Research Article
Abstract
Pancreatic cancer (PC) is notoriously resistant to both chemotherapy and immunotherapy, presenting a major therapeutic challenge. Epigenetic modifications play a critical role in PC progression, yet their contribution to chemoimmunotherapy resistance remains poorly understood. Here, we identified the transcription factor ZEB1 as a critical driver of chemoimmunotherapy resistance in PC. ZEB1 knockdown synergized with gemcitabine and anti–PD-1 therapy, markedly suppressed PC growth, and prolonged survival in vivo. Single-cell and spatial transcriptomics revealed that ZEB1 ablation promoted tumor pyroptosis by recruiting and activating GZMA+CD8+ T cells in the tumor core through epigenetic upregulation of CXCL16. Meanwhile, ZEB1 blockade attenuates CD44+ neutrophil–induced CD8+ T cell exhaustion by reducing tumor-derived SPP1 secretion, which otherwise promotes exhaustion through activation of the PD-L1/PD-1 pathway. Clinically, high ZEB1 expression correlated with chemoresistance, immunosuppression, and diminished CXCL16 levels in patients with PC. Importantly, the epigenetic inhibitor mocetinostat (targeting ZEB1) potentiated the efficacy of chemoimmunotherapy, including anti–PD-1 and CAR T therapies, in patient-derived organoids, xenografts, and orthotopic models. Our study unveils ZEB1 as a master epigenetic regulator of chemoimmunotherapy resistance and proposes its targeting as a transformative strategy for PC treatment.
Authors
Shaobo Zhang, Yumeng Hu, Zhijun Zhou, Gaoyuan Lv, Chenze Zhang, Yuanyuan Guo, Fangxia Wang, Yuxin Ye, Haoran Qi, Hui Zhang, Wenming Wu, Min Li, Mingyang Liu
Abstract
We describe here a shared surface and cell wall protein, endoglucanase 2 (Eng2), expressed on the etiological agents that cause the endemic systemic mycoses of North America — Blastomyces, Coccidioides, and Histoplasma. We demonstrate that, despite sequence variation of the protein across these related fungi, exposure to Eng2 vaccinated and protected inbred and humanized HLA-DR4 strains of mice against lethal experimental infections with these fungi by eliciting adaptive immunity mediated by CD4+ T cells. We also show that CD4+ T cell precursors against Eng2 were detectable in naive individuals and that patients who had recovered from these infections evinced a memory and recall CD4+ T cell response to Eng2 and its immunodominant epitopes that we have mapped. We created and cataloged new tools and information, such as immunodominant peptide epitopes of Eng2 from each fungus recognized by inbred mice and humans, and we engineered peptide–MHC II tetramers to track T cells in inbred and HLA-DR4–humanized mice. These tools and tetramers will be useful for those who study these infections in mice and humans. Last, because most patients demonstrated immune memory and recall responses against Eng2, our work offers tools for the diagnosis of this collection of infectious diseases across North America.
Authors
Uju J. Okaa, Cleison Ledesma Taira, Lucas dos Santos Dias, Hannah Dobson, Gregory C. Kujoth, Althea Campuzano, E. Jane Homan, George R. Thompson, Chiung-Yu Hung, George S. Deepe Jr, Marcel Wüthrich, Bruce S. Klein
Abstract
B lymphocytes play major adaptive immune roles, producing antibodies and driving T cell responses. However, how immunometabolism networks support B cell activation and differentiation in response to distinct receptor stimuli remains incompletely understood. To gain insights, we systematically investigated acute primary human B cell transcriptional, translational, and metabolomic responses to B cell receptor (BCR), TLR9, CD40-ligand (CD40L), IL-4, or combinations thereof. T cell–independent BCR/TLR9 costimulation, which drives malignant and autoimmune B cell states, highly induced transaminase branched chain amino acid transaminase 1 (BCAT1), which localized to lysosomal membranes to support branched chain amino acid synthesis and mTORC1 activation. BCAT1 inhibition blunted BCR/TLR9, but not CD40L/IL-4–triggered B cell proliferation, IL-10 expression, and BCR/TLR pathway–driven lymphoma xenograft outgrowth. These results provide a valuable resource, reveal receptor-mediated immunometabolism remodeling to support key B cell phenotypes, and identify BCAT1 as an activated B cell therapeutic target.
Authors
Rui Guo, Yizhe Sun, Matthew Y. Lim, Hardik Shah, Joao A. Paulo, Rahaman A. Ahmed, Weixing Li, Yuchen Zhang, Haopeng Yang, Liang Wei Wang, Daniel Strebinger, Nicholas A. Smith, Meng Li, Merrin Man Long Leong, Michael Lutchenkov, Jin Hua Liang, Zhixuan Li, Yin Wang, Rishi Puri, Ari Melnick, Michael R. Green, John M. Asara, Adonia E. Papathanassiu, Duane R. Wesemann, Steven P. Gygi, Vamsi K. Mootha, Benjamin E. Gewurz
Abstract
A cornerstone of research to improve cancer outcomes involves studies of model systems to identify causal drivers of oncogenesis, understand mechanisms leading to metastases, and develop new therapeutics. Although most cancer types are represented by large cell line panels that reflect diverse neoplastic genotypes and phenotypes found in patients, prostate cancer is notable for a very limited repertoire of models that recapitulate the pathobiology of human disease. Of these, the lymph node carcinoma of the prostate (LNCaP) cell line has served as the major resource for basic and translational studies. Here, we delineated the molecular composition of LNCaP and multiple substrains through analyses of whole-genome sequences, transcriptomes, chromatin structure, androgen receptor (AR) cistromes, and functional studies. Our results determined that LNCaP exhibits substantial subclonal diversity, ongoing genomic instability, and phenotype plasticity. Several oncogenic features were consistently present across strains, but others were unexpectedly variable, such as ETV1 expression, Y chromosome loss, a reliance on WNT and glucocorticoid receptor activity, and distinct AR alterations maintaining AR pathway activation. These results document the inherent molecular heterogeneity and ongoing genomic instability that drive diverse prostate cancer phenotypes and provide a foundation for the accurate interpretation and reproduction of research findings.
Authors
Arnab Bose, Armand Bankhead III, Ilsa Coleman, Thomas Persse, Wanting Han, Patricia Galipeau, Brian Hanratty, Tony Chu, Jared Lucas, Dapei Li, Rabeya Bilkis, Pushpa Itagi, Sajida Hassan, Mallory Beightol, Minjeong Ko, Ruth Dumpit, Michael Haffner, Colin Pritchard, Gavin Ha, Peter S. Nelson
Abstract
Checkpoint inhibitors targeting CTLA-4 and PD-1 revolutionized the treatment of cancer patients, but their use is limited by the emergence of immune-related adverse events (irAEs). We assessed autoreactive B cell frequencies in the blood of cancer patients before and after treatment with checkpoint inhibitors by testing the reactivity of recombinant antibodies cloned from single B cells. We found that anti–PD-1 and anti–CTLA-4 combination therapy induced the emergence of autoreactive mature naive B cells, whereas central B cell tolerance remained functional. In contrast, anti–PD-1 alone did not alter autoreactive B cell counterselection. Anti–CTLA-4 injections in humanized mice also resulted in the production of autoreactive B cells, whereas anti–PD-1 did not. We conclude that CTLA-4 but not PD-1 is required for the removal of developing autoreactive mature naive B cells and that CTLA-4 blockade broadens the peripheral B cell repertoire, which likely contains clones that promote not only irAEs but also antitumor responses.
Authors
Elif Çakan, Meng Wang, Yile Dai, Adrien Mirouse, Clarence Rachel Villanueva-Pachas, Delphine Bouis, Joshua M. Boeckers, Ruchi Gera, Sally Yraita, Leslie Clapp, Ana Luisa Perdigoto, Fabien R. Delmotte, Christopher Massad, Antonietta Bacchiocchi, Aaron M. Ring, Yuval Kluger, Harriet M. Kluger, Kevan C. Herold, Eric Meffre
Abstract
Activating mutations in PIK3CA, the gene encoding the catalytic p110α subunit of PI3K, are some of the most frequent genomic alterations in breast cancer. Alpelisib, a small-molecule inhibitor that targets p110α, is a recommended drug for patients with PIK3CA-mutant advanced breast cancer. However, clinical success for PI3K inhibitors (PI3Kis) has been limited by their narrow therapeutic window. The lipid phosphatase PTEN is a potent tumor suppressor and a major negative regulator of the PI3K pathway. Unsurprisingly, inactivating mutations in PTEN correlate with tumor progression and resistance to PI3K inhibition due to persistent PI3K signaling. Here, we demonstrate that PI3K inhibition leads rapidly to the inactivation of PTEN. Using a functional genetic screen, we show that this effect is mediated by a USP10-GSK3β signaling axis, in which USP10 stabilizes GSK3β, resulting in GSK3β-mediated phosphorylation of the C-terminal tail of PTEN. This phosphorylation inhibits PTEN dimerization and thus prevents its activation. Downregulation of GSK3β or USP10 resensitizes PI3Ki-resistant breast cancer models and patient-derived organoids to PI3K inhibition and induces tumor regression. Our study establishes that enhancing PTEN activity is a new strategy to treat PIK3CA mutant tumors and provides a strong rationale for pursuing USP10 inhibitors in the clinic.
Authors
Nishi Kumari, Sarah C.E. Wright, Christopher M. Witham, Laia Monserrat, Marta Palafox, John L.C. Richard, Carlotta Costa, Moshe Elkabets, Mark Agostino, Theresa Klemm, Melissa Eccles, Alex Garnham, Ting Wu, Jonas A. Nilsson, Nikita Walz, Veena Venugopal, Anthony Cerra, Natali Vasilevski, Stephanie Bridgeman, Sona Bassi, Azad Saei, Moutaz Helal, Philipp Neundorf, Angela Riedel, Mathias Rosenfeldt, Jespal Gill, Nikolett Pahor, Oliver Hartmann, Jacky Chung, Sachdev S. Sidhu, Nina Moderau, Sudhakar Jha, Jordi Rodon, Markus E. Diefenbacher, David Komander, Violeta Serra, Pieter Johan Adam Eichhorn
Abstract
3-O-sulfation of heparan sulfate (HS) is the key determinant for binding and activation of antithrombin III (AT). This interaction is the basis of heparin treatment to prevent thrombotic events and excess coagulation. Antithrombin-binding HS (HSAT) is expressed in human tissues but is thought to be expressed in the subendothelial space, mast cells, and follicular fluid. Here, we show that HSAT is ubiquitously expressed in the basement membranes of epithelial cells in multiple tissues. In the pancreas, HSAT is expressed by healthy ductal cells, and its expression is increased in premalignant pancreatic intraepithelial neoplasia lesions but not in pancreatic ductal adenocarcinoma (PDAC). Inactivation of HS3ST1, a key enzyme in HSAT synthesis, in PDAC cells eliminated HSAT expression, induced an inflammatory phenotype, suppressed markers of apoptosis, and increased metastasis in an experimental mouse PDAC model. HSAT-positive PDAC cells bind AT, which inhibits the generation of active thrombin by tissue factor and factor VIIa. Furthermore, plasma from patients with PDAC showed accumulation of HSAT, suggesting its potential as a marker of tumor formation. These findings suggest that HSAT exerts a tumor-suppressing function through recruitment of AT and that the decrease in HSAT during progression of pancreatic tumorigenesis increases inflammation and metastatic potential.
Authors
Thomas Mandel Clausen, Ryan J. Weiss, Jacob R. Tremblay, Benjamin P. Kellman, Joanna Coker, Leo A. Dworkin, Jessica P. Rodriguez, Ivy M. Chang, Timothy Chen, Vikram Padala, Richard Karlsson, Hyemin Song, Kristina L. Peck, Satoshi Ogawa, Daniel R. Sandoval, Hiren J. Joshi, Gaowei Wang, L. Paige Ferguson, Nikita Bhalerao, Allison Moores, Tannishtha Reya, Maike Sander, Thomas C. Caffrey, Jean L. Grem, Alexandra Aicher, Christopher Heeschen, Dzung Le, Nathan E. Lewis, Michael A. Hollingsworth, Paul M. Grandgenett, Susan L. Bellis, Rebecca L. Miller, Mark M. Fuster, David W. Dawson, Dannielle D. Engle, Jeffrey D. Esko
Abstract
Pulmonary fibrosis (PF) has been called a fibroproliferative disease, yet the functional importance of proliferating fibroblasts to PF has not been systematically examined. In response to alveolar injury, quiescent alveolar fibroblasts differentiate into fibrotic fibroblasts that express high amounts of collagens. However, what role, if any, proliferation plays in the accumulation of fibrotic fibroblasts has remained unclear. Using 5-ethynyl-2′-deoxyuridine (EdU) incorporation, genetic lineage tracing, and single-cell RNA-Seq, we delineated the proliferation dynamics of lung fibroblasts during post-injury fibrogenesis. We found substantial DNA replication in progeny of alveolar fibroblasts in 2 independent models of PF. Lineage labeling revealed clonal expansion of these fibroblast descendants principally in regions of fibrotic remodeling. The transcriptome of proliferating fibroblasts closely resembled that of fibrotic fibroblasts, suggesting that fibroblasts can first differentiate into fibrotic fibroblasts and then proliferate. Genetic ablation of proliferating fibroblasts and selective inhibition of cytokinesis in alveolar fibroblast descendants significantly mitigated PF and rescued lung function. Furthermore, fibroblasts in precision-cut lung slices from human fibrotic lungs exhibited higher proliferation rates than did those in nondiseased lungs. Together, this work establishes fibroblast proliferation as a critical driver of PF and suggests that specifically targeting fibroblast proliferation could be a new therapeutic strategy for fibrotic diseases.
Authors
Christopher Molina, Tatsuya Tsukui, Imran S. Khan, Xin Ren, Wenli Qiu, Michael Matthay, Paul Wolters, Dean Sheppard
Abstract
Few drugs are available for rare diseases due to economic disincentives. However, tailored medications for extremely rare disorders (N-of-1) offer a ray of hope. Artificial antisense oligonucleotides (ASOs) are now best known for their use in spinal muscular atrophy (SMA). The success of nusinersen/Spinraza for SMA indicates the potential of ASO therapies for other rare conditions. We propose a strategy to develop N-of-1 ASOs for treating one form of trichothiodystrophy (TTD), a rare condition with multisystem abnormalities and reduced life expectancy, associated with instability and greatly reduced amounts of the DNA-repair/transcription factor TFIIH. The therapeutic targets carry mutations in GTF2H5, encoding the TFIIH-p8 subunit. This approach was inspired by the diagnosis and molecular dissection of a xeroderma pigmentosum (XP) case with mutations in GTF2H4, encoding the TFIIH-p52 subunit. This is newly classified as a ninth XP complementation–group, XP-J, identified 5 decades after the discovery of the other XP complementation–groups. The p8-p52 interaction is required to support the TFIIH-complex formation, and the patient’s p52 C-terminal truncation results in the complete absence of p8 in TFIIH. However, intriguingly, TFIIH remained stable in vivo, and the patient with XP-J did not exhibit any TTD-features. The aim of our ASO-design is to induce a C-terminal truncation of p52 and we have successfully stabilized TFIIH in p8-deficient cells from patients with TTD-A.
Authors
Yuka Nakazawa, Lin Ye, Yasuyoshi Oka, Hironobu Morinaga, Kana Kato, Mayuko Shimada, Kotaro Tsukada, Koyo Tsujikawa, Yosuke Nishio, Hiva Fassihi, Shehla Mohammed, Alan R. Lehmann, Tomoo Ogi
Abstract
The Integrator complex plays essential roles in RNA polymerase II (RNAPII) transcription termination and RNA processing. Here, we identify INTS6, a subunit of the Integrator complex, as a novel gene associated with neurodevelopmental disorders (NDDs). Through analysis of large NDD cohorts and international collaborations, we identified 23 families harboring monoallelic likely gene-disruptive or de novo missense variants in INTS6. Phenotypic characterization revealed shared features, including language and motor delays, autism, intellectual disability, and sleep disturbances. Using a nervous-system conditional KO (cKO) mouse model, we show that Ints6 deficiency disrupts early neurogenesis, cortical lamination, and synaptic development. Ints6 cKO mice had a thickened ventricular zone/subventricular zone, thinning of the cortical plate, reduced neuronal differentiation, and increased apoptosis in cortical layer 6. Behavioral assessments of heterozygous mice revealed deficits in social novelty preference, spatial memory, and hyperactivity, mirroring phenotypes observed in individuals with INTS6 variants. Molecular analyses further revealed that INTS6 deficiency alters RNAPII dynamics, disrupts transcriptional regulation, and impairs synaptic gene expression. Treatment with a CDK9 inhibitor (CDK9i) reduced RNAPII phosphorylation, thereby limiting its binding to target genes. Notably, CDK9i reversed neurosphere overproliferation and rescued the abnormal dendritic spine phenotype caused by Ints6 deficiency. This work advances understanding of INTS-related NDD pathogenesis and highlights potential therapeutic targets for intervention.
Authors
Xiaoxia Peng, Xiangbin Jia, Hanying Wang, Jingjing Chen, Xiaolei Zhang, Senwei Tan, Xinyu Duan, Can Qiu, Mengyuan Hu, Haiyan Hou, Ilaria Parenti, Alma Kuechler, Frank J. Kaiser, Alicia Renck, Raymond Caylor, Cindy Skinner, Joseph Peeden, Benjamin Cogne, Bertrand Isidor, Sandra Mercier, Gael Nicolas, Anne-Marie Guerrot, Flavio Faletra, Luciana Musante, Lior Cohen, Gaber Bergant, Goran Čuturilo, Borut Peterlin, Andrea Seeley, Kristine Bachman, Julian A. Martinez-Agosto, Conny van Ravenswaaij-Arts, Dennis Bos, Katherine H. Kim, Tobias Bartolomaeus, Zelia Schmederer, Rami Abou Jamra, Erfan Aref-Eshghi, Wenjing Zhao, Yongyi Zou, Zhengmao Hu, Qian Pan, Faxiang Li, Guodong Chen, Jiada Li, Zhangxue Hu, Kun Xia, Jieqiong Tan, Hui Guo
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ISSN: 0021-9738 (print), 1558-8238 (online)