Osteosarcoma (OS) in pediatric, adolescent, and young adult (AYA) patients is an aggressive bone cancer with limited treatment options. Dysregulation of the CDK4/6–cyclin D axis and the PI3K/mTOR pathway contributes to OS pathogenesis, providing a biological rationale for co-targeting these signaling nodes. However, pharmacologic CDK4/6 inhibition can trigger compensatory activation of the PI3K/mTOR pathway, restoring D-type cyclin expression and partially reactivating CDK4/6 signaling. Thus, dual inhibition of the CDK4/6 and PI3K/mTOR pathways not only addresses two parallel oncogenic drivers but may also prevent potential CDK4/6 inhibitor resistance mediated by feedback activation of PI3K/mTOR. In this study, we tested the hypothesis that coordinated targeting of these pathways would improve tumor control in preclinical OS models. In vitro sensitivity analyses using palbociclib and voxtalisib demonstrated additive to synergistic OS growth suppression, with palbociclib inducing G1 arrest and senescence, and the combination enhancing autophagy. Furthermore, the efficacy, tolerability, and mechanisms of palbociclib and voxtalisib, alone or in combination, were evaluated in molecularly defined primary treatment-naïve, and relapsed/metastatic OS models. In the relapsed/metastatic PDX77-TT2 model, short-term palbociclib exposure activated PI3K/mTOR signaling, whereas the combination of palbociclib and voxtalisib in long-term studies produced marked tumor suppression and extended survival. In the primary treatment-naïve PDX96 model, long-term palbociclib exposure generated a robust CDK4/6 pharmacodynamic response. The addition of voxtalisib reinforced autophagy, sustained CDK pathway inhibition, and improved overall tumor control. In an OS lung-colonization model, CDK4/6 inhibition alone markedly reduced OS lung nodules, with combination therapy providing comparable suppression. Dual CDK4/6–PI3K/mTOR inhibition achieves tumor control across various OS models, supporting the use of genomically guided, pathway-targeted strategies for pediatric and AYA OS.

Active vitamin D [1,25(OH)2D3; 1,25D] synthesis is finely balanced in kidney proximal tubules by the catabolic enzyme CYP24A1 and anabolic CYP27B1. Fibroblast growth factor 23 (FGF23) and 1,25D lower 1,25D by increasing CYP24A1 and suppressing CYP27B1, opposing the actions of parathyroid hormone (PTH). Following FGF23 injections, scRNAseq identified E twenty-six (ETS) member ETV1 as specifically induced in PT S1-S2 cells with Cyp24a1. ETV1 was rapidly recruited to Cyp24a1 enhancers mediating FGF23 and PTH responses, overlapping with VDR, whereas PTH nearly eliminated ETV1 occupancy (4,790 sites to 22). In vitro, ETV1 induced CYP24A1, and ETV1-VDR interactions were greatly enhanced by 1,25D. Deletion of Etv1 from mouse kidney epithelium caused FGF23 resistance with elevated iFGF23, and a PTH mimetic salt-inducible kinase inhibitor enhanced COP1-mediated ETV1 degradation. Together, ETV1 is identified as a mediator of reciprocal FGF23 and PTH control of renal vitamin D metabolism, revealing novel mechanisms governing endocrine mineral homeostasis.

Advancements in chimeric antigen receptor (CAR) T-cell therapy for treating diffuse large B-cell lymphoma (DLBCL) have been limited by an incomplete understanding of CAR T-cell differentiation in patients. Here, we show via single-cell, multi-modal, and longitudinal analyses, that CD8+ CAR T cells from DLBCL patients successfully treated with axicabtagene ciloleucel undergo two distinct waves of clonal expansion in vivo. The first wave is dominated by an exhausted-like effector memory phenotype during peak expansion (day 8-14). The second wave is dominated by a terminal effector phenotype during the post-peak persistence period (day 21-28). Importantly, the two waves have distinct ontogeny from the infusion product and are biologically uncoupled. Precursors of the first wave exhibit more effector-like signatures, whereas precursors of the second wave exhibit more stem-like signatures. We demonstrate that CAR T-cell expansion and persistence are mediated by clonally, phenotypically, and ontogenically distinct CAR T-cell populations that serve complementary clinical purposes.

Immunomodulatory agents are an important recent advance in cancer therapy, but utility is often limited by tumor immune evasion mechanisms. Strategic therapeutic activation of intracellular antiviral immune responses offers an opportunity to reverse immune evasion mechanisms and improve treatment outcomes. Anti-cancer agents such as, DNA methyltransferase inhibitors (DNMTis) induce re-expression of endogenous retroviruses (ERVs), leading to cytosolic double-stranded RNA (dsRNA) accumulation that activates interferon/inflammasome signaling. Moreover, poly (ADP ribose) polymerase inhibitors (PARPi) increase cytosolic dsDNA, activating stimulator of interferon (IFN) genes (STING). We reported that DNMTis in combination with PARPis induce STING-dependent signaling in a process termed pathogen mimicry response (PMR). Although we and others have demonstrated that mitochondria (mt) are an important gateway for antiviral inflammasome signaling, the underlying mechanism in cancer remains to be fully elucidated. In this regard, our studies of the little-known gene, NFX1-type zinc finger–containing 1 (ZNFX1), show that ZNFX1 acts as a master nucleic acid (dsRNA/DNA) sensor for mt gateway function. Bioinformatics analysis in primary ovarian tumors from TCGA and clinical trial RNAseq datasets shows that increased ZNFX1 expression tracks with tumor stage and grade but inversely correlates with a mt dysfunction signature. In a panel of ovarian cancer (OC) cell lines, transfection of dsRNA/DNA mimics or DNMTi azacytidine (AZA) and PARPi (talazoparib [TAL]) treatments induce increased ZNFX1 expression and binding to mt antiviral protein (MAVs) localized on the mt outer membrane. Functional studies of mt dysfunction in OC cells further show that dsRNA/DNA as well as above viral mimicry drugs increase mt reactive oxygen species (ROS) as measured by mitosox flow cytometry. AZA and TAL treatments also increase fragmented mtDNA and oxidative mtDNA base damage, as measured by long range PCR and 8-oxoguanine (8-oxoG) ELISA assays. These drug treatments also increase release of mtDNA into the cytosol, resulting in STING-dependent inflammasome signaling and cytokine release. Notably, ZNFX1 knockout (KO) attenuates these dynamics, further supported by bioinformatics analysis of RNA seq data, thus defining ZNFX1 as a gene as essential for IFN/inflammasome signaling induced by mtDNA damage. Pathway analysis of ZNFX1 KO vs wild-type RNAseq data, combined with in vitro and in vivo validation assays, demonstrate increased proliferation and epithelial to mesenchymal transition, suggesting that not only is ZNFX1 a master regular of the above mt dynamics but also a new tumor suppressor in OC. Abrogating ZNFX1 expression in OC cells triggers increased cell proliferation, invasive capacity and, increased tumor growth in vivo. Taken together, this work then suggests novel approaches to improve immune therapy responses in OC through manipulating ZNFX1. Citation Format: Feyruz V Rassool, Lora Stojanovic, Rachel Abbotts, Kaushlendra Tripathi, Saranya Rajendran, Colin M Coon, Elnaz Abbasi, Sheng Liu, Jun Wan, Michael J Topper, Stephen B Baylin, Kenneth P Nephew. ZNFX1 is a master regulator and tumor suppressor in epigenetically-induced pathogen mimicry, mitochondrial dysfunction and STING-dependent signaling in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr PR001.

Abstract Immunomodulatory agents are an important recent advance in cancer therapy, but utility is often limited by tumor immune evasion mechanisms. Strategic therapeutic activation of intracellular antiviral immune responses offers an opportunity to reverse immune evasion mechanisms and improve treatment outcomes. Anti-cancer agents such as, DNA methyltransferase inhibitors (DNMTis) induce re-expression of endogenous retroviruses (ERVs), leading to cytosolic double-stranded RNA (dsRNA) accumulation that activates interferon/inflammasome signaling. Moreover, poly (ADP ribose) polymerase inhibitors (PARPi) increase cytosolic dsDNA, activating stimulator of interferon (IFN) genes (STING). We reported that DNMTis in combination with PARPis induce STING-dependent signaling in a process termed pathogen mimicry response (PMR). Mitochondria (mt) are an important gateway for antiviral inflammasome signaling, but are not fully understood in cancer. Our studies of the little-known gene, NFX1-type zinc finger-containing 1 (ZNFX1), show that it acts as a master nucleic acid (dsRNA/DNA) sensor for mt gateway function. Bioinformatics analysis in primary ovarian tumors from TCGA and clinical trial RNAseq datasets, shows that increased ZNFX1 expression tracks with tumor stage and grade but inversely correlates with a mt dysfunction signature. In studies of high-grade and endometrial serous carcinoma (OC) cell lines (N=3), transfection of dsRNA/DNA mimics or DNMTi azacytidine (AZA) and PARPi (talazoparib [TAL]) treatments induce increased ZNFX1 expression and binding to mt antiviral protein (MAVs) localized on the mt outer membrane. Functional studies of mt dysfunction in OC cells, show that dsRNA/DNA as well as above viral mimicry drugs increase mt reactive oxygen species (ROS) as measured by mitosox flow cytometry. AZA and TAL treatments also increase fragmented mtDNA and oxidative mtDNA base damage, as measured by long range PCR and 8-oxoguanine (8-oxoG) ELISA assays. These drug treatments also increase release of mtDNA into the cytosol, resulting in STING-dependent inflammasome signaling and cytokine release. Notably, ZNFX1 knockout (KO) attenuates these dynamics, including in bioinformatics of RNA seq data, thus defining this gene as essential for IFN/inflammasome signaling induced by mtDNA damage. Further pathway analysis of ZNFX1 KO vs wild-type (WT) RNAseq data suggest increased proliferation and epithelial to mesenchymal transition (EMT) that was validated by in vitro and in vivo assays. Not only is ZNFX1 a master regular of the above mt dynamics, but it is a tumor suppressor in OC. Abrogating ZNFX1 expression in OC cells triggers increased cell proliferation, invasive capacity and, in-vivo, increased tumor growth. This work then suggests novel approaches to improve immune therapy responses in OC through manipulating ZNFX1. Citation Format: Lora Stojanovic, Rachel Abbotts, Kaushlendra Tripathi, Collin M. Coon, Sheng Liu, Jun Wan, Michael Topper, Stephen Baylin, Kenneth Nephew, Feyruz Rassool. ZNFX1 is a master regulator and tumor suppressor in epigenetically induced pathogen mimicry, mitochondrial dysfunction and STING-dependent signaling in 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 2838.

DNA methyltransferase (DNMT) and PARP inhibitors induce a stimulator of IFN gene-dependent pathogen mimicry response (PMR) in ovarian and other cancers. In this study, we showed that combining DNMT and PARP inhibitors upregulates expression of the nucleic acid sensor NFX1-type zinc finger-containing 1 (ZNFX1) protein. ZNFX1 mediated the induction of PMR in mitochondria, serving as a gateway for stimulator of IFN gene-dependent IFN/inflammasome signaling. Loss of ZNFX1 in ovarian cancer cells promoted proliferation and spheroid formation in vitro and tumor growth in vivo. In patient ovarian cancer databases, expression of ZNFX1 was elevated in advanced stage disease, and ZNFX1 expression alone significantly correlated with an increase in overall survival in a phase III trial for patients with therapy-resistant ovarian cancer receiving bevacizumab in combination with chemotherapy. RNA sequencing revealed an association between inflammasome signaling through ZNFX1 and abnormal vasculogenesis. Together, this study identified that ZNFX1 is a tumor suppressor that controls PMR signaling through mitochondria and may serve as a biomarker to facilitate personalized therapy in patients with ovarian cancer.Significance: DNMT and PARP inhibitors induce a nucleic acid sensor, ZNFX1, that serves as a mitochondrial gateway to STING-dependent inflammasome signaling with tumor suppressor properties in ovarian cancer.

Retinal neovascularization impairs visual function and is a hallmark of several neovascular eye diseases, including retinopathy of prematurity (ROP) and proliferative diabetic retinopathy (PDR). Current treatments include intravitreal injections of anti-vascular endothelial growth factor (VEGF) biologics, but these therapeutics are often accompanied by high treatment burden and resistance to therapy. Prior studies indicate that APE1/Ref-1, a multifunctional protein with both endonuclease (APE1) and redox-mediated transcriptional regulatory activity (Ref-1), activates multiple pro-angiogenic and pro-inflammatory signaling pathways by chemically reducing key cysteine residues in transcription factors, thereby activating them. Here, we investigated the previously unexplored role of Ref-1 in retinal neovascularization. We demonstrate that Ref-1 is highly expressed in endothelial cells in human PDR and in the oxygen-induced retinopathy (OIR) mouse model of retinal neovascularization. Ref-1 is also highly expressed in microglia and astrocytes in OIR. A small molecule Ref-1 redox inhibitor, APX2009, decreased retinal neovascularization in OIR after systemic delivery. In vitro, hypoxic endothelial cells did not exhibit upregulation of Ref-1 but rather increased Ref-1 nuclear localization. APX2009 decreased hypoxic endothelial cell proliferation and HIF-1 alpha transcriptional activation. Thus, Ref-1 redox activity may be a novel therapeutic target for the treatment of retinal neovascularization, making APX2009 a promising systemic therapeutic approach for the treatment of vascular retinopathies such as ROP and PDR.

DNA methyltransferase and poly(ADP-ribose) polymerase inhibitors (DNMTis, PARPis) induce a stimulator of interferon (IFN) genes (STING)-dependent pathogen mimicry response (PMR) in ovarian (OC) and other cancers. We now show that combining DNMTis and PARPis upregulates expression of a little-studied nucleic-acid sensor, NFX1-type zinc finger-containing 1 protein (ZNFX1). We demonstrate that ZNFX1 is a novel master regulator for PMR induction in mitochondria, serving as a gateway for STING-dependent PMR. In patient OC databases, high ZNFX1 expression levels correlate with advanced stage disease. ZNFX1 expression alone significantly correlates with an increase in overall survival in a phase 3 trial for therapy-resistant OC patients receiving bevacizumab in combination with chemotherapy. In correlative RNA-seq data, inflammasome signaling through ZNFX1 correlates with abnormal vasculogenesis. ZNFX1 controls PMR signaling through the mitochondria and may serve as a biomarker to facilitate offering personalized therapy in OC patients, highlighting the strong translational significance of our findings.

Background: Recently, long non-coding RNAs (lncRNAs) have emerged as novel human-specific (i.e. non-conserved) regulators of cardiovascular development and disease, which possess diverse functions through interacting with other molecules, including DNA, RNA, protein, and lipid. We identified a human lncRNA, LIPTER, which mediates lipid droplet (LD) transport to regulate lipid metabilism of human cardiomyocytes (CMs). Mechanistically, LIPTER binds phospholipids PA and PI4P on the LD membranes and the MYH10 protein, connecting LDs to the cytoskeleton and facilitating LD transport to mitochondria. LIPTER deficiencies led to prominent LD accumulation, mitochondrial dysfunction, and death of human iPS cell-derived CMs. Since downregulation of LIPTER and enahnced LD accumulation are associated with cardiac dysfunction and heart failure in patients with metabolic disorders, such as obesity and diabetes mellitus, we thereby seek to explore the preclinical potential of LIPTER for the therapy of human metabolic disorder associated cardiac dysfunction and heart failure. Hypothesis: We hypothesize that transgenic overexpression of the human lncRNA LIPTER in mouse heart could attenuate metabolic syndrome-associated myocardium lipid accumulation and cardiac dysfunction, as well as prevent isoproterenol-induced heart failure through increasing the fatty acid oxidation (FAO) of mouse heart. Goals: To evaluate the preclinical potential of human lncRNA LIPTER for the therapy of cardiac dysfunction and heart failure by using mouse cardiac dysfunction and heart failure models. Methods: We established a LIPTER transgenic overexpression mouse line (LIPTER Tg ). Both WT and LIPTER Tg mice were fed with high fat diet for 10 months to induce cardiac lipid accumulation and dysfunction. Additionally, heart failure was induced by the chronic isoproterenol administration. After treatment, mice were subjected to histological and molecular analyses. Results: We found LIPTER Tg significantly enhanced FAO of mouse heart, reduced cardiac lipid accumulation and fibrosis, and alleviated cardiac dysfunction of high-fat-diet fed mice, as well as preserved cardiac function of mice post isoproterenol administration. Conclusions: We unveil a crucial role of human lncRNA LIPTER in regulating lipid metabolism of human CMs and testify its clinical potential for treating cardiac dysfunction and heart failure.

Intracellular α-ketoglutarate is an indispensable substrate for the Jumonji family of histone demethylases (JHDMs) mediating most of the histone demethylation reactions. Since α-ketoglutarate is an intermediate of the tricarboxylic acid cycle and a product of transamination, its availability is governed by the metabolism of several amino acids. Here, we show that asparagine starvation suppresses global histone demethylation. This process is neither due to the change of expression of histone-modifying enzymes nor due to the change of intracellular levels of α-ketoglutarate. Rather, asparagine starvation reduces the intracellular pool of labile iron, a key co-factor for the JHDMs to function. Mechanistically, asparagine starvation suppresses the expression of the transferrin receptor to limit iron uptake. Furthermore, iron supplementation to the culture medium restores histone demethylation and alters gene expression to accelerate cell death upon asparagine depletion. These results suggest that suppressing iron-dependent histone demethylation is part of the cellular adaptive response to asparagine starvation.

Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid tissue collection/processing protocol to perform scRNA-seq of breast biopsies of healthy women and identify 23 breast epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters are applied to analyze transcriptomes of ~3,000 breast cancers. Gene signatures derived from mature luminal cell clusters are enriched in ~68% of breast cancers, whereas a signature from a luminal progenitor cluster is enriched in ~20% of breast cancers. Overexpression of luminal progenitor cluster-derived signatures in HER2+, but not in other subtypes, is associated with unfavorable outcome. We identify TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts, and their expression analyses in >550 breast cancers enable prognostically relevant subclassification of ER+ breast cancers.

Additional file 5: Table S3. ARID1A ChIP-seq paired genes.