of CAR design and its modulation of the TIME in mediating the efficacy of adoptive immunotherapy for high-grade glioma.
Significance:
CAR T-cell immunotherapies hold great potential for treating brain cancers; however, they are hindered by a challenging immune environment that dampens their effectiveness. In this study, we show that the CAR design influences the makeup of the immune environment in brain tumors, underscoring the need to target specific immune components to improve CAR T-cell performance, and highlighting the significance of using models with functional immune systems to optimize this therapy.
Neurodevelopmental Outcomes Prediction in Newborns with Seizures Caused by KCNQ2 Gene Defects
Authors: Huang Zhelan , Liu Bo , Xiao Tiantian , Wang Yaqiong , Lu Yulan , Hu Liyuan , Cheng Guoqiang , Li Zhihua , Wang Laishuan , Zhang Rong , Wang Jin , Cao Yun , Dong Xinran , Yang Lin , Zhou Wenhao
Published: December 2023

Introduction: Pathogenic variant in the KCNQ2 gene is a common genetic etiology of neonatal convulsion. However, it remains a question in KCNQ2-related disorders that who will develop into atypical developmental outcomes. Methods: We established a prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects based on the Gradient Boosting Machine (GBM) model with a training set obtained from the Human Gene Mutation Database (HGMD, public training dataset). The features used in the prediction model were, respectively, based on clinical features only and optimized features. The validation set was obtained from the China Neonatal Genomes Project (CNGP, internal validation dataset). Results: With the HGMD training set, the prediction results showed that the area under the receiver-operating characteristic curve (AUC) for predicting atypical developmental outcomes was 0.723 when using clinical features only and was improved to 0.986 when using optimized features, respectively. In feature importance ranking, both variants pathogenicity and protein functional/structural features played an important role in the prediction model. For the CNGP validation set, the AUC was 0.596 when using clinical features only and was improved to 0.736 when using optimized features. Conclusion: In our study, functional/structural features and variant pathogenicity have higher feature importance compared with clinical information. This prediction model for the neurodevelopmental outcomes of newborns with seizures caused by KCNQ2 gene defects is a promising alternative that could prove to be valuable in clinical practice.
Doação de sangue durante a pandemia da Covid-19: conhecimentos, práticas e atitudes dos estudantes de medicina
Authors: Purim Kátia Sheylla Malta , Bezerra Ingrid Corrêa , Jesus João Vitor Weckerlin de , Machado Renan Kruchelski , Rocha Rodrigo Ribas da Rocha , Silva Thiago Dorneles da
Published: December 2023

Doação voluntária de sangue é um ato desafiador, em especial, durante períodos de crise sanitária. O propósito deste estudo transversal foi analisar os conhecimentos, práticas e atitudes dos estudantes de medicina, do ciclo básico ao internato, quanto à doação de sangue durante a pandemia da Covid-19. O trabalho foi realizado entre maio e dezembro de 2021, via Google forms. Para motivo de comparação, a amostra (n=327) foi dividida em doadores (n=183) e não doadores (n=144) de sangue e utilizado teste qui-quadrado e teste exato de Fisher, sendo considerado estatisticamente significantes perguntas que obtiveram valores com p<0,05. Os resultados indicam que, mesmo sendo a minoria de ambos os grupos, ainda há uma quantidade significativa de estudantes de medicina que apresentam pouco domínio sobre o processo de doação de sangue, além de estarem permeados por medo e desinformação sobre a segurança da coleta. Fatos estes, ainda mais perceptíveis durante o período da pandemia, no qual o percentual de doadores foi de 30,6%. Desta forma, ressalta-se a necessidade de estratégias educacionais criativas e contextualizadas para esclarecer e sensibilizar melhor os jovens para este ato de solidariedade.
Anatomia de A a Z
Authors: Souza Sara Luiza Custódio de , Batista Núbia de Castro , Soares Evelise Aline , Saez Daniel Martinez , Marques Petrus Pires , Guerra Flávia Da Ré
Published: December 2023

Os termos médicos utilizados na morfologia eram provenientes de um nome próprio, com o intuito de homenagear os que descobriram ou apresentaram a estrutura anatômica, conhecidos como epônimos. Buscando unificar a linguagem anatômica e facilitar o processo de ensino, em 1989 foi criado o Comitê Federativo Internacional de Terminologia Anatômica (FICAT), cujo propósito era revisar os epônimos e atualizar a terminologia anatômica. Com o objetivo de apresentar os fundamentos e conhecimentos sobre a origem das terminologias anatômicas nas mídias sociais, a Liga Acadêmica de Anatomia da Universidade Federal de Alfenas (LAANAT/UNIFAL-MG), por meio do projeto de extensão “Anatomia de A a Z”, divulgou conhecimentos científicos acerca da etimologia anatômica. Foram feitas postagens semanais no Instagram e no Facebook, a partir de publicações elaboradas pelos ligantes, supervisionadas pelos professores coordenadores e desenvolvidas no aplicativo Canva. Cada postagem seguiu sequencialmente as letras do alfabeto (de A a Z) e eram compostas da etimologia de duas estruturas anatômicas. Frente a uma análise de dados, observamos que em 23 publicações, alcançamos 712 curtidas, 194 compartilhamentos, 44publicações salvas, 4739 contas alcançadas e 6608 impressões. A LAANAT promoveu, de forma clara e objetiva, a divulgação de conhecimentos das terminologias anatômicas ao público geral.
Professor Antonio Candido
Authors: Candido Antonio
Published: December 2023

Concedida a Daniel Cantinelli Sevillano, sob a orientação do professor Sedi Hirano, em 20-05-2003, em ocasião das comemorações dos 70 anos da Faculdade de Filosofia, Letras e Ciências Humanas. Originalmente publicada em Informe. Informativo da Faculdade de Filosofia, Letras e Ciências Humanas da Universidade de São Paulo, v. 1, n. 4, p. 24-30, São Paulo, jul-ago /2004.
“O amor desse homem pela arte de escrever” Lima pelos olhos de Lins
Authors: Nitrini Sandra , Hazin Elizabeth , Barreto Francismar Ramírez
Published: December 2023

Apresentação por Elizabeth Hazin, Francismar Ramírez Barreto e Sandra Nitrini.
Articulando Saberes: a Curricularização da Extensão e a Disciplina "Educação, Saúde e Assistência Social: Redes Complementares na Proteção Social Básica"
Authors: Kruppa Sonia Maria Portella , Martins Cleide Lavieri , Pereira Érica Gomes , Musumeci Leonardo Rafael , Bógus Cláudia Maria , Louvison Marília Cristina Prado , Silva Zilda Pereira da , Gryschek Anna Luiza de Fátima Pinho Lins
Published: December 2023

O presente artigo traz um relato de experiência do primeiro oferecimento, em 2021, da disciplina PRG0021 “Educação, saúde e assistência social: redes complementares na proteção social básica”, à luz das diretrizes e desafios da curricularização da extensão universitária. Para tanto, além de contextualizar o debate sobre curricularização da extensão, recupera o processo de criação da disciplina como uma sucessão de diferentes articulações entre unidades universitárias; entre estas e os serviços locais de políticas sociais e seus territórios; entre os próprios serviços das políticas de educação, saúde e assistência social; entre a formação inicial e continuada; entre a extensão, o ensino e a pesquisa. Ressalta-se nesse processo a importância do fomento a projetos interunidades pela Pró-Reitoria de Graduação da Universidade de São Paulo. E, por fim, sistematiza-se alguns de seus aprendizados a fim de inspirar propostas futuras de curricularização da extensão em outras disciplinas de graduação.
Necessary Role of Ceramides in the Human Microvascular Endothelium During Health and Disease
Authors: SenthilKumar Gopika , Katunaric Boran , Zirgibel Zachary , Lindemer Brian , Jaramillo-Torres Maria J. , Bordas-Murphy Henry , Schulz Mary E. , Pearson Paul J. , Freed Julie K.
Published: December 2023

Background:

Elevated plasma ceramides and microvascular dysfunction both independently predict adverse cardiac events. Despite the known detrimental effects of ceramide on the microvasculature, evidence suggests that activation of the shear-sensitive, ceramide-forming enzyme NSmase (neutral sphingomyelinase) elicits formation of vasoprotective nitric oxide (NO). Here, we explore a novel hypothesis that acute ceramide formation through NSmase is necessary for maintaining NO signaling within the human microvascular endothelium. We further define the mechanism through which ceramide exerts beneficial effects and discern key mechanistic differences between arterioles from otherwise healthy adults (non–coronary artery disease [CAD]) and patients diagnosed with CAD.

Methods:

Human arterioles were dissected from discarded surgical adipose tissue (n=166), and vascular reactivity to flow and C2-ceramide was assessed. Shear-induced NO and mitochondrial hydrogen peroxide (H
2
O
2
) production were measured in arterioles using fluorescence microscopy. H
2
O
2
fluorescence was assessed in isolated human umbilical vein endothelial cells.

Results:

Inhibition of NSmase in arterioles from otherwise healthy adults induced a switch from NO to NOX-2 (NADPH-oxidase 2)–dependent H
2
O
2
-mediated flow-induced dilation. Endothelial dysfunction was prevented by treatment with sphingosine-1-phosphate (S1P) and partially prevented by C2-ceramide and an agonist of S1P-receptor 1 (S1PR1); the inhibition of the S1P/S1PR1 signaling axis induced endothelial dysfunction via NOX-2. Ceramide increased NO production in arterioles from non-CAD adults, an effect that was diminished with inhibition of S1P/S1PR1/S1P-receptor 3 signaling. In arterioles from patients with CAD, inhibition of NSmase impaired the overall ability to induce mitochondrial H
2
O
2
production and subsequently dilate to flow, an effect not restored with exogenous S1P. Acute ceramide administration to arterioles from patients with CAD promoted H
2
O
2
as opposed to NO production, an effect dependent on S1P-receptor 3 signaling.

Conclusion:

These data suggest that despite differential downstream signaling between health and disease, NSmase-mediated ceramide formation is necessary for proper functioning of the human microvascular endothelium. Therapeutic strategies that aim to significantly lower ceramide formation may prove detrimental to the microvasculature.
Trends in Ductus Arteriosus Stent Versus Blalock‐Taussig‐Thomas Shunt Use and Comparison of Cost, Length of Stay, and Short‐Term Outcomes in Neonates With Ductal‐Dependent Pulmonary Blood Flow: An Observational Study Using the Pediatric Health Information Systems Database
Authors: Lemley Bethan A. , Wu Lezhou , Roberts Amy L. , Shinohara Russell T. , Quarshie William O. , Qureshi Athar M. , Smith Christopher L. , Dori Yoav , Gillespie Matthew J. , Rome Jonathan J. , Glatz Andrew C. , Amaral Sandra , O'Byrne Michael L.
Published: December 2023

Background

The modified Blalock‐Taussig‐Thomas shunt is the gold standard palliation for securing pulmonary blood flow in infants with ductal‐dependent pulmonary blood flow. Recently, the ductus arteriosus stent (DAS) has become a viable alternative.

Methods and Results

This was a retrospective multicenter study of neonates ≤30 days undergoing DAS or Blalock‐Taussig‐Thomas shunt placement between January 1, 2017 and December 31, 2020 at hospitals reporting to the Pediatric Health Information Systems database. We performed generalized linear mixed‐effects modeling to evaluate trends in intervention and intercenter variation, propensity score adjustment and inverse probability weighting with linear mixed‐effects modeling to analyze length of stay and cost of hospitalization, and generalized linear mixed modeling to analyze differences in 30‐day outcomes. There were 1874 subjects (58% male, 61% White) from 45 centers (29% DAS). Odds of DAS increased with time (odds ratio [OR] 1.23, annually,
P
<0.01 [95% CI, 1.10–1.38]) with significant intercenter variation (median OR, 3.81 [95% CI, 2.74–5.91]). DAS was associated with shorter hospital length of stay (ratio of geometric means, 0.76 [95% CI, 0.63–0.91]), shorter intensive care unit length of stay (ratio of geometric means, 0.77 [95% CI, 0.61–0.97]), and less expensive hospitalization (ratio of geometric means, 0.70 [95% CI, 0.56–0.87]). Intervention was not significantly associated with odds of 30‐day transplant‐free survival (OR,1.18 [95% CI, 0.70–1.99]) or freedom from catheter reintervention (OR, 1.02 [95% CI, 0.65–1.58]), but DAS was associated with 30‐day freedom from composite adverse outcome (OR, 1.51 [95% CI, 1.11–2.05]).

Conclusions

Use of DAS is increasing, but there is variability across centers. Though odds of transplant‐free survival and reintervention were not significantly different after DAS, and DAS was associated with shorter length of stay and lower in‐hospital costs.
Changing Trends in Mechanical Circulatory Support Use and Outcomes in Patients Undergoing Percutaneous Coronary Interventions for Acute Coronary Syndrome Complicated With Cardiogenic Shock: Insights From a Nationwide Registry in Japan
Authors: Nishimoto Yuji , Inohara Taku , Kohsaka Shun , Sakakura Kenichi , Kawai Tsutomu , Kikuchi Atsushi , Watanabe Tetsuya , Yamada Takahisa , Fukunami Masatake , Yamaji Kyohei , Ishii Hideki , Amano Tetsuya , Kozuma Ken ,   J‐PCI Registry Investigators
Published: December 2023

Background

Temporal trends in the management of acute coronary syndrome complicated with cardiogenic shock after the revision of guideline recommendations for intra‐aortic balloon pump (IABP) use and the approval of the Impella require further investigation, because their impact remains uncertain.

Methods and Results

Using the Japanese Percutaneous Coronary Intervention (J‐PCI) registry database from 2019 to 2021, we identified 12 171 patients undergoing percutaneous coronary intervention for acute coronary syndrome complicated with cardiogenic shock under mechanical circulatory support. The patients were stratified into 3 groups: (1) IABP alone, (2) Impella, and (3) venoarterial extracorporeal membrane oxygenation (VA‐ECMO); the VA‐ECMO group was further stratified into (3a) VA‐ECMO alone, (3b) VA‐ECMO in combination with IABP, and (3c) VA‐ECMO in combination with Impella. The quarterly prevalence and outcomes were reported. The use of IABP alone decreased significantly from 63.5% in the first quarter of 2019 to 58.3% in the fourth quarter of 2021 (
P
for trend=0.01). Among 4245 patients requiring VA‐ECMO, the use of VA‐ECMO in combination with IABP decreased significantly from 78.7% to 67.3%, whereas the use of VA‐ECMO in combination with Impella increased significantly from 4.2% to 17.0% (
P
for trend <0.001 for both). After adjusting for the confounders, the risk difference in the fourth quarter of 2021 relative to the first quarter of 2019 for in‐hospital mortality was not significant (adjusted odds ratio, 0.84 [95% CI, 0.69–1.01]).

Conclusions

Our study revealed substantial changes in the use of different mechanical circulatory support modalities in acute coronary syndrome complicated with cardiogenic shock, but they did not significantly improve the outcomes.
Development as Structural Violence in Ethiopia
Authors: Getahun Binayew Tamrat
Published: December 2023

Development should not be done in a way that endangers the environment, human life, or non-human life that depends on it. However, in Ethiopia, economic development was carried out with little or no concern for the environment or indigenous and minority groups whose livelihoods directly depended on natural resources. Based on an examination of primary and secondary sources through the lens of structural violence theory, this article argues that Ethiopia’s economic growth was not equitable and happened at the expense of the country’s natural resources. Using the Negede Woyto of Lake Tana as a case study, this paper investigated how economic development projects in Ethiopia impacted minority communities. The conclusion reached was that the eprdf-led government actively worked to inflict structural violence on minority groups in the Lake Tana region, using sustainable economic development as a justification.
Scythians and ξεινικὰ νόμαια
Authors: Sinitsyn Alexander
Published: December 2023

Herodotus’ logos about Scythians and ξεινικὰ νόμαια—amusing and ominous, as is typical of him, yet insightful—consists of two stories about the sad lots of Anacharsis and Scyles; the story begins with a statement that Scythians shun practicing customs of other peoples, particularly those of Hellas; it ends as an adage asserting the initial statement: that is the way Scythians guard their customs (4.76–80). Herodotus describes the barbarian neighbors’ attitude towards foreign and alien customs. But these two examples are about their own, Scythian, heroes or rather antiheroes. Both the philhellenes forswear their native religion and customs and abandon themselves to Greek ritual practices; therefore, they suffer for their behavior. The author of the article holds that Herodotus was sympathetic to Scythians’ resentment against ξεινικὰ νόμαια. The Greek historian speaks about piety and patriotism of Scythians, who believe that the offence against νόμαια is a threat to the very foundation of their culture.