tbuckley/cabot-search huggingface dataset:
Abstract 1937: How circulating tumor cells disguise
Authors: Dorothea Schott, Monika Pizon, Andreas Riess, Katharina Pachmann
Journal: Cancer Research (2025)

Background: The most threatening aspect of malignant tumors is their ability to develop metastases in distant organs eventually leading to fatal outcome. These metastases must be derived from cells seeded into the circulation from the primary tumor. It is, however, well known that the majority of metastases do not develop during growth of the primary tumor but only months or even years after the removal of the primary tumor. Circulating tumor cells have been claimed to rapidly disappear from the blood after surgical removal of the primary tumor leading to the assumption that they are eradicated with a half- life of few hours. Therefore, already the presence of circulating tumor cells has been (over) interpreted as a sign of metastatic disease. Indeed, initially, we, like most other approaches for circulating tumor cell detection, did not find any tumor cells right after surgery. However, using a standardized approach (1) we were able to detect increased numbers of tumor cells in blood days after surgery not only in lung (2) but also in breast cancer (3). Rapid disappearance of cells shed from the tumor is not necessarily due to eradication of these cells by the immune system but dormant cells obviously can survive due to recirculation into foreign tissues or encryption. The question is: How can cancer cells conceal in the circulation? Methods: Using the maintrac® approach including resting the samples for 24 hours at room temperature on the shelf lead to detection of cells previously concealed from detection with anti-EpCAM antibody. In addition the presence of platelets was monitored using red fluorescing anti CD36 or anti-CD41/CD61 antibody. Results: The maintrac® approach allowed detection of live tumor cells seeded at any time into the circulation. When, accidentally, we stained cells and platelets right after blood draw we found aggregations of red fluorescing platelets which upon inspection in transmitted light were shown to be clustered on cells. In time lapse photography on individual cells for 24 hrs it was observed that platelets were increasingly released from the cells and anti-EpCAM staining became more and more apparent. This indicates that platelets initially clustered around epithelial tumor cells prevent anti-EpCAM from binding to the cells and only if platelets are released the cells can be identified as positive cells. Most possibly hypoxic conditions induce release of the platelets. Conclusion: Rapid disappearance of cells shed from the tumor may be due to occultation of the cells by platelets. Since platelets express PD-L1 this may contribute to suppress anti-cancer immune cell activity. Citation Format: Dorothea Schott, Monika Pizon, Andreas Riess, Katharina Pachmann. How circulating tumor cells disguise [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 1937.
Alpha-synuclein mutations mislocalize cytoplasmic p300 compromising autophagy, which is rescued by ACLY inhibition
Authors: Sung Min Son, Farah H Siddiqi, Ana Lopez, Rizwan Ansari, Sylwia D Tyrkalska, So Jung Park, Tilo Kunath, Emmanouil Metzakopian, Angeleen Fleming, David C Rubinsztein
Journal: Neuron (2025)

Triplications and certain point mutations in the SNCA gene, encoding alpha-synuclein (α-Syn), cause Parkinson's disease (PD). Here, we demonstrate that the PD-causing A53T α-Syn mutation and elevated α-Syn expression perturb acetyl-coenzyme A (CoA) and p300 biology in human neurons and in the CNS of zebrafish and mice. This dysregulation is mediated by activation of ATP-citrate lyase (ACLY), a key enzyme that generates acetyl-CoA in the cytoplasm, via two mechanisms. First, ACLY activity increases acetyl-CoA levels, which activate p300. Second, ACLY activation increases LKB1 acetylation, which inhibits AMPK, leading to increased cytoplasmic and decreased nuclear p300. This lowers histone acetylation and increases acetylation of cytoplasmic p300 substrates, like raptor, which causes mechanistic target of rapamycin complex 1 (mTORC1) hyperactivation, thereby impairing autophagy. ACLY inhibitors rescue pathological phenotypes in PD neurons, organoids, zebrafish, and mouse models, suggesting that this pathway is a core feature of α-Syn toxicity and that ACLY may be a suitable therapeutic target.
Abstract 1535: Glycogen metabolism is critical for cancer-associated fibroblast proliferation and immunosuppressive activity
Authors: Xudong Zhu, Yuning Zhou, Zhijie Yin, Jinpeng Liu, Chi Wang, B.Mark Evers, Qingding Wang
Journal: Cancer Research (2025)

Background: Metabolic reprogramming is a characteristic feature of both cancer cells and their neighboring cells in the immunosuppressive tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are the major sources of secreted cytokines contributing to the immunosuppressive activity in the TME. Dysregulation of glycogen metabolism is integral to cancer cell proliferation and metastasis. The purpose of this study was to identify whether glycogen metabolism is important for CAF proliferation and cytokine production. Methods: CAFs were isolated from colorectal cancer (CRC) patient samples and cultured in conditioned medium (CM) derived from HCT116 human CRC cells. The expression of glycogen phosphorylase liver form (PYGL), glycogen phosphorylase brain form (PYGB), hexokinase 2 (HK2), lactate dehydrogenase A (LDHA), IL6, CLCF1, LIF, and CXCL6 was determined by either real time (RT)-PCR or western blot. Glycogen levels were determined using a Glycogen Analysis Kit. Cell proliferation was determined using WST-1. Results: (i) Data set analysis identified an elevated glucose metabolism in CAFs compared to normal fibroblasts. (ii) Treatment of CAFs with CM derived from HCT116 cells resulted in activated glycogen metabolism as noted by elevated protein expression of glycogen synthase, PYGL, PYGB, and the reduced level of glycogen in CAFs. In addition, CM increased glucose metabolism in CAFs as noted by significantly increased expression of HK2 and LDHA. Moreover, CM increased the expression of IL6 family cytokines such as IL6, CLCF1, LIF and CXCL6 in CAFs. (iii) Inhibition of glycogen metabolism by treatment with the PYG inhibitor, CP-91149, significantly repressed CAF proliferation and reduced the expression of these cytokines. Consistently, knockdown of PYGB or PYGL significantly decreased the level of these cytokines in CAFs. (iv) Inhibition of glycogen synthase by treatment with the glycogen synthase inhibitor, MZ-101, or knockdown of glycogen synthase 1 decreased the expression of these cytokines in CAFs. Conclusion: Our results demonstrate that glycogen metabolism is crucial for promoting CAF proliferation and cytokine production. Importantly, our findings suggest that targeting glycogen metabolism in CAFs reshapes the immunosuppressive TME and may enhance the efficacy of immunotherapy for CRC. Citation Format: Xudong Zhu, Yuning Zhou, Zhijie Yin, Jinpeng Liu, Chi Wang, B.Mark Evers, Qingding Wang. Glycogen metabolism is critical for cancer-associated fibroblast proliferation and immunosuppressive activity [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 1535.
Abstract 2043: Circulating tumor DNA (ctDNA) mutation analysis at baseline (BSL) and end of treatment (EOT) with sacituzumab govitecan (SG) and clinical impact on efficacy in patients (pts) with HR+/HER2- metastatic breast cancer (mBC): Biomarker results from TROPiCS-02
Authors: Hope S. Rugo, Yi Zhang, Shan Tang, Frederik Marmé, Peter Schmid, Javier Cortés, Sara M. Tolaney, Oh Kyu Yoon, Wendy Verret, Meghna Das Thakur, Aditya Bardia
Journal: Cancer Research (2025)

Abstract Background: SG is approved in pretreated HR+/HER2- mBC based on the TROPiCS-02 study (NCT03901339). Mutations in specific genes may affect efficacy of SG, including PIK3CA/TP53 (common in BC, may impact outcomes) and TACSTD2/TOP1 (may confer resistance to Trop-2-directed ADCs like SG). We assessed specific mutations at BSL and EOT in TROPiCS-02 to identify genes that may be involved in acquired SG resistance. Methods: Randomized pts received SG or chemotherapy treatment of physician’s choice (TPC). Plasma samples were collected at BSL and EOT, and ctDNA was analyzed using Guardant Health’s Infinity RUO ctDNA panel. Specific genes were analyzed to determine association with clinical outcomes (progression-free survival [PFS] and overall survival [OS]). Unbiased analysis at EOT was used to identify genes associated with SG resistance. Results: Pt characteristics, PFS, and OS were similar between the intent-to-treat (ITT; N=543) and ctDNA (46% of ITT) populations. PFS and OS benefit was observed with SG vs TPC regardless of PIK3CA or TP53 mutation status (Table). At BSL and EOT, no TACSTD2 mutations were observed in the SG arm. At BSL, 3 TOP1 mutations (I435V, D122H, M319I) were detected in 2 pts, and at EOT, 1 new TOP1 mutation (G717V) was detected in the SG arm (184 days treatment). At BSL 64% of pts had ≥1 deleterious variant in the 69-gene DDR panel. No clear expansion or clearance of individual DDR genes or variants was observed at EOT. Conclusions: Survival benefit was observed with SG vs TPC in pts with and without PIK3CA and TP53 mutations, similar to the ITT population. Our matched BSL to EOT analyses did not identify any genes that were clear drivers of SG resistance in pretreated HR+/HER2- mBC. Future analyses would benefit from paired biopsies at BSL and at disease progression to identify potential drivers of SG resistance. Citation Format: Hope S. Rugo, Yi Zhang, Shan Tang, Frederik Marmé, Peter Schmid, Javier Cortés, Sara M. Tolaney, Oh Kyu Yoon, Wendy Verret, Meghna Das Thakur, Aditya Bardia. Circulating tumor DNA (ctDNA) mutation analysis at baseline (BSL) and end of treatment (EOT) with sacituzumab govitecan (SG) and clinical impact on efficacy in patients (pts) with HR+/HER2- metastatic breast cancer (mBC): Biomarker results from TROPiCS-02. [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 2043.
Abstract 3828: Understanding the molecular underpinnings of breast cancer brain metastases: implications for early detection and treatment
Authors: Melanie Spears, Megan Hopkins, Rania Chehade, Italo Fernandes, Vida Talebian, Jane Bayani, Katarzyna Jerzak
Journal: Cancer Research (2025)

Abstract Brain metastases (BrM) are a major cause of morbidity and mortality among patients with metastatic breast cancer. Women with metastatic HER2-positive (HER2+) and triple-negative breast cancer (TNBC) have a particularly high propensity to develop BrM, with up to half developing BrM during their lifetime. Currently, apart from assignment of risk by breast cancer subtype, risk factors for the development of BrM are lacking. Given that BrM are associated with a poor prognosis, particularly among patients with TNBC, there is a critical need for biomarkers to identify patients at high risk of BrM for whom future screening and/or prevention strategies can be employed. In this study we performed whole transcriptomic profiling of 53 brain metastases in triplicate with spatial resolution using Bruker’s Digital Spatial Profiler, Whole Transcriptome Assay. Patients with breast cancer BrM who were treated with surgery, whole brain radiotherapy (WBRT) and/or stereotactic radiosurgery (SRS) between 2008 and 2018 were selected, representative sections of tumor were cored and microarrayed prior to spatial transcriptomic profiling of the tumor and tumor microenvironment. Across both HER2+ and TNBC subtypes, spatial deconvolution revealed a high proportion of CD4+ and CD8+ naïve T-cells in the tumor compartments compared to the tumor microenvironment whereas macrophages were the most abundant immune cell type irrespective of subtype in the tumor microenvironment. Differential gene expression analysis demonstrated that higher expression levels of known HER2 mediated genes including MED1, STARD3 and GRB7 were present in the HER2+ brain subtypes. Markers for stem cell features were more prevalent within tumor compartments of TNBC BrM compared to HER2+ BrM. In conclusion, this study characterized the tumor and tumor microenvironment of breast cancer BrM using spatial transcriptomics, identifying molecular underpinnings that may be targeted for BrM prevention and/or treatment. Citation Format: Melanie Spears, Megan Hopkins, Rania Chehade, Italo Fernandes, Vida Talebian, Jane Bayani, Katarzyna Jerzak. Understanding the molecular underpinnings of breast cancer brain metastases: implications for early detection and treatment [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 3828.
Abstract 3808: Bidirectional glutamine transport prevents mitochondrial stress in B-cell transformation
Authors: Ruifeng Sun, Gauri Deb, Kohei Kume, Yanzhi Feng, Johanna Scott, Thomas Graeber, Markus Müschen
Journal: Cancer Research (2025)

Comparing cell surface proteome changes during B-cell transformation, we found strong induction of SLC7A5, which simultaneously mediates leucine uptake and glutamine export. However, the significance of glutamine export is unknown.Slc7a5 deletion in transformed B cells (BCR-ABL1), but not primary resting B-cells, resulted in accumulated intracellular glutamine, reduced cell proliferation and viability, and prolonged survival of transplant recipients. Interestingly, glutamine deprivation, and pharmacological glutamine sequestration, partially rescued cell fitness, suggesting abnormal accumulation of glutamine impedes malignant transformation.Mechanistically, Slc7a5 deletion and glutamine accumulation resulted in integrated mitochondrial stress response, which signals through mTORC1 to activate ATF4 expression. Treatment with rapamycin significantly rescued growth disadvantage of Slc7a5-deficient cells, whereas treatment with p70 S6K1 inhibitor (PF-470671) had no rescue effect. These results suggested that activated mTORC1 in Slc7a5-deficient cells induced ATF4-mediated stress response rather than global protein synthesis. Chemogenomic screen with a selective SLC7A5 inhibitor in human B-cell leukemia revealed that deletion of genes involved in integrated stress response, including ATF4, led to synthetic lethality. By contrast, deletion of genes involved in mitochondrial tRNA aminoacylation and protein translation had rescue effects. Consistently, alleviation of mitochondrial stress by inhibiting protein synthesis with CHX completely rescued cell defects. In addition, metabolomic analysis and isotope tracing of (15N)2-glutamine revealed that Slc7a5-deficient cells directed glutamine metabolism towards purine synthesis, at the expense of glutathione and NAD+ synthesis. This is consistent with previous findings that mTORC1-ATF4 axis directly induced purine synthesis. Despite the critical role of glutaminolysis in cancer metabolism, our study show that SLC7A5-mediated glutamine export is critical in preventing mitochondrial stress and that abnormal accumulation of glutamine could be detrimental. Citation Format: Ruifeng Sun, Gauri Deb, Kohei Kume, Yanzhi Feng, Johanna Scott, Thomas Graeber, Markus Müschen. Bidirectional glutamine transport prevents mitochondrial stress in B-cell transformation [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 3808.
Abstract 5485: A new 30-color spectral flow cytometry panel for T cell characterization
Authors: David Draper, Brogan Yarzabek, Stacey Roys, Anita J. Zaitouna, Philip Lapinski, Amber Rowse, Scott Wise
Journal: Cancer Research (2025)

Abstract Spectral flow cytometers have facilitated the development of antibody panels with 30 colors or more to provide deep insights into the immune response. With a focus on T cell therapies, Labcorp has developed the 30-color immunophenotyping panel using the Cytek Aurora™ Spectral Flow Cytometer. The panel backbone includes 1 viability dye and 10 lineage markers to profile T cell, NK, and B cell subsets. 19 additional functional markers enable the characterization of activation, exhaustion, cytotoxicity, and proliferation in each subset, plus memory T cell subset delineation. Antibody-fluorophore combinations in a novel 30-color spectral flow cytometry panel were carefully considered and the resulting panel was developed utilizing primary PBMCs cultured with IL-2 and anti-CD3/CD28 to activate T cell subsets. Modulation of the expression levels for each functional marker was validated via comparisons made to unstimulated PBMCs. The most notable changes observed were in the expression of CCR7, CD25, ICOS, and Granzyme B which were expressed at levels between 60-95% of CD8+ T cells. Checkpoints including PD-1, LAG-3, TIM-3, and TIGIT were also upregulated, albeit to a lesser extent (&amp;lt;50% of CD8+ T cells). For memory phenotypes, analysis of CD45RA, CD45RO, CCR7, CD95, CD62L, and CD103 were combined to delineate Tn, Teff, Tte, Tcm, Tem, and Trm subsets. To provide an additional unbiased and wholistic analysis, t-SNE was conducted to deliver a comprehensive interpretation T cell functionality in the context of various exhausted phenotypic profiles. Finally, Nanostring® analysis using the nCounter® CAR-T Characterization panel was performed to further validate the modulation of gene sets underlying the TCR-driven PBMC activation. As expected, the transcriptomic analysis mirrored the flow cytometry immunophenotyping data with regard to activation and immunosuppressive gene modulation downstream of the TCR signaling. Taken together, a lymphoid panel was developed that measured multiple phenotypic and activity markers in T cells. Importantly, our data demonstrate how spectral flow cytometry can be applied to assess T cell therapies in preclinical tumor-bearing mouse models or clinical trials. Citation Format: David Draper, Brogan Yarzabek, Stacey Roys, Anita J. Zaitouna, Philip Lapinski, Amber Rowse, Scott Wise. A new 30-color spectral flow cytometry panel for T cell characterization [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 5485.
Abstract 6414: Epigenetic signatures of oral HPV-related cancer risk in HIV-positive subjects from Puerto Rico
Authors: Jurelis Torres-Reyes, Mayra S. Haedo-Cruz, Juliana M. Serrano-Rodríguez, Jeannette L. Salgado-Montilla, Maria M. Sánchez-Vázquez, Magaly Martínez-Ferrer, Gabriel Borges-Velez, Josué Pérez-Santiago
Journal: Cancer Research (2025)

Abstract Background: Advances in antiretroviral therapy (ART) have not reduced the disproportional incidence and prevalence of oral Human Papillomavirus (HPV) and oropharyngeal cancers in people with HIV (PWH), suggesting ART alone may not fully restore immunity. While DNA methylation is an epigenetic marker strongly linked with aging and cancer, the putative role of epigenetic regulation in HPV-related cancers, particularly in PWH, remains scarce. Methods: We evaluated the methylation profiles from saliva of 16 sexually active PWH (9 HPV-, and 7 HPV+). Oral rinse samples were collected and analyzed for HPV infection and genotyped using the DNA ELISA kit HPV SPF10 and RHA kit HPV SPF10-LiPA25. We measured the genome-wide methylation levels using the Illumina Infinium Methylation BeadChip arrays. We performed enrichment and functional analyses of differentially methylated loci and genes with differential methylation using GREAT and Metascape, respectively. Physical and functional protein-protein interaction networks were constructed using STRINGdatabase. Results: We identified 521 loci with significant differences in the levels of DNA methylation (p&amp;lt;0.1). There was genome-wide hypermethylation in HPV+ participants. Differential methylation analysis associated to cis-regulatory elements showed that 136 loci were associated to one gene, and 381 loci were associated to two or more genes, while four loci were not associated to any genes. Functional analysis of gene-associated loci with differential methylation illustrated significantly impacted biological processes and pathways, including: regulation of G1/S transition of mitotic cell cycle, RAC1 GTPase cycle, oxidative stress response, MAPK cascade, among others (adjusted p&amp;lt;0.05). Additionally, physical and functional interaction networks showed H3C12 as a major hub with 8 interactions with other genes including EGF, RBFOX3, NTRK3, and SIN3B. Conclusion: We found a distinct methylation profile by HPV status associated with cancer-related genes, which may represent novel biomarkers of early identification for HPV-related cancers in PWH in Puerto Rico. Reprogramming DNA methylation patterns may be a safe way to identify, prevent, or treat HPV persistence. Citation Format: Jurelis Torres-Reyes, Mayra S. Haedo-Cruz, Juliana M. Serrano-Rodríguez, Jeannette L. Salgado-Montilla, Maria M. Sánchez-Vázquez, Magaly Martínez-Ferrer, Gabriel Borges-Velez, Josué Pérez-Santiago. Epigenetic signatures of oral HPV-related cancer risk in HIV-positive subjects from Puerto Rico [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 6414.