Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas.

How cancer-associated chromatin abnormalities shape tumor-immune interaction remains incompletely understood. Recent studies have linked DNA hypomethylation and de-repression of retrotransposons to anti-tumor immunity through the induction of interferon response. Here, we report that inactivation of the histone H3K36 methyltransferase NSD1, which is frequently found in squamous cell carcinomas (SCCs) and induces DNA hypomethylation, unexpectedly results in diminished tumor immune infiltration. In syngeneic and genetically engineered mouse models of head and neck SCCs, NSD1-deficient tumors exhibit immune exclusion and reduced interferon response despite high retrotransposon expression. Mechanistically, NSD1 loss results in silencing of innate immunity genes, including the type III interferon receptor IFNLR1, through depletion of H3K36 di-methylation (H3K36me2) and gain of H3K27 tri-methylation (H3K27me3). Inhibition of EZH2 restores immune infiltration and impairs the growth of Nsd1-mutant tumors. Thus, our work uncovers a druggable chromatin cross talk that regulates the viral mimicry response and enables immune evasion of DNA hypomethylated tumors.

Serine starvation silences estrogen receptor signaling through histone hypoacetylation.

Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.

A Process Algebraic Approach to Predict and Control Uncertainty in Smart IoT Systems for Smart Cities Based on Permissible Probabilistic Equivalence.

Process algebra is one of the most suitable formal methods to model smart IoT systems for smart cities. Each IoT in the systems can be modeled as a process in algebra. In addition, the nondeterministic behavior of the systems can be predicted by defining probabilities on the choice operations in some algebra, such as PALOMA and PACSR. However, there are no practical mechanisms in algebra either to measure or control uncertainty caused by the nondeterministic behavior in terms of satisfiability of the system requirements. In our previous research, to overcome the limitation, a new process algebra called dTP-Calculus was presented to verify probabilistically the safety and security requirements of smart IoT systems: the nondeterministic behavior of the systems was defined and controlled by the static and dynamic probabilities. However, the approach required a strong assumption to handle the unsatisfied probabilistic requirements: enforcing an optimally arbitrary level of high-performance probability from the continuous range of the probability domain. In the paper, the assumption from the previous research is eliminated by defining the levels of probability from the discrete domain based on the notion of Permissible Process and System Equivalences so that satisfiability is incrementally enforced by both Permissible Process Enhancement in the process level and Permissible System Enhancement in the system level. In this way, the unsatisfied probabilistic requirements can be incrementally enforced with better-performing probabilities in the discrete steps until the final decision for satisfiability can be made. The SAVE tool suite has been developed on the ADOxx meta-modeling platform to demonstrate the effectiveness of the approach with a smart EMS (emergency medical service) system example, which is one of the most practical examples for smart cities. SAVE showed that the approach is very applicable to specify, analyze, verify, and especially, predict and control uncertainty or risks caused by the nondeterministic behavior of smart IoT systems. The approach based on dTP-Calculus and SAVE may be considered one of the most suitable formal methods and tools to model smart IoT systems for smart cities.

Process Algebraic Approach for Probabilistic Verification of Safety and Security Requirements of Smart IoT (Internet of Things) Systems in Digital Twin.

Process algebra can be considered one of the most practical formal methods for modeling Smart IoT Systems in Digital Twin, since each IoT device in the systems can be considered as a process. Further, some of the algebras are applied to predict the behavior of the systems. For example, PALOMA (Process Algebra for Located Markovian Agents) and PACSR (Probabilistic Algebra of Communicating Shared Resources) process algebras are designed to predict the behavior of IoT Systems with probability on choice operations. However, there is a lack of analytical methods in the algebras to predict the nondeterministic behavior of the systems. Further, there is no control mechanism to handle undesirable nondeterministic behavior of the systems. In order to overcome these limitations, this paper proposes a new process algebra, called dTP-Calculus, which can be used (1) to specify the nondeterministic behavior of the systems with static probability, (2) verify the safety and security requirements of the nondeterministic behavior with probability requirements, and (3) control undesirable nondeterministic behavior with dynamic probability. To demonstrate the feasibility and practicality of the approach, the SAVE (Specification, Analysis, Verification, Evaluation) tool has been developed on the ADOxx Meta-Modeling Platform and applied to a SEMS (Smart Emergency Medical Service) example. In addition, a miniature digital twin system for the SEMS example was constructed and applied to the SAVE tool as a proof of concept for Digital Twin. It shows that the approach with dTP-Calculus on the tool can be very efficient and effective for Smart IoT Systems in Digital Twin.

Modeling Method to Abstract Collective Behavior of Smart IoT Systems in CPS.

This paper presents a new modeling method to abstract the collective behavior of Smart IoT Systems in CPS, based on process algebra and a lattice structure. In general, process algebra is known to be one of the best formal methods to model IoTs, since each IoT can be represented as a process; a lattice can also be considered one of the best mathematical structures to abstract the collective behavior of IoTs since it has the hierarchical structure to represent multi-dimensional aspects of the interactions of IoTs. The dual approach using two mathematical structures is very challenging since the process algebra have to provide an expressive power to describe the smart behavior of IoTs, and the lattice has to provide an operational capability to handle the state-explosion problem generated from the interactions of IoTs. For these purposes, this paper presents a process algebra, called dTP-Calculus, which represents the smart behavior of IoTs with non-deterministic choice operation based on probability, and a lattice, called n:2-Lattice, which has special join and meet operations to handle the state explosion problem. The main advantage of the method is that the lattice can represent all the possible behavior of the IoT systems, and the patterns of behavior can be elaborated by finding the traces of the behavior in the lattice. Another main advantage is that the new notion of equivalences can be defined within n:2-Lattice, which can be used to solve the classical problem of exponential and non-deterministic complexity in the equivalences of Norm Chomsky and Robin Milner by abstracting them into polynomial and static complexity in the lattice. In order to prove the concept of the method, two tools are developed based on the ADOxx Meta-Modeling Platform: SAVE for the dTP-Calculus and PRISM for the n:2-Lattice. The method and tools can be considered one of the most challenging research topics in the area of modeling to represent the collective behavior of Smart IoT Systems.

The lysine-specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer.

Genome-wide studies in tumor cells have indicated that chromatin-modifying proteins are commonly mutated in human cancers. The lysine-specific methyltransferase 2C (KMT2C/MLL3) is a putative tumor suppressor in several epithelia and in myeloid cells. Here, we show that downregulation of KMT2C in bladder cancer cells leads to extensive changes in the epigenetic status and the expression of DNA damage response and DNA repair genes. More specifically, cells with low KMT2C activity are deficient in homologous recombination-mediated double-strand break DNA repair. Consequently, these cells suffer from substantially higher endogenous DNA damage and genomic instability. Finally, these cells seem to rely heavily on PARP1/2 for DNA repair, and treatment with the PARP1/2 inhibitor olaparib leads to synthetic lethality, suggesting that cancer cells with low KMT2C expression are attractive targets for therapies with PARP1/2 inhibitors.

Targeting DNA repair in cancer: current state and novel approaches.

DNA damage response, DNA repair and genomic instability have been under study for their role in tumor initiation and progression for many years now. More recently, next-generation sequencing on cancer tissue from various patient cohorts have revealed mutations and epigenetic silencing of various genes encoding proteins with roles in these processes. These findings, together with the unequivocal role of DNA repair in therapeutic response, have fueled efforts toward the clinical exploitation of research findings. The successful example of PARP1/2 inhibitors has also supported these efforts and led to numerous preclinical and clinical trials with a large number of small molecules targeting various components involved in DNA repair singularly or in combination with other therapies. In this review, we focus on recent considerations related to DNA damage response and new DNA repair inhibition agents. We then discuss how immunotherapy can collaborate with these new drugs and how epigenetic drugs can rewire the activity of repair pathways and sensitize cancer cells to DNA repair inhibition therapies.

Resolving DNA Damage: Epigenetic Regulation of DNA Repair.

Epigenetic research has rapidly evolved into a dynamic field of genome biology. Chromatin regulation has been proved to be an essential aspect for all genomic processes, including DNA repair. Chromatin structure is modified by enzymes and factors that deposit, erase, and interact with epigenetic marks such as DNA and histone modifications, as well as by complexes that remodel nucleosomes. In this review we discuss recent advances on how the chromatin state is modulated during this multi-step process of damage recognition, signaling, and repair. Moreover, we examine how chromatin is regulated when different pathways of DNA repair are utilized. Furthermore, we review additional modes of regulation of DNA repair, such as through the role of global and localized chromatin states in maintaining expression of DNA repair genes, as well as through the activity of epigenetic enzymes on non-nucleosome substrates. Finally, we discuss current and future applications of the mechanistic interplays between chromatin regulation and DNA repair in the context cancer treatment.

A comparative study between clinical grading of anterior chamber flare and flare reading using the Kowa laser flare meter.

To assess the accuracy of standard clinical grading of aqueous flare in uveitis according to the Standardization of Uveitis Nomenclature consensus, and compare the results with the readings of the laser flare meter, Kowa 500. Two examiners clinically graded the flare in 110 eyes. The flare was then measured using the Kowa laser flare meter. Twenty-nine eyes were graded as anterior chamber flare +2; for 18 of these, the clinicians were in agreement, the rest differed by the order of one grade. The range of the laser flare meter for these eyes was 5.2-899.1 photons/ms. The median value was 41.4. Seventy-four eyes were graded with flare +1. Agreement was established in 51 of these eyes. Disagreement for the rest was again by the order of 1, and the flare meter range was 1.1-169.9 photons/ms, median value 18.4. For the clinical measure of flare 0, the clinicians disagreed on three out of five eyes. The flare meter readings ranged from 2.5 to 14.1 photons/ms, median value 9.9. Only two eyes were graded with flare +3 and there was one step disagreement on both of them. We found little evidence of association between the flare readings and intraocular pressure or age. Our findings suggest that clinical evaluation of aqueous flare is subjective. Compared with the Kowa laser flare meter's numeric readings, the discrepancies observed indicate that clinical grading is an approximate science. The laser flare meter provides an accurate, reproducible, non-invasive assessment of aqueous flare that can prove valuable in research and clinical decisions.

Adult-Onset Foveomacular Vitelliform Dystrophy With Unilateral Presentation: A Case Series.

Adult-onset foveomacular vitelliform dystrophy (AOFVD) is a rare condition affecting the macula that presents diagnostic and management challenges due to its varied manifestations and clinical overlap with other retinal disorders. As vitelliform lesions can occur in various conditions, such as Best disease and age-related macular degeneration, clinical presentation, multimodal imaging findings, and genetic testing can aid in accurate diagnosis. Although AOFVD typically affects both eyes, unilateral involvement can occur. This study presents four cases of unilateral AOFVD in female patients aged 43 to 66 years. Each patient was monitored for two years with fundoscopy and multimodal imaging, including color fundus photography, optical coherence tomography (OCT), OCT-angiography, fluorescein angiography, and fundus autofluorescence (FAF). All patients presented with a characterized solitary, subfoveal, yellow lesion on fundoscopy. FAF revealed intense hyperautofluorescence corresponding with the lesions. OCT revealed the accumulation of homogenous hyperreflective material between the retinal pigment epithelium and photoreceptors. No abnormal findings were observed in the fellow eyes. Subfoveal choroidal thickness was measured at 355 µm, 545 µm, 486 µm, and 669 µm in the affected eyes. While AOFVD typically manifests bilaterally, these cases demonstrate a unique unilateral presentation, highlighting the importance of comprehensive examination and differential diagnosis. Distinguishing cases with unilateral presentation from other conditions can be more challenging, so awareness of this unusual phenotype and its clinical characteristics must be raised. Choroidal thickness measurements provide additional insights into AOFVD pathophysiology, suggesting a potential association with the pachychoroid spectrum.

Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors.

The interplay between metabolism and chromatin signaling is implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway, which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen, we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDACs). This association is observed across cultured cells, mouse models, and patient-derived xenografts. Integrative epigenomic, transcriptomic, and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors.

Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy.

While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of the squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Up-regulation of the major p63 isoform ΔNp63α, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together, these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression.

A Novel Modified Surgical Approach for FIL SSF Lens.

This study aimed to describe a novel modified surgical technique for FIL SSF lens (Rome, Italy: Soleko) implantation. A retrospective study of FIL SSF lens implantation on six eyes of six patients with subluxated or dislocated intraocular lens (IOL). Standard pars plana vitrectomy (PPV) was performed in all patients. The subluxated or dislocated IOL was removed from a 2.4 corneal incision. From the same incision, the folded FIL SSF lens was inserted. Then lens plugs were extremized through a 23G scleral incision inside two 4 mm pockets that were created at the beginning of the operation. In two cases one pocket had to be converted into a triagonal-shaped scleral flap. All scleral pockets were sutured with 7.0 Vicryl suture and the conjunctiva with 7.0 Vicryl. In the follow-up period of six months, the lens is centered and not tilted. The refractive outcome is within the expectations. Visual acuity is improved in all patients. No haptic exposure and no other complications were noted in all cases. FIL SSF lens is a good option for treating aphakia. This modified implantation technique is safe, fast, and easy. It is also versatile, combining the advantages of both previously described techniques, as it gives the option of flap conversion if needed. Larger studies and prospective comparative studies can highlight the best and more appropriate technique.

Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors.

Interplay between metabolism and chromatin signaling have been implicated in cancer initiation and progression. However, whether and how metabolic reprogramming in tumors generates specific epigenetic vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor mutations that cause aberrant activation of the NRF2 antioxidant pathway and drive aggressive and chemo-resistant disease. We performed a chromatin-focused CRISPR screen and report that NRF2 activation sensitized LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDAC). This association was consistently observed across cultured cells, syngeneic mouse models and patient-derived xenografts. HDAC inhibition causes widespread increases in histone H4 acetylation (H4ac) at intergenic regions, but also drives re-targeting of H4ac reader protein BRD4 away from promoters with high H4ac levels and transcriptional downregulation of corresponding genes. Integrative epigenomic, transcriptomic and metabolomic analysis demonstrates that these chromatin changes are associated with reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest that metabolic alterations such as NRF2 activation could serve as biomarkers for effective repurposing of HDAC inhibitors to treat solid tumors.

Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy.

While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Upregulation of the major p63 isoform ΔNp63α, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression.

Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma.

Interplay between chromatin-associated complexes and modifications critically contribute to the partitioning of epigenome into stable and functionally distinct domains. Yet there is a lack of systematic identification of chromatin crosstalk mechanisms, limiting our understanding of the dynamic transition between chromatin states during development and disease. Here we perform co-dependency mapping of genes using CRISPR-Cas9-mediated fitness screens in pan-cancer cell lines to quantify gene-gene functional relationships. We identify 145 co-dependency modules and further define the molecular context underlying the essentiality of these modules by incorporating mutational, epigenome, gene expression and drug sensitivity profiles of cell lines. These analyses assign new protein complex composition and function, and predict new functional interactions, including an unexpected co-dependency between two transcriptionally counteracting chromatin complexes - polycomb repressive complex 2 (PRC2) and MLL-MEN1 complex. We show that PRC2-mediated H3K27 tri-methylation regulates the genome-wide distribution of MLL1 and MEN1. In lymphoma cells with EZH2 gain-of-function mutations, the re-localization of MLL-MEN1 complex drives oncogenic gene expression and results in a hypersensitivity to pharmacologic inhibition of MEN1. Together, our findings provide a resource for discovery of trans-regulatory interactions as mechanisms of chromatin regulation and potential targets of synthetic lethality.

Cancer Evolution in Precision Medicine Era.

Recent advances in our understanding of cancer, driven mainly by the emergence of new technologies have highlighted that heterogeneity shapes not only the genetic profile of tumors but also their epigenetic and gene expression profile [...].

HDAC Inhibitors: Dissecting Mechanisms of Action to Counter Tumor Heterogeneity.

Intra-tumoral heterogeneity presents a major obstacle to cancer therapeutics, including conventional chemotherapy, immunotherapy, and targeted therapies. Stochastic events such as mutations, chromosomal aberrations, and epigenetic dysregulation, as well as micro-environmental selection pressures related to nutrient and oxygen availability, immune infiltration, and immunoediting processes can drive immense phenotypic variability in tumor cells. Here, we discuss how histone deacetylase inhibitors, a prominent class of epigenetic drugs, can be leveraged to counter tumor heterogeneity. We examine their effects on cellular processes that contribute to heterogeneity and provide insights on their mechanisms of action that could assist in the development of future therapeutic approaches.

Activation of the NRF2 antioxidant program generates an imbalance in central carbon metabolism in cancer.

During tumorigenesis, the high metabolic demand of cancer cells results in increased production of reactive oxygen species. To maintain oxidative homeostasis, tumor cells increase their antioxidant production through hyperactivation of the NRF2 pathway, which promotes tumor cell growth. Despite the extensive characterization of NRF2-driven metabolic rewiring, little is known about the metabolic liabilities generated by this reprogramming. Here, we show that activation of NRF2, in either mouse or human cancer cells, leads to increased dependency on exogenous glutamine through increased consumption of glutamate for glutathione synthesis and glutamate secretion by xc- antiporter system. Together, this limits glutamate availability for the tricarboxylic acid cycle and other biosynthetic reactions creating a metabolic bottleneck. Cancers with genetic or pharmacological activation of the NRF2 antioxidant pathway have a metabolic imbalance between supporting increased antioxidant capacity over central carbon metabolism, which can be therapeutically exploited.