Citations

Showing 10 of 108036 citations.

Abstract 2294: Monitoring glioma treatment response through longitudinal analysis of cell-free DNA in cerebrospinal fluid: Insights from a comprehensive study using next-generation sequencing
Cecile, Riviere-Cazaux, Dong, Xiaoxi , Mo, Wei , Du, Pan , Jia, Shidong , Burns, Terence, Dai, Chao

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 2294-2294

10.1158/1538-7445.am2024-2294 Get It

Abstract Background: Assessing treatment response in gliomas with high fidelity remains challenging. Cell-free DNA (cfDNA) is increasingly recognized as a liquid biomarker in plasma and cerebrospinal fluid (CSF), showing promise in optimizing therapeutic regimens for various cancers. While CSF has been explored as a source of cfDNA for gliomas, understanding the dynamics of cfDNA abundance and sequencing changes during treatment and recurrence is essential. Leveraging our biobank of longitudinal CSF specimens obtained through CSF access devices, we aimed to determine the potential utility of CSF cfDNA as a monitoring tool for treatment response in glioma patients. Materials and methods: Longitudinal CSF specimens were collected through Ommaya reservoirs (NCT04692337) or ventriculoperitoneal shunts (NCT04692324) from patients with brain tumors, including gliomas. cfDNA was extracted from 1-5 mL of CSF based on available sample volumes and quantified using Qubit. Next-Generation sequencing using PredicineCARE or PredicineSCORE low-pass whole genome sequencing (LPWGS) was performed based on the available cfDNA. Results: CSF collected before versus after resection showed an increase in quantified cfDNA (2.97x, range: 1.58-5.26x), indicating the impact of increased parenchymal disruption and closer contact with CSF. Subsequently, CSF cfDNA decreased during chemoradiation and adjuvant treatment and increased at recurrence, even in patients co-enrolled in immunotherapy trials for IL-7 agonists and pembrolizumab. Notably, copy number burden (CNB) increased at recurrence in three patients with known disease progression and decreased throughout immunotherapy treatment in one patient despite concerns of pseudoprogression. In a patient with a hypermutated glioblastoma, CSF cfDNA revealed over 59 genomic alterations, including MAP2K1, KIT, and PDGFRA. Another patient with a progressing EGFR-amplified GBM showed over 200 new variants in the final sample, with EGFR copy number increasing from 2 to over 30. Conclusion: Analysis of cfDNA throughout a patient’s disease course, encompassing resection and treatment with standard-of-care and experimental therapies, may aid in disease monitoring and treatment response. Further evaluation in a larger patient cohort is needed to determine the sensitivity of changes in mutations, CNB, and cfDNA quantity for glioma disease burden. Citation Format: Riviere-Cazaux Cecile, Xiaoxi Dong, Chao Dai, Wei Mo, Pan Du, Shidong Jia, Terence Burns. Monitoring glioma treatment response through longitudinal analysis of cell-free DNA in cerebrospinal fluid: Insights from a comprehensive study using next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2294.
Abstract 2303: Identifying and stratifying circulating tumor cell cluster subtypes in metastatic breast cancer patients and evaluating their clinical outcomes
Aryasomayajula, Aravind, Alpaugh, R. Katherine , Chumsri, Saranya , Tang, Cha‐Mei , Priore, Giuseppe Del, Adams, Daniel L. , Reduzzi, Carolina , Williams, William V. , Cristofanilli, Massimo

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 2303-2303

10.1158/1538-7445.am2024-2303 Get It

Abstract Background: Circulating tumor cell clusters (CTCCs) are aggregated groups of tumor cells that detached from primary tumors and circulate the bloodstream. However, while Circulating Tumor Cells (CTCs) are a well studied phenomenon, CTCCs remain relatively unexplored and ill-defined, with only a few descriptive investigations evaluating their clinical utility. Adding to CTCC complexity is that various subtypes exist, including homotypic clusters consisting of a homogenous population of tumor cells and heterotypic CTCCs made of CTCs with immune/stromal white blood cells (WBCs). Furthermore, CTCs can undergo Epithelial-Mesenchymal Transition (EMT), a process characterized by loss of epithelial traits and upregulation of mesenchymal traits, and can form clustered EMTs (CEMTs). Moreover, CTCs can fuse with macrophages forming Tumor Macrophage Hybrid Cells, aka Cancer-Associated Macrophage Like cells (CAMLs) when in circulation. We enumerated all these types of cells and complex aggregates in the peripheral blood of patients with metastatic breast cancer (mBC). Methods: We enumerated the 6 populations from patient samples enrolled in IRB aproved prospective pilot studies. Whole peripheral blood (7.5mL) was filtered and stained with cytokeratin (CK) & CD45/CD14 to identify CTCs. CTCs were defined as an intact DAPI nuclei and strong filamentous CK. Homotypic CTCCs were defined as ≥2 CTCs attached together. Heterotypic CTCCs were defined as ≥1 CTC attached to ≥1 WBC. EMTs were defined as having DAPI nuclei and weak non-filamentous CK. CEMTS were defined as ≥2 EMTs. CAMLs were defined as having an enlarged polynucleated DAPI, and positive for CD45/CD14 or non-filamentous CK. Median progression free survival (mPFS) and median overall survival (mOS) over 24 months (m) were evaluated. Results: We evaluated the blood of 79 mBC patients. Single CTCs were found in 57% of patients (n=34/79), homotypic CTCCs 15% (n=12/79), heterotypic CTCCs 66% (n=27/79), EMTs 56% (n=44/79), CEMTs 23% (n=18/79) and CAMLs 97% (n=77/79). Over 24 ms, patierns with detectable heterotypic CTCCs & homotypic CTCCs had the shortest response times at mPFS=2.8 & mOS=5.8 ms, or mPFS=2.1 & mOS=4.3 ms, respectively. This was followed by CTCs mPFS=3.7 & mOS=13.7 ms, EMTs mPFS=4.3 & mOS=14.4 ms, CAMLs mPFS=4.3 & mOS=14.4 ms, and CEMT mPFS=4.7 & mOS=13.2 ms. Additionally, CTCCs were rare in HER2+ patients at 4.4% (n=1/23), but no associations to other hormone statuses were found. Conclusion: CTCCs appear to represent an array of subtypes with different biological and clinical meanings. Here we enumerated CTCC subtypes in the blood of mBC patients and stratified the various types to clinical outcomes. These data suggest CTCCs are clinically important and further understanding of their biology in the context of tumor pathogenesis is needed. Citation Format: Daniel L. Adams, Carolina Reduzzi, Aravind Aryasomayajula, R. Katherine Alpaugh, Saranya Chumsri, Cha-Mei Tang, Giuseppe Del Priore, William V. Williams, Massimo Cristofanilli. Identifying and stratifying circulating tumor cell cluster subtypes in metastatic breast cancer patients and evaluating their clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2303.
Abstract 2958: Melphalan-treated multiple myeloma cells exhibit a senescent-like dormancy phenotype
Guilatco, Angelo Jose, Sannuli, Neal I., Kirkland, James L. , Kourelis, Taxiarchis , Weivoda, Megan , Diaz‐delCastillo, Marta , Borges, Gabriel Álvares , Ritting, Megan L. , Aalam, Syed Mohammed Musheer , Kannan, Nagarajan , Tchkonia, Tamar , Lin, Yi , Drake, Matthew T. , Andersen, Thomas Levin

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 2958-2958

10.1158/1538-7445.am2024-2958 Get It

Abstract Multiple myeloma (MM) is an incurable plasma cell (PC) cancer in which all patients are expected to relapse. Cytotoxic agents such as high-dose melphalan (HDM), which is used as a myeloablative agent prior to autologous stem cell transplant (ASCT) in MM, drive therapy-induced senescence (TIS) in non-cancerous tissues. We hypothesized that HDM similarly activates TIS pathways in surviving MM cells and this response may correlate with patient outcomes post-ASCT. To test this, we developed an in vitro model in which 5TGM1 mouse MM cells are cultured with 10uM melphalan (HDM) or vehicle (Veh) for 6 hours, followed by co-culture in normal media with primary mouse bone marrow stromal cells. Cultures were maintained for 10 days and imaged to quantify cumulative population doublings (CPDs). 5TGM1 were then isolated by FACS to measure telomere-associated DNA damage foci (TAFs), sensitivity to senolytic drugs, and senescence gene expression (RT-qPCR and scRNA-seq). To translate these studies, scRNA-seq was used to analyze CD138+ PCs from MM patient bone marrow post-ASCT. Additionally, longitudinal bone biopsies from MM patients at diagnosis and post-ASCT were stained for CD138+ PCs; PC burden was quantified using artificial intelligence assisted histology (HALO). HDM-5TGM1 exhibited stable growth arrest (decreased CPDs) and sustained DNA damage (increased TAFs) compared to Veh-5TGM1. HDM-5TGM1 were also significantly more sensitive to senolytic ablation (Dasatinib+Quercetin or Fisetin). HDM-5TGM1 showed increased senescence (Cdkn1a, Cdkn1c, Glb1), anti-apoptosis (Bcl2l1), and senescence associated secretory phenotype (Ccl5, Icam1, Mmp13) genes, as well as myeloid markers found to be increased in MM dormancy (Axl, Fcer1g, Mpeg1). Analysis by scRNA-seq revealed that HDM-5TGM1 were G0/G1 arrested, and gene set enrichment analysis (GSEA) confirmed upregulation of senescence pathways with downregulation of DNA replication and cell cycle pathways. Consistent with RT-qPCR results, these cells exhibited myeloid gene expression. Analysis of patient CD138+ PCs post-ASCT by scRNA-seq also revealed a myeloid-like cluster. Of interest, of the 491 genes upregulated in this cluster, 268 were also upregulated in HDM-5TGM1. CD138+ PCs could also be detected in patient bone biopsies post-ASCT, although PC burden was significantly reduced post-ASCT. Surprisingly, the percent reduction in PC burden post-ASCT was greater in relapsed (≤3 years) vs non-relapsed patients. Further, in relapsed patients, PC burden post-ASCT positively correlated with time in remission. Altogether, these findings demonstrate that HDM can induce senescence features and a myeloid-dormancy signature in surviving MM cells. This phenotype is associated with longer durable response, suggesting that activation of TIS may be a strategy to extend PFS. Further, senolytic therapy may be a novel approach to eliminate dormant MM cells and prevent relapse. Citation Format: Angelo Jose Guilatco, Marta Diaz-del-Castillo, Gabriel Alvares Borges, Neal I. Sannuli, Megan L. Ritting, Syed Mohammed Aalam, Nagarajan Kannan, Tamar Tchkonia, James L. Kirkland, Yi Lin, Taxiarchis Kourelis, Matthew T. Drake, Thomas Levin Andersen, Megan Weivoda. Melphalan-treated multiple myeloma cells exhibit a senescent-like dormancy phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2958.
Abstract 297: Role of purine metabolism in CLL cell pathobiology and CLL disease progression
McCabe, Chantal E. , O’Brien, Daniel R. , Chen, Yi , Tan, Fenlai , Anthony, Stephen P. , Chen, Yu , Sinha, Sutapa , Han, Weiguo , Wang, Zhiquan , Rabe, Kari G. , Slager, Susan L. , Parikh, Sameer A. , Braggio, Esteban , Dai, Bing, Shen, Yue, Kay, Neil E.

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 297-297

10.1158/1538-7445.am2024-297 Get It

Abstract The treatment of Chronic lymphocytic leukemia (CLL) has been revolutionized in recent years, however CLL is still incurable, and the leukemic cells often develop drug resistance. Previous studies show that the interaction of CLL cells with the bone marrow (BM) microenvironment promotes spontaneous and drug induced survival. But the nature of this interaction is still in need of a full understanding. To pursue this we discerned RNA profiles using RNA-seq in paired CLL cells isolated from untreated blood and BM (n=6) and in untreated patients CLL cells (n=4) cultured alone or cocultured with BM stromal cells (BMSCs). CLL cells from blood/BM and CLL cells cultured alone or with BMSCs were examined by Western blot (WB), untargeted metabolomics (LCMS+GCMS) and preclinical drug sensitivity assays. We found upregulation of 232 genes in CLL cells from BM vs the paired blood and 917 genes in cocultured CLL cells compared to CLL cells cultured alone (p&lt0.05, fold change &gt1.5). Here we detected only 13 genes that overlap between BM and cocultured CLL cells. When we analyzed the expression of these 13 genes in blood CLL cells from a cohort of 162 untreated patients by RNA-seq we found a positive relationship between 4 (PNP, C16orf54, MOB3A, CDK2AP2) with CLL patient clinical outcome including overall survival (OS), progression free survival (PFS), and time to first treatment (TTFT) [multivariable Cox proportional hazards models, p&lt0.05]. Out of the 4 genes, purine nucleoside phosphorylase (PNP), an enzyme in the purine salvage pathway, showed the most significant association for patient’s OS, PFS, and TTFT. Metabolomic profiling indicated an increased level of purine salvage pathway metabolites adenosine, inosine, and hypoxanthine in cocultured CLL cells. WB analysis using blood CLL cells from untreated patients showed a variable PNP protein expression (high, low/no PNP) and induction in PNP protein levels were found in blood CLL cells expressing low/no PNP only when in contact with BM/BMSCs. But PNP inhibitor forodesine did not show any significant killing in high vs low/no PNP group. When we treated CLL cells from untreated patients with Bcl2 inhibitors venetoclax, S55746 and LP-118 (Bcl-2/Bcl-xl inhibitor, Newave), CLL cells showed increasing sensitivity to the Bcl2 inhibitors associated with their PNP expression (high&gtlow&gtno PNP). But a covalent and non-covalent BTKi LP-168 (Newave) cultured with CLL cells showed no difference in drug sensitivity associated with CLL PNP levels. In contrast CLL cells when treated with both venetoclax and LP-168, showed more drug sensitivity in the high PNP expressing CLL cells vs low/no PNP. These results indicate that active purine metabolism in CLL cells can contribute to differential novel agent drug responses of CLL patients. Future studies to understand the exact mechanism of how PNP relates to this differential drug sensitivity should be instructive in regard to alternate maneuvers to treat CLL. Citation Format: Sutapa Sinha, Weiguo Han, Zhiquan Wang, Kari G. Rabe, Susan L. Slager, Chantal E. McCabe, Daniel R. O'Brien, Sameer A. Parikh, Esteban Braggio, Yi Chen, Fenlai Tan, Stephen P. Anthony, Yu Chen, Bing Dai, Yue Shen, Neil E. Kay. Role of purine metabolism in CLL cell pathobiology and CLL disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 297.
Abstract 2972: Senescent macrophages drive tumorigenesis by limiting antitumor immunity
Prieto, Luis I.

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 2972-2972

10.1158/1538-7445.am2024-2972 Get It

Abstract A big challenge in oncology is tumor heterogeneity, as the same type of tumor can manifest differently across patients. Our current cancer therapies focus on targeting malignant cells without considering how the tumor microenvironment influence tumorigenesis or changes in response to treatment. Therefore, identifying effective therapies that restrict tumor growth and progression while restoring optimal tissue and organ function is imperative. Here, we propose a potential strategy to delay the frequency of lung tumorigenesis and reduce progression by selectively targeting tumor-promoting senescent cells that arise with advancing age, prolonging antitumor immunity. Using lung tumor-prone mice, we found that senescent cells, specifically senescent alveolar macrophages, accumulate early in hyperplastic lesions. Mechanistically, these macrophages upregulate the cell cycle regulator p16Ink4a; express the cell surface protein CXCR1; they are distinct from other established subsets; are sensitive to senolytic interventions; have a tumor-promoting secretome, including SPP1; and express immunosuppressive factors that modulate the antitumor immune response. Selective clearance of senescent macrophages attenuates adenoma development, indicating they, at least in part, promote tumorigenesis. Importantly, we observed alveolar macrophages with these properties accumulating in treatment-naive human early-stage lung adenocarcinoma in situ, indicating that the cellular senescence program in macrophages is a conserved etiology. We also found that senescent alveolar macrophages accumulate in otherwise naturally aged normal mouse lungs and their persistence correlates with increased inflammation. Collectively, our findings suggest that targeting senescent macrophages may constitute a potential therapeutic intervention to postpone or attenuate lung cancer during the early stages of the disease. Citation Format: Luis I. Prieto. Senescent macrophages drive tumorigenesis by limiting antitumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2972.
Incremental Value of a Metabolic Risk Score for Heart Failure Mortality: A Population-Based Study
Joo, Jungnam , Shearer, Joseph J. , Wolska, Anna , Remaley, Alan T. , Otvos, James D. , Connelly, Margery A. , Sampson, Maureen , Larson, Nicholas B. , Park, Hoyoung , Conners, Katherine M. , Turecamo, Sarah , Roger, Véronique L. , Bielinski, Suzette , Larson, Nicholas B , Park, Hoyoung , Roger, Veronique L , Bielinski, Suzette J.

Mayo Clinic

Circulation: Genomic and Precision Medicine | March 22, 2024 | Volume: 17 | Issue: 2 | Pages: No page available

10.1161/circgen.123.004312 | PMID 38516784 Get It

BACKGROUND: Heart failure is heterogeneous syndrome with persistently high mortality. Nuclear magnetic resonance spectroscopy enables high-throughput metabolomics, suitable for precision phenotyping. We aimed to use targeted metabolomics to derive a metabolic risk score (MRS) that improved mortality risk stratification in heart failure. METHODS: Nuclear magnetic resonance was used to measure 21 metabolites (lipoprotein subspecies, branched-chain amino acids, alanine, GlycA (glycoprotein acetylation), ketone bodies, glucose, and citrate) in plasma collected from a heart failure community cohort. The MRS was derived using least absolute shrinkage and selection operator penalized Cox regression and temporal validation. The association between the MRS and mortality and whether risk stratification was improved over the Meta-Analysis Global Group in Chronic Heart Failure clinical risk score and NT-proBNP (N-terminal pro-B-type natriuretic peptide) levels were assessed. RESULTS: The study included 1382 patients (median age, 78 years, 52% men, 43% reduced ejection fraction) with a 5-year survival rate of 48% (95% CI, 46%–51%). The MRS included 9 metabolites measured. In the validation data set, a 1 standard deviation increase in the MRS was associated with a large increased rate of death (hazard ratio, 2.2 [95% CI, 1.9–2.5]) that remained after adjustment for Meta-Analysis Global Group in Chronic Heart Failure score and NT-proBNP (hazard ratio, 1.6 [95% CI, 1.3–1.9]). These associations did not differ by ejection fraction. The integrated discrimination and net reclassification indices, and Uno’s C statistic, indicated that the addition of the MRS improved discrimination over Meta-Analysis Global Group in Chronic Heart Failure and NT-proBNP. CONCLUSIONS: This MRS developed in a heart failure community cohort was associated with a large excess risk of death and improved risk stratification beyond an established risk score and clinical markers.
Abstract 4299: A lineage-specific role of oncogenic protein kinase Cι in lung adenocarcinoma
Nguyen, Duy T. , Yin, Ning , Weems, Capella, Jamieson, Lee, Murray, Nicole R., Fields, Alan P. , Yin, Ning, Meneses, Kayleah M.

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 4299-4299

10.1158/1538-7445.am2024-4299 Get It

Abstract Lung adenocarcinoma (LUAD), the most prevalent subtype of lung cancer, can arise from two different cell populations: alveolar type 2 (AT2) cells and bronchiolar club cells. By utilizing genomic data from the cancer genome atlas program, human LUAD cell lines, and the well-characterized LSL-KrasG12D/Trp53-/- (KP) mouse model, we demonstrated that tumors arising from club cells are much more aggressive and follow a different trajectory of tumorigenesis when compared to those arising from AT2 cells. Intriguingly, our data strongly suggest that expression and signaling activity of protein kinase C iota (PKCι) can profoundly affect the cell of origin and oncogenic signaling pathways employed by resultant tumors. Specifically, KP-mediated transformation of club cells appears to be dependent on PKCι-ELF3-NOTCH3 and PKCι-YAP1 signaling axes, while AT2 cell malignancy is dependent on the PKCι-independent WNT signaling. In addition, club-cell-origin tumors exhibit an enrichment of cancer stem cells and increased infiltration of immunosuppressive myeloid cells in comparison to AT2-cell-origin tumors. This results in accelerated progression and increased likelihood of metastasis by LUAD tumors that originate from club cells. Taken together, our results indicate that PKCι expression and signaling activity can profoundly influence the cells of origin, tumor trajectories, and therapeutic vulnerabilities of LUAD tumors. Citation Format: Duy T. Nguyen, Ning Yin, Capella R. Weems, Lee Jamieson, Kayleah Meneses, Yi Liu, Nicole R. Murray, Alan P. Fields. A lineage-specific role of oncogenic protein kinase Cι in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4299.
Abstract 4959: Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline
Wang, Panwen , Yu, Yue , Kocher, Jean-Pierre A., Lin, Yi, Li, Ying , Dong, Haidong , Yu, Yue, Zhang, Shuwen , Sun, Zhifu , Wang, Junwen

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 4959-4959

10.1158/1538-7445.am2024-4959 Get It

Abstract Introduction: Single-cell RNA-sequencing (scRNA-seq) pairing with single-cell T-Cell-Receptor-sequencing (scTCR-seq) enables profiling of gene expression and TCR repertoires in individual T cells, elevating our understanding of T-cell-mediated immunity. Here, we present immunopipe, a comprehensive and flexible pipeline (https://github.com/pwwang/immunopipe) for analyzing the paired data. Besides the command-line tool, it offers a user-friendly web interface that allows users with varying programming expertise to configure, initiate, and monitor the pipeline. By combining extensive functionality with ease of use, immunopipe empowers users to unlock valuable insights from the data, which notably advances our understanding of immune response and fosters the development of innovative immunotherapies. Results: Immunopipe is a comprehensive analytical pipeline for scRNA-seq and scTCR-seq data, offering various modules leveraging existing tools and novel methods to ensure data quality and enable downstream analytics. It performs quality control for scRNA-seq data, clusters cells based on gene expression to facilitate the identification of cell populations and provides insights into T-cell heterogeneity and functional diversity through T-cell selection and clustering. Enrichment analysis identifies markers and pathways for T-cell characterization. Our automated T-cell annotation tool annotates cell types accurately and hierarchically. For scTCR-seq data, immunopipe analyzes TCR clones, including clonality, diversity, gene usage, and repertoire overlap. Clone residency analysis examines the presence of clones across samples. Integrative analyses combine scRNA-seq and scTCR-seq data, providing a comprehensive understanding of the cellular landscape. Immunopipe incorporates diverse cell group information to analyze T-cell populations, which enables granular perspectives of the data for comprehensive insights. Immunopipe offers a flexible platform, allowing users to customize the analyses as needed. It supports both core and optional analyses through configuration, where users have control over the adjustable parameters. The pipeline relies on cell grouping information that can be referenced from metadata or modified to generate new variables for analysis and data filtering. Immunopipe can be executed locally or on scheduler platforms, and a docker image is provided for compatibility and simplified installation. It also offers a web interface that facilitates configuration, execution monitoring, and access to results. Conclusion: Immunopipe is a flexible and user-friendly pipeline for analyzing scRNA-seq and scTCR-seq data. It empowers researchers to gain valuable insights that could enhance the understanding of immune responses and facilitate the development of innovative immunotherapies. Citation Format: Panwen Wang, Haidong Dong, Yue Yu, Shuwen Zhang, Zhifu Sun, Jean-Pierre A. Kocher, Junwen Wang, Lin Yi, Ying Li. Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4959.
Abstract 496: Insights into correlation between nanomechanical properties and cytokines expression during gold nanoparticle endocytosis
Wang, Enfeng , Kulkarni, Tanmay , Angom, Ramcharan Singh , Mukhopadhyay, Debabrata , Bhattacharya, Santanu

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 496-496

10.1158/1538-7445.am2024-496 Get It

Abstract Gold nanoparticles for therapeutic interventions have become a widely popular source due to the ease in surface chemistry available for modification. Several studies undertaken focusses on the size, shape of nanoparticles as well as the signaling mechanisms and yet, knowledge regarding the alteration in membrane dynamics such as nanomechanical properties and cytokines involved during their uptake has not been studies before. To overcome the knowledge deficit, we employed atomic force microscopy and qRT-PCR techniques to acquire nanomechanical attributes and cytokines expressions respectively, in Panc-1 and AsPC-1 cell lines treated with surface modified gold nanoparticles for 1- and 24-hours’ time point. In nanomechanics paradigm, impetus was given on both linear attributes such as membrane stiffness, deformation, and adhesion as well as non-linear attributes such as drained Poisson’s ratio, diffusion coefficient and pore size. On the other hand, qRT-PCR technique yielded alterations in relative mRNA expressions of pro-tumorigenic cytokines such as CCL2, CXCL1, CXCL2, CXCL3, IL8, IL11, IL18 and TGFβ-1. Further, using Pearson’s correlation, we deduced the dependency between nanomechanical properties and cytokines expressions. We evaluated several criteria such as receptor dependent vs independent, PEGylated vs non-PEGylated and 1 hr vs 24hrs, to deduce correlations between cytokines and nanomechanical attributes. In Panc-1 cell line, we observed that PEGylation vs non-PEGylation of gold nanoparticles demonstrated most significant correlations, whereas in AsPC-1 cell line, receptor independent mechanism played a pivotal role in establishing significant correlations. For instance, D_C and P_D were highly correlated with CXCL1, CXCL2 and TGFβ-1 when non-PEGylated gold nanoparticles were up taken by Panc-1 cells. Similarly, D_C and P_D were highly correlated consistently with our cytokine panel except for TGFβ-1. In AsPC-1 cell line, deformation was significantly correlated with CCL2, CXCL2, CXCL3 and IL-8 whereas, D_C and P_D were significantly correlated with CCL2, CXCL1, CXCL3, IL-18 and TGFβ-1 in receptor independent scenario. This study demonstrated that during the uptake of gold nanoparticles, non-linear nanomechanical attributes are detrimental over linear attributes. Moreover, Surface modified gold nanoparticles induce varying levels of alteration in pro-tumorigenic cytokines. Taken together, this study boosts our insights into correlations describing cytokines regulating nanomechanical attributes in endocytosis paradigm. Citation Format: Tanmay Kulkarni, Enfeng Wang, Ramcharan Singh Angom, Debabrata Mukhopadhyay, Santanu Bhattacharya. Insights into correlation between nanomechanical properties and cytokines expression during gold nanoparticle endocytosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 496.
Abstract 4995: Impact of radiotherapy on extracellular vesicle mediated anti-tumor immunity in oligometastatic prostate cancer
Uzendu, Chisom, Lavoie, Roxane R. , Lucien-Matteoni, Fabrice, Kim, Yohan , Dong, Haidong , Park, Sean S.

Mayo Clinic

Cancer Research | March 22, 2024 | Volume: 84 | Issue: 6_Supplement | Pages: 4995-4995

10.1158/1538-7445.am2024-4995 Get It

Abstract Metastasis-ablative radiotherapy is a new therapeutic approach that prolongs survival in patients with advanced cancers. Tumour irradiation can elicit an immunogenic cell death resulting in the expansion of tumour-reactive T cells and eradication of both irradiated and distant non-irradiated metastases, referred to as the “abscopal effect”. This abscopal response, nevertheless, is observed in a minority of patients suggesting uncharacterized mechanisms that prevent robust systemic anti-tumor immune response. Tumour-derived extracellular vesicles (TdEVs) have recently emerged as mediators of antitumor immunity but their immunomodulatory role in response to radiotherapy remains largely unknown. Recent clinical studies by our lab have demonstrated that circulating levels of tumour-derived extracellular vesicles (tdEVs) are elevated in response to radiotherapy and high tdEV concentrations are associated with reduced levels of peripheral cytotoxic CD8+ T cells and higher risk of disease recurrence in advanced prostate cancer. Based on our findings, we hypothesize that radiotherapy induces the release of tumor-derived EVs that suppress anti-tumor immunity. Prostate cancer cells (PC3 and DU145) were irradiated with clinically used doses of ionizing radiation (20Gy x 1 or 10Gy x 3 fractions) and tdEVs were co-cultured with human CD8+ T cells to measure their proliferation and cytotoxic activity. Increased levels of tdEVs were released by tumour cells treated with radiotherapy. A higher frequency of impaired T cell cytotoxic activity and a reduction in CD8 T cell proliferation was found in the 10Gy x 3 radiation regimen. Proteomic analysis and western blot showed an increased expression of the immune checkpoint molecule B7-H3 on the tumour cell surface and tdEVs in response to radiotherapy. While coculture of CD8 T cells with B7-H3 depleted tdEVs led to recovery of T-cell cytotoxic ability, overexpression of the B7-H3 in tdEVs inhibited cytotoxic activity. This study provides a rationale for future studies in which we will test the immune-mediated effects of radiotherapy-induced tdEVs in immunocompetent mouse models and investigate B7-H3 blockade as a therapeutic approach to boost abscopal response in the treatment of advanced prostate cancer. Citation Format: Chisom J. Uzendu, Yohan Kim, Roxane R. Lavoie, Haidong Dong, Sean Park, Fabrice Lucien-Matteoni. Impact of radiotherapy on extracellular vesicle mediated anti-tumor immunity in oligometastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4995.