tbuckley/cabot-search huggingface dataset:
UBE2T/CDC42/CD276 signaling axis mediates brain metastasis of triple-negative breast cancer via lysosomal autophagy
Authors: Liang Liang Shi, Yan Chen, Ming Xing Xie, Qian Zhi Chen, Xin Wei Qiao, Qi Hong Cheng, Lin Li, Rong Fu, Tao Liang, Xiaobing Jiang, Min Jie Wang, Jin Yao, Jun Jun Li
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background Advanced triple-negative breast cancer (TNBC) is prone to brain metastasis (BrM). The precise molecular mechanism responsible for this phenomenon has not yet been completely established, so it is vital to comprehend the molecular mechanism behind it. Methods The protein chip analysis was conducted to identify any abnormal UBE2T protein expression in TNBC, especially BrM. Here, we used public databases and bioinformatics analysis as well as clinical samples from different cohorts to investigate the interrelationship between UBE2T/CDC42/CD276. This predicted relationship was then repeatedly validated using different in vivo and in vitro experimental methods. Additionally, multiple experimental approaches were implemented, encompassing western blotting, Co-IP, GST pull-down, flow cytometry, mass spectrometry, immunofluorescence, immunohistochemistry, and qRT-PCR to reveal the molecular mechanism of UBE2T-mediated immune escape and BrM. Results Our results indicate that expressed at elevated levels in breast cancer, UBE2T is negatively linked to patient prognosis, especially in BrM of TNBC. Data from clinical samples from our different cohorts and TCGA indicate a significant correlation between UBE2T and immunosuppression. Mechanistically, UBE2T directly interacts with CDC42, promoting its K48-linked polyubiquitination and proteasomal degradation, thereby inhibiting CDC42 from degrading CD276 via the autophagy-lysosomal pathway, indirectly upregulating CD276 and thereby impairing the CD8 + T cells function, ultimately mediating tumor immune escape and BrM. Finally, animal experimental results also showed that inhibition of UBE2T elevated the TNBC sensitivity to immune checkpoint CD276 blockade and inhibited BrM of TNBC. Conclusions In conclusion, our results indicate a new mechanism whereby UBE2T-mediated ubiquitination positively controls the UBE2T/CDC42/CD276 axis to upregulate tumor cell expression of CD276 and thereby impair CD8 + T cells function, ultimately leading to tumor cell immune escape and BrM.
Oncolytic virus OH2 extends survival in patients with PD-1 pretreated melanoma: phase Ia/Ib trial results and biomarker insights
Authors: Xuan Wang, Hui Tian, Zhihong Chi, Lu Si, Xinan Sheng, Han Hu, Xiangyong Gu, Siming Li, Caili Li, Bin Lian, Li Zhou, Lili Mao, Bixia Tang, Xieqiao Yan, Xiaoting Wei, Juan Li, Binlei Liu, Jun Guo, Yan Kong, Chuanliang Cui
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background OH2 is an oncolytic virus derived from herpes simplex virus type 2. A phase Ia/Ib clinical trial in China was conducted in patients with unresected stage III–IV melanoma, the majority of whom had the acral type, to assess the safety and preliminary efficacy of OH2. Methods The trial enrolled patients with histologically confirmed unresectable stage III or advanced stage IV melanoma. In phase Ia, nine patients received OH2 single-dose treatment across three dose levels (10 6 , 10 7 , and 10 8 CCID 50 /mL, where CCID 50 represents cell culture infectious dose 50%) while six patients underwent multidose therapy. Phase Ib expanded the proposed dose. Antitumor efficacy was evaluated using the Response Evaluation Criteria in Solid Tumors and immune-RECIST guidelines. NCT04386967 is the clinical trial identifier. Results All 44 patients were enrolled. OH2 was well tolerated without serious adverse events (AEs) or deaths reported. No Grade 3 or higher treatment-related AEs occurred. In phase Ia, the 1-year survival rate was 92.9% (95% CI, 59.1% to 99.0%), with a median overall survival of 28.9 months (95% CI, 12.7 to not reached). In phase Ib, 10 patients achieved immune-partial response (iPR)/partial response (PR), yielding an objective response rate (ORR) of 37.0% (95% CI, 19.4% to 57.6%), with 6 patients still responding. The rate of the durable response (PR or complete response lasting at least 6 months) was at least 29.6% (8/27). Notably, 7 of 12 III–IVM1a patients who previously received programmed cell death protein-1 (PD-1) therapy achieved iPR/PR, with an ORR of 58.3% (95% CI, 27.7% to 84.8%) and a disease control rate of 75.0% (95% CI, 42.8% to 94.5%). Biomarker analysis indicated that elevated baseline neutrophil activation state correlated with poorer clinical outcomes. A phase III clinical trial is ongoing in China ( NCT05868707 ). Conclusions OH2 oncolytic virotherapy exhibited a favorable safety profile without dose-limiting toxicities (DLTs) and demonstrated durable antitumor efficacy in patients with melanoma, especially in those who had progressed on anti-PD-1 treatment. Trial registration number ClinicalTrials.gov identifier NCT04386967 .
Single-chain variable fragment affinity tuning can optimize anti-AML CAR-NK cell functionality
Authors: Ruyan Rahnama, Monika Kizerwetter, Huilin Yang, Ilias Christodoulou, Christian Guaraca, Natalie Jordan Holl, Jun Choe, Stamatia C Vorri, Megan Zinsky, Danielle G Jones, Nikol Garcia Espinoza, Yun-Huai Kuo, Marianna Zahurak, Ravi Varadhan, Jamie B. Spangler, Challice L. Bonifant
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background Natural Killer (NK) cells have intrinsic anticancer activity that can be redirected toward acute myeloid leukemia (AML) with chimeric antigen receptor (CAR) engineering. Here, we study the functional consequences of CAR binding affinity and targeted epitope on CAR-NK cell activation, cytolytic synapse formation, and antitumor activity. Methods We characterized NK-92 and primary NK cell populations expressing variant affinity AML-specific CARs containing single-chain variable fragments (scFvs, 26292 or 7G3) targeting two epitopes on CD123. 26292 affinity variants were discovered through directed evolution of an error-prone mutagenic library, while 7G3 affinity variants were previously reported. The resulting CAR-NK cell panel was studied with in vitro binding, activation, and cytotoxicity studies and in mouse xenograft models. Results 26292 and 7G3 CARs of variable CD123 binding affinities were highly expressed in NK cells and conferred antigen-specific activation in vitro. High-resolution imaging demonstrated greater clustering of high-affinity 7G3 CAR-NK cells and consequent AML target cell death in a short-term time lapse. Low-affinity 7G3 CAR-NK cells exhibited enhanced antigen density discrimination with greater membrane-proximal signaling, cytokine production, and cytotoxicity. In longer-term assays, low-affinity 7G3 CAR-NK cells demonstrated more sustained killing of AML cells. In vivo testing highlighted greater expansion of low-affinity 7G3 CAR-NK cells in two xenograft models. Conclusions Expression of 26292 and 7G3 CARs with a range of CD123 binding affinities in NK cells leads to antigen-specific activation and cytotoxicity against AML. Affinity-based differences in functional activation and antitumor activity are dependent on time course and are scFv/epitope specific.
Combinatorial <i>in vivo</i> genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis
Authors: Jess D Hebert, Yuning J Tang, Márton Szamecz, Laura Andrejka, Steven S Lopez, Dmitri A Petrov, Gábor Boross, Monte M Winslow
Journal: Molecular Biology and Evolution (2025)

Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.
Single cell RNA sequencing of hematopoietic cells in fresh and frozen human atheroma tissue
Authors: Herra Ahmad, J k Gopakumar, Daniel C Nachun, Lisa Ma, Jessica D’Addabbo, Xianxi Huang, Tiffany Koyano, Jack Boyd, Y Joseph Woo, Robyn Fong, Oliver Aalami, Patricia K Nguyen, Siddhartha Jaiswal
Journal: Cardiovascular Research (2025)

Single-cell RNA sequencing (scRNA-seq) is a powerful method for exploring the cellular heterogeneity within human atheroma but typically requires fresh tissue to preserve cell membrane integrity, limiting the feasibility of large-scale biobanking for later analysis. The aim of this study was to determine whether cryopreservation of fragile and necrotic atheroma tissue affects the viability and transcriptomic profiles of hematopoietic cells in subsequent scRNA-seq analysis, enabling the use of cryopreserved atheroma samples for future research. We performed scRNA-seq on five paired fresh and cryopreserved atheroma samples - three from coronary arteries and two from carotid arteries. Each sample was enzymatically digested, sorted for CD45+ hematopoietic cells, and processed using the 10X Genomics scRNA-seq workflow. Half of each sample was processed immediately, while the other half was cryopreserved in liquid nitrogen for an average of five weeks before thawing and processing. In carotid artery samples, we noted the absence of LYVE1+ macrophages, likely due to the loss of the adventitial layer during endarterectomy procedures. Our results indicated that cryopreservation modestly affected cellular integrity, leading to an increase in the relative abundance of mitochondrial RNA in frozen samples. Minimal differences were observed between fresh and cryopreserved samples in uniquely detected transcripts, cell clustering, or transcriptional profiles within hematopoietic populations. Our study demonstrates that cryopreserved human atheroma samples can be successfully profiled using scRNA-seq, with comparable transcriptomic data to that obtained from fresh samples. These findings suggest that cryopreservation is a viable method for biobanking atheroma tissues, facilitating large-scale studies without the need for immediate sample processing.
Repeated OGTT Versus Continuous Glucose Monitoring for Predicting Development of Stage 3 Type 1 Diabetes: A Longitudinal Analysis
Authors: Aster K. Desouter, Bart Keymeulen, Ursule Van de Velde, Annelien Van Dalem, Bruno Lapauw, Christophe De Block, Pieter Gillard, Nicole Seret, Eric V. Balti, Elena R. Van Vooren, Willem Staels, Sara Van Aken, Marieke den Brinker, Sylvia Depoorter, Joke Marlier, Hasan Kahya, Frans K. Gorus
Journal: Diabetes Care (2025)

Evidence for using continuous glucose monitoring (CGM) as an alternative to oral glucose tolerance tests (OGTTs) in presymptomatic type 1 diabetes is primarily cross-sectional. We used longitudinal data to compare the diagnostic performance of repeated CGM, HbA1c, and OGTT metrics to predict progression to stage 3 type 1 diabetes. Thirty-four multiple autoantibody-positive first-degree relatives (FDRs) (BMI SD score [SDS] <2) were followed in a multicenter study with semiannual 5-day CGM recordings, HbA1c, and OGTT for a median of 3.5 (interquartile range [IQR] 2.0-7.5) years. Longitudinal patterns were compared based on progression status. Prediction of rapid (<3 years) and overall progression to stage 3 was assessed using receiver operating characteristic (ROC) areas under the curve (AUCs), Kaplan-Meier method, baseline Cox proportional hazards models (concordance), and extended Cox proportional hazards models with time-varying covariates in multiple record data (n = 197 OGTTs and concomitant CGM recordings), adjusted for intraindividual correlations (corrected Akaike information criterion [AICc]). After a median of 40 (IQR 20-91) months, 17 of 34 FDRs (baseline median age 16.6 years) developed stage 3 type 1 diabetes. CGM metrics increased close to onset, paralleling changes in OGTT, both with substantial intra- and interindividual variability. Cross-sectionally, the best OGTT and CGM metrics similarly predicted rapid (ROC-AUC = 0.86-0.92) and overall progression (concordance = 0.73-0.78). In longitudinal models, OGTT-derived AUC glucose (AICc = 71) outperformed the best CGM metric (AICc = 75) and HbA1c (AICc = 80) (all P < 0.001). HbA1c complemented repeated CGM metrics (AICc = 68), though OGTT-based multivariable models remained superior (AICc = 59). In longitudinal models, repeated CGM and HbA1c were nearly as effective as OGTT in predicting stage 3 type 1 diabetes and may be more convenient for long-term clinical monitoring.
Regulatory T cells converted from Th1 cells in tumors suppress cancer immunity via CD39
Authors: Sang-Nee Tan, Jing Hao, Jing Ge, Yazheng Yang, Liguo Liu, Jia Huang, Meng Lin, Xiaohong Zhao, Genyu Wang, Zhiying Yang, Ling Ni, Chen Dong
Journal: The Journal of Experimental Medicine (2025)

Regulatory T (Treg) cells are known to impede antitumor immunity, yet the regulatory mechanisms and functional roles of these cells remain poorly understood. In this study, through the characterization of multiple cancer models, we identified a substantial presence of peripherally induced Treg cells in the tumor microenvironment (TME). Depletion of these cells triggered antitumor responses and provided potent therapeutic effects by increasing functional CD8+ T cells. Fate-mapping and transfer experiments revealed that IFN-γ-expressing T helper (Th) 1 cells differentiated into Treg cells in response to TGF-β signaling in tumors. Pseudotime trajectory analysis further revealed the terminal differentiation of Th1-like Treg cells from Th1 cells in the TME. Tumor-resident Treg cells highly expressed T-bet, which was essential for their functions in the TME. Additionally, CD39 was highly expressed by T-bet+ Treg cells in both mouse and human tumors, and was necessary for Treg cell-mediated suppression of CD8+ T cell responses. Our study elucidated the developmental pathway of intratumoral Treg cells and highlighted novel strategies for targeting them in cancer patients.
No added sugar: CCDC134 stabilizes ER chaperone Gp96 for TLR biogenesis
Authors: Antje Blumenthal, Leslie C. Domínguez Cadena
Journal: The Journal of Experimental Medicine (2025)

Bernaleau et al. (https://doi.org/10.1084/jem.20240825) show that CCDC134 located in the ER is required for TLR biogenesis by controlling the N-glycosylation, folding, and stabilization of the ER chaperone Gp96.
Reinforcing cancer immunotherapy with engineered porous hollow mycobacterium tuberculosis loaded with tumor neoantigens
Authors: Ming-Hui Chen, Jie Jiang, Hengyu Chen, Ri-Hong Wu, Weijing Xie, Shu-Zhen Dai, Wu-Ping Zheng, Guang-Hong Tan, Feng-Ying Huang
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background Enhancing antigen cross-presentation is essential for the development of a tumor neoantigen vaccine. One approach is to stimulate antigen-presenting cells (APCs) to uptake neoantigens. Mycobacterium tuberculosis (MTb) contains pathogen-associated molecular patterns (PAMPs) recognized by APCs and adhesion molecules that facilitate MTb invasion of APCs. Therefore, we suggest using MTb as a carrier to enhance APC phagocytosis of neoantigens, thereby promoting antigen cross-presentation. Methods The successful preparation of the MTb carrier (phMTb) was confirmed through electron and confocal microscopy. Fluorescence microscopy was used to detect PAMPs and adhesion molecules on phMTb as well as to observe its role in aiding dendritic cells (DCs) in antigen uptake into endosomes or lysosomes. Flow cytometry was used to assess the retention of PAMPs and adhesion molecules on phMTb, investigate antigen uptake by DCs, evaluate their activation and maturation status, examine the presentation of tumor neoantigens, and analyze immune cells in draining lymph nodes and tumor tissues. The efficacy of phMTb vaccine formulations in combination with anti-programmed cell death protein 1 (PD-1) antibody therapy was assessed using the MC38 mouse tumor models. Adverse effects were evaluated through H&amp;E staining of major organs, assessment of reproductive capability and detection of biochemical indices. Results The engineered porous hollow phMTb carrier successfully encapsulated model tumor neoantigens, with or without the adjuvant CpG. The phMTb retained PAMPs and adhesion molecules on its surface, similar to the parental MTb, thereby enhancing DC uptake of phMTb and its formulations containing tumor neoantigens and CpG. Vaccines formulated with phMTb facilitated DC maturation, activation, cross-presentation of tumor neoantigens, and promoted migration of phMTb-laden DCs to lymph nodes, enhancing effector and memory CD8 + T lymphocyte function. In murine tumor models, immunization with phMTb-formulated neoantigen vaccines elicited a robust tumor-specific cytotoxic T lymphocyte immune response with minimal adverse effects. Additionally, vaccination with phMTb-formulated neoantigen vaccines effectively reversed the tumor’s immune-suppressive microenvironment. Concurrent administration of the PD-1 antibody with the phMTb-formulated neoantigen vaccine exhibited significant synergistic therapeutic effects. Conclusions The results of our study highlight the potential clinical translation of personalized tumor neoantigen vaccines using the phMTb carrier.
CENP-A/CENP-B uncoupling in the evolutionary reshuffling of centromeres in equids
Authors: Eleonora Cappelletti, Francesca M. Piras, Marialaura Biundo, Elena Raimondi, Solomon G. Nergadze, Elena Giulotto
Journal: Genome biology (2025)

While CENP-A is the epigenetic determinant of the centromeric function, the role of CENP-B, a centromeric protein binding a specific DNA sequence, the CENP-B-box, remains elusive. In the few mammalian species analyzed so far, the CENP-B box is contained in the major satellite repeat that is present at all centromeres, with the exception of the Y chromosome. We previously demonstrated that, in the genus Equus, numerous centromeres lack any satellite repeat. In four Equus species, CENP-B is expressed but does not bind the majority of satellite-based centromeres, or the satellite-free ones, while it is localized at several ancestral, now-inactive, centromeres. Centromeres lacking CENP-B are functional and recruit normal amounts of CENP-A and CENP-C. The absence of CENP-B is related to the lack of CENP-B boxes rather than to peculiar features of the protein itself. CENP-B boxes are present in a previously undescribed repeat which is not the major satellite bound by CENP-A. Comparative sequence analysis suggests that this satellite was centromeric in the equid ancestor, lost centromeric function during evolution, and gave rise to a shorter CENP-A bound repeat not containing the CENP-B box but enriched in dyad symmetries. We propose that the uncoupling between CENP-B and CENP-A may have played a role in the extensive evolutionary reshuffling of equid centromeres. This study provides new insights into the complexity of centromere organization in a largely biodiverse world where the majority of mammalian species still have to be studied.
Cellular deconstruction of the human skeletal muscle microenvironment identifies an exercise-induced histaminergic crosstalk
Authors: Thibaux Van der Stede, Alexia Van de Loock, Guillermo Turiel, Camilla Hansen, Andrea Tamariz-Ellemann, Max Ullrich, Eline Lievens, Jan Spaas, Nurten Yigit, Jasper Anckaert, Justine Nuytens, Siegrid De Baere, Ruud Van Thienen, Anneleen Weyns, Laurie De Wilde, Peter Van Eenoo, Siska Croubels, John R Halliwill, Pieter Mestdagh, Erik A Richter, Lasse Gliemann, Ylva Hellsten, Jo Vandesompele, Katrien De Bock, Wim Derave
Journal: Cell Metabolism (2025)

Plasticity of skeletal muscle is induced by transcriptional and translational events in response to exercise, leading to multiple health and performance benefits. The skeletal muscle microenvironment harbors myofibers and mononuclear cells, but the rich cell diversity has been largely ignored in relation to exercise adaptations. Using our workflow of transcriptome profiling of individual myofibers, we observed that their exercise-induced transcriptional response was surprisingly modest compared with the bulk muscle tissue response. Through the integration of single-cell data, we identified a small mast cell population likely responsible for histamine secretion during exercise and for targeting myeloid and vascular cells rather than myofibers. We demonstrated through histamine H1 or H2 receptor blockade in humans that this paracrine histamine signaling cascade drives muscle glycogen resynthesis and coordinates the transcriptional exercise response. Altogether, our cellular deconstruction of the human skeletal muscle microenvironment uncovers a histamine-driven intercellular communication network steering muscle recovery and adaptation to exercise.
Piezo2 in sensory neurons regulates systemic and adipose tissue metabolism
Authors: Fabian S Passini, Bavat Bornstein, Sarah Rubin, Yael Kuperman, Sharon Krief, Evi Masschelein, Tevie Mehlman, Alexander Brandis, Yoseph Addadi, Shira Huri-Ohev Shalom, Erik A Richter, Tal Yardeni, Amir Tirosh, Katrien De Bock, Elazar Zelzer
Journal: Cell Metabolism (2025)
Distinct cellular mechanisms underlie chemotherapies and PD-L1 blockade combinations in triple-negative breast cancer
Authors: Yuanyuan Zhang, Hongyan Chen, Hongnan Mo, Ning Zhao, Xiaoying Sun, Baolin Liu, Ranran Gao, Binghe Xu, Zemin Zhang, Zhihua Liu, Fei Ma
Journal: Cancer Cell (2025)

Combining immune checkpoint blockade (ICB) with chemotherapy shows promise for treating triple-negative breast cancer (TNBC), though the mechanisms remain incompletely understood. Here, we integrate published and new single-cell RNA sequencing (scRNA-seq) data to investigate the tumor immune microenvironment (TIME) in TNBC patients treated with paclitaxel (PTX), nab-paclitaxel (Nab-PTX), and their combinations with the anti-PD-L1 antibody atezolizumab (ATZ). Compared to ATZ plus PTX, ATZ plus Nab-PTX rewires TCF7+ stem-like effector memory CD8+ T cells (Tsem) and CD4+ T follicular helper (Tfh) cells. Nab-paclitaxel, unlike PTX, also reshapes the myeloid compartment, expanding mast cells and pro-inflammatory macrophages. Our analyses in human TNBC and murine models underscore the crucial role of mast cells in orchestrating anti-tumor immune responses, likely by promoting the recruitment and activation of T and B cells. In vivo experiments demonstrate that activating mast cells alongside PD-L1 blockade attenuates TNBC progression, suggesting mast cells as a promising adjunct for enhancing ICB therapy efficacy.