Wang, Linghua

Abstract Innate immune cells of macrophage family predominate tumor immune microenvironment of CNS malignancies. Although macrophages exhibit myriads of protective functions such as clearance of malignant cells, immune surveillance, inflammation resolution and tissue repair, they are generally linked to immunosuppression in gliomas. To identify anti-glioma myeloid cell effectors, we performed directionally concatenated ligand-receptor (L-R) interactome analyses from dendritic cells (DC) and microglia (MG) to lymphoid (CD4+T, Tregs, CD8+T, NK and NKT) cells identified by single cell transcriptomics analyses of ~145,000 tumor-associated CD45+ leukocytes from tumor brains of eighteen high-grade and low-grade glioma patients. Amongst DC-specific (e.g. adhesion molecules) and MG-specific (e.g. chemokine family) interactomes, we identified LGALS9 encoding Galectin-9 as the most pertinent interactions (e.g. SORL1 encoding sortilin-related receptor 1) in MG of IDH-wild type gliomas. Spectral cytometry, immunohistochemistry and western blotting analyses of MG, macrophage, DC, lymphoid cells and tumor cells confirmed abundant expression of Galectin-9 in glioma-associated MG and not in Nestin+ tumor cells. Furthermore, differential gene enrichment analyses revealed transcripts associated with cellular adhesion (coronin 1A, integrin) and phagocytosis (FcγR, phospholipase D, Rab family proteins etc.) was significantly upregulated in Galectin-9hi compared to Galectin-9lo/- MG and macrophages predicting putative role of Galectin-9 in tumor cell adhesion and phagocytosis. Using glioblastoma relevant patient derived ex vivo primary microglia (pMGs; 707, 2103, 1805) and glioma stem cell (GSC) co-culture model system, we evaluated the functional role of Galectin-9. Confocal imaging analyses of co-cultured pMGs with GSC revealed that siRNA or neutralizing antibody mediated downregulation of Galectin-9 led to significantly impaired adhesion (p<0.001) between pMGs and GSC. Not only adhesion but even phagocytosis of GSC was dramatically attenuated (p<0.0001) across all Galectin-9 silenced or neutralized pMGs. Altogether, our study underscores unappreciated role of Galectin-9 in MG as regulator of glioma cell adhesion and phagocytosis that can be harnessed for glioblastoma immunotherapy.

Abstract Background: Cancer-associated fibroblasts (CAFs) are a highly diverse cell population that plays a crucial role in shaping the tumor microenvironment (TME). Their spatial interactions within the TME remain to be systematically characterized, and the factors driving their phenotypic heterogeneity are not yet fully understood. Recent advancements in single-cell spatial transcriptomics technologies and cell segmentation approaches enable the precise measurement of thousands of transcripts at subcellular resolution. Combined with innovative bioinformatics, these advancements have unlocked unprecedented opportunities for in-depth characterization of CAFs and their interactions within the TME. Methods: We conducted a comprehensive spatial transcriptomic analysis of CAFs across 8 cancer types, using the CosMx and MERSCOPE platforms to profile nearly 6 million cells as part of our discovery cohorts. We developed a novel computational method to spatially cluster CAF subpopulations and defined four distinct spatial CAF subtypes. We further examined their phenotypic differences, spatial niche organization, and interactions with neighboring cells. Additionally, we investigated the influence of CAF subtypes on immune cell phenotypes and infiltration levels. To validate our findings, we employed multiple spatial platforms, including Visium, Xenium, COMET, CODEX, and IMC, to ensure reproducibility across diverse technologies. Moreover, we performed correlative studies in large-cohorts with rich clinical data to evaluate the clinical significance of these CAF subtypes. Results: Our approach provided an unprecedented high-resolution examination of the spatial phenotypes of CAFs in large, complex tissues, uncovering novel insights. We comprehensively characterized CAFs across various solid tumor types and identified four conserved spatial CAF subtypes. These subtypes are characterized by distinct cell organizational patterns, neighboring cell compositions, interaction networks, and transcriptomic features. Moreover, they demonstrate significant correlations with the abundance, distribution, and phenotypes of tumor-infiltrating immune cells, as well as associations with tumor histopathological features and clinical outcomes. Conclusions: Our study provides a pan-cancer, high-resolution characterization of CAF spatial organization and interactions in solid tumors and identified conserved spatial CAF subtypes linked to distinct organizational patterns. Our findings reveal that the transcriptomic states and phenotypes of CAFs are significantly shaped by their interactions with neighboring cancer and immune cells. Beyond offering novel insights into the spatial heterogeneity of CAFs, this work paves the way for developing strategies to effectively target and modulate CAFs for therapeutic benefit. Citation Format: Yunhe Liu, Ansam Sinjab, Jimin Min, Guangchun Han, Francesca Paradiso, Yuanyuan Zhang, Yang Liu, Ruiping Wang, Guangsheng Pei, Kyung Serk Cho, Enyu Dai, Akshay Basi, Jared K. Burks, Kimal I. Rajapakshe, Yanshuo Chu, Jiahui Jiang, Daiwei Zhang, Xinmiao Yan, Paola A. Guerrero, Alejandra Serrano, Mingyao Li, Tae Hyun Hwang, Andrew Futreal, Jaffer A. Ajani, Luisa M Solis Soto, Amir A. Jazaeri, Humam Kadara, Anirban Maitra, Linghua Wang. Spatial subtypes and cellular interactions of cancer-associated fibroblasts revealed by single-cell spatial omics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 166.

Summary: The transition from 2D to 3D spatial profiling marks a revolutionary era in cancer research, offering unprecedented potential to enhance cancer diagnosis and treatment. This commentary outlines the experimental and computational advancements and challenges in 3D spatial molecular profiling, underscoring the innovation needed in imaging tools, software, artificial intelligence, and machine learning to overcome implementation hurdles and harness the full potential of 3D analysis in the field.

Abstract Background: The methylthioadenosine phosphorylase (MTAP) gene encodes an essential enzyme for the salvage pathway of adenosine synthesis and is frequently lost in different types of cancer including urothelial bladder carcinoma. Therefore, MTAP-deficient tumors are theoretically very sensitive to anti-folate agents such as pemetrexed that can effectively block the de novo pathway of adenosine synthesis and as a result, create a state of synthetic lethality. We thus hypothesize that tumor MTAP gene deficiency is associated with response to pemetrexed therapy in bladder cancer. Methods: In this study, we investigated MTAP gene deficiency rates in the TCGA database and confirmed MTAP protein loss by immunohistochemistry using a tumor tissue microarray containing bladder tumor tissues from 151 patients. We then performed in vitro and in vivo studies using MTAP-proficient and MTAP-deficient human bladder cancer cell lines. Functional loss of MTAP was verified with mass spectrometry, which detects its substrate methylthioadenosine (MTA) levels. We also correlated these pre-clinical studies with clinical response data on patients with metastatic bladder cancer treated with pemetrexed. Results: We identified that 27.8% bladder cancer patients have MTAP protein deficiency, which is consistent with exome sequencing data from the TCGA database. In vitro data showed MTAP-deficient human bladder cancer cell lines were significantly more sensitive to pemetrexed, with IC50 at least 40 times lower than MTAP-proficient cell lines. Subsequent knockdown of the MTAP gene in MTAP-proficient cell lines increased sensitivities to pemetrexed treatment. Consistent with the in vitro data, pemetrexed significantly inhibited the growth of MTAP-deficient or knockdown xenograft tumors but not MTAP-proficient tumors. Furthermore, 4 of 4 (100%) patients with MTAP-deficient metastatic bladder cancer responded to pemetrexed treatment, whereas only 1 of 11 (9%) patients with MTAP-proficient metastatic bladder cancer responded to pemetrexed. Conclusion: Our data demonstrate that MTAP gene loss in urothelial bladder cancer leads to a metabolic state of synthetic lethality with pemetrexed therapy. Therefore, bladder tumor MTAP loss should be further investigated as a potential biomarker for selection of patients for anti-folate therapy. Citation Format: Jianfeng Chen, Omar Alhalabi, Guangchun Han, Wei-Lien Wang, Xin-Qiao Zhang, Jian H. Song, Lidia P. Lopez, Sumankalai Ramachandran, Anh G. Hoang, Tyrone Garnett, Matthew Campbell, Amishi Y. Shah, Jennifer Wang, Arlene O. Siefker-Radtke, Shi-Ming Tu, Mark Titus, Charles C. Guo, Gary E. Gallick, Eleni Efstathiou, William F. Benedict, Christopher J. Logothetis, Thai H. Ho, Linghua Wang, Jianjun Gao. MTAP gene deficiency creates vulnerability to anti-folate therapy in urothelial bladder carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 385.

4521 Background: The MTAP gene encodes an essential enzyme for the salvage pathway of nucleotide synthesis and is frequently deleted in UBC. Anti-folate agents such as pemetrexed can effectively inhibit the de novo pathway of nucleotide synthesis and as a result, create a synthetic lethality in MTAP deficient UBC. We hypothesize that MTAP gene loss correlates with enhanced response to pemetrexed in UBC. Methods: We investigated MTAP gene deletion rates in the TCGA database and determined MTAP protein loss rates by immunohistochemistry (IHC) using a UBC tissue microarray (TMA) from 151 patients (pts). We then performed in vitro and in vivo studies using MTAP proficient and MTAP deficient bladder cancer cell lines. At the clinical level, we performed a retrospective analysis based on MTAP status of pts treated with pemetrexed as 2nd line at our institution between 2014 and 2018. We are now enrolling pts in a single-arm, open-label, phase II clinical trial (NCT02693717) with pemetrexed in pts with MTAP deficient UBC. Results: Per our TCGA and TMA IHC analyses, MTAP deficiency rate was 25.9% and 27.8%, respectively. MTAP deficient UBC cell lines were at least 40 times more sensitive to pemetrexed than MTAP proficient lines. Knockdown of the MTAP gene increased apoptosis rate by pemetrexed from approximately 20% to 60%. Additionally, pemetrexed significantly inhibited the growth of MTAP deficient or knockdown xenograft tumors but not MTAP proficient tumors. Retrospective analysis of 12 pts using RECIST criteria indicated that all 4 MTAP deficient UBC pts responded to pemetrexed whereas only 1 of 8 (12.5%) MTAP proficient UBC pts responded. Of the 6 pts enrolled on the clinical trial, 3 (50%) had complete or partial response, 1 had stable disease, 1 was not evaluable and 1 had disease progression. Combined analysis of the entire experience demonstrates a higher response rate in MTAP deficient UBC (70%) as compared to MTAP proficient UBC (12.5%). Conclusions: Our preclinical and clinical data demonstrate that MTAP loss in UBC leads to a state of synthetic lethality when treated with pemetrexed and should be further investigated as a novel biomarker to predict response to anti-folate agents.