Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.

PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition

Multiple cancers exhibit aberrant protein arginine methylation by both type I arginine methyltransferases, predominately protein arginine methyltransferase 1 (PRMT1) and to a lesser extent PRMT4, and by type II PRMTs, predominately PRMT5. Here, we perform targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across 12 cancer cell lines. We find that inhibition of type I and II PRMTs suppresses phosphorylated and total ATR in cancer cells. Loss of ATR from PRMT inhibition results in defective DNA replication stress response activation, including from PARP inhibitors. Inhibition of type I and II PRMTs is synergistic with PARP inhibition regardless of homologous recombination function, but type I PRMT inhibition is more toxic to non-malignant cells. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves survival in both BRCA-mutant and wild-type patient-derived xenografts without toxicity. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to sensitize tumors to PARP inhibition.

Mitochondria-targeting nano therapy altering IDH2-mediated EZH2/EZH1 interaction as precise epigenetic regulation in glioblastoma

Glioblastoma (GBM) is a complex brain cancer with frequent relapses and high mortality and still awaits effective treatment. Mitochondria dysfunction is a pathogenic condition in GBM and could be a prime therapeutic target for ceasing GBM progression. Strategies to overcome brain solid tumor barriers and selectively target mitochondria within specific cell types may improve GBM treatment. Here, we present hypericin-conjugated gold nanoparticles (PEG-AuNPs@Hyp) where hypericin is a mitochondrion-targeting agent exhibiting multimodal therapy by critically impacting the IDH2 gene (Isocitrate dehydrogenase) and its interaction with polycomb methyltransferase EZH1/2 for GBM therapy. It significantly localizes in mitochondria by enhanced cellular uptake in the human GBM cell lines/three-dimensional (3D) culture model under red-light exposure. It triggers oxidative stress and changes the mitochondrial potential, with increased Bax/Bcl2 ratio enhancing GBM cell death. The suppressed expression of mutated IDH2 and polycomb group of proteins upon PEG-AuNPs@Hyp/light exposure regulates mitochondria-targeting-mediated GBM metabolism with epigenetic repression of complex machinery function. Polyubiquitination and proteasomal degradation of EZH1 indicate the implication of these polycomb proteins in GBM progression. Chromatin immunoprecipitation reveals the IDH2 and EZH1/EZH2 direct interaction, confirming the role played by IDH2 in modulating the expression of EZH1 and EZH2. In vivo studies further displayed better tumor ablation in a GBM tumor-bearing nude mouse model. The present multimodal nanoformulation compromised the functional dependency of polycomb on mitochondrial IDH2 and established the mechanism of GBM inhibition.

Coupled catalytic dephosphorylation and complex phosphate ion-exchange in networked hierarchical lanthanum carbonate grafted asymmetric bio-composite membrane

The remediation of non-reactive phosphate pollutants in the aquatic system is essential for protecting the ecological niche. In this work, a highly robust protein nanoparticles networked rare-earth metal carbonate-grafted bio-composite membrane (abbreviated as REMC) was fabricated via chemical crosslinking of three-dimensional (3D) hierarchical lanthanum carbonate (mREM) and casein nanoparticles (CsNPs) for selective rejection of non-reactive phosphates. The main components of the REMC membrane are mREM and CsNPs, which were prepared via SDS/CTAB templated homogeneous precipitation and the coacervation/desolvation hybrid method, respectively. The active lanthanum ion (La³⁺) on the 3D spherulitic surface of mREM exhibited excellent phosphate adsorption capacity (maximum adsorption capacity was 358 mg.g^-1) across a wide pH range and in a multi-ionic environment. A series of batch testing and characterizations revealed that the active La³⁺ and dominating phosphate centers in the REMC membrane framework enable non-enzymatic phosphatase-like activity, cleaving the phosphate ester bond of organic phosphates and releasing free phosphate anions. These released phosphate ions are retained in the REMC membrane via an ion exchange mechanism, where they contribute to improved phosphate removal capacities. Furthermore, CsNPs have a dual function in the membrane, acting as a matrix in the REMC membrane framework and contributing to phosphate ion sequestrations in a synergistic manner. The catalysis of para-nitrophenyl phosphates (pNPP) to paranitrophenol (pNP) in a sequential dephosphorylation by REMC offers an estimate of reaction kinetics and elucidates the underlying mechanism of improved phosphate selectivity in a multi-ionic environment. Furthermore, phosphate specificity, homogeneous binding capacity, reusability, and visual observation of REMC membrane saturation binding direct it's useful economic, industrial applications in aqueous phosphate contaminant removal, which could be beneficial for the active recovery of the aquatic ecosystem.

A non-viral nano-delivery system targeting epigenetic methyltransferase EZH2 for precise acute myeloid leukemia therapy

Acute myeloid leukemia (AML), which is common in the elderly population, accounts for poor long-term survival with a high possibility of relapse. The associated lack of currently developed therapeutics is directing the search for new therapeutic targets relating to AML. EZH2 (Enhancer of Zeste Homolog 2) is a histone methyltransferase member of the polycomb-group (PcG) family, and its significant overexpression in AML means it has emerged as a potential epigenetic target. Here, we propose the human serum albumin (HSA) nanoparticle based delivery of small interfering RNA (siRNA), which can target EZH2-expressing genes in AML. EZH2 specific siRNA loaded in a polyethyleneimine (PEI) conjugated HSA nanocarrier can overcome the systemic instability of siRNA and precisely target the AML cell population for increased EZH2 gene silencing. A stable nanosized complex (HSANPs-PEI@EZH2siRNA), achieved via the electrostatic interaction of PEI and EZH2 siRNA, shows increased systemic stability and hemocompatibility, and enhanced EZH2 gene silencing activity in vitro, compared to conventional transfection reagents. HSANPs-PEI@EZH2siRNA-treated AML cells showed downregulated EZH2, which is associated with a reduced level of Bmi-1 protein, and H3K27me3 and H2AK119ub modification. The ubiquitin-mediated proteasomal degradation pathway plays a critical role in the downregulation of associated proteins following HSANPs-PEI@EZH2siRNA exposure to AML cells. c-Myb is the AML-responsive transcription factor that directly binds on the EZH2 promoter and was downregulated in HSANPs-PEI@EZH2siRNA-treated AML cells. The systemic exposure to HSANPs-PEI@EZH2siRNA of AML engrafted immunodeficient nude mice displayed efficient EZH2 gene silencing and a reduced AML cell population in peripheral blood and bone marrow. The present study demonstrates a non-viral siRNA delivery system for epigenetic targeting based superior anti-leukemic therapy.

Recuperative effect of metformin loaded polydopamine nanoformulation promoting EZH2 mediated proteasomal degradation of phospho-α-synuclein in Parkinson's disease model

Posttranslational modification and agglomeration of α-synuclein (α-Syn), mitochondrial dysfunction, oxidative stress and loss of dopaminergic neurons are hallmark of Parkinson's disease (PD). This paper evaluates neuroprotection efficacy of nature inspired biocompatible polydopamine nanocarrier for metformin delivery (Met encapsulated PDANPs) by crossing blood brain barrier in in vitro, 3D and in vivo experimental PD models. The neuroprotective potential was arbitrated by downregulation of phospho-serine 129 (pSer129) α-Syn, with reduction in oxidative stress, prevention of apoptosis and anti-inflammatory activities. The neuroprotective mechanism proved novel interaction of epigenetic regulator EZH2 mediated ubiquitination and proteasomal degradation of aggregated pSer129 α-Syn. In summary, this study divulges the neuroprotective role of Met loaded PDANPs by reversing the neurochemical deficits by confirming an epigenetic mediated nanotherapeutic approach for the PD prevention.

A NIR-responsive indocyanine green-genistein nanoformulation to control the polycomb epigenetic machinery for the efficient combinatorial photo/chemotherapy of glioblastoma

Combinatorial photodynamics and chemotherapy have drawn enormous attention as therapeutic modalities via precise stimuli-responsive drug delivery for glioblastoma, which can overcome the limitations associated with conventional therapies. Herein, we have prepared an indocyanine green tagged, genistein encapsulated casein nanoformulation (ICG-Gen@CasNPs) that exhibits the near infra-red region responsive controlled release of genistein and enhanced cellular uptake in the human glioblastoma monolayer and a three-dimensional raft culture model via the enhanced retention effect. ICG-Gen@CasNPs, with the integrated photosensitizer indocyanine green within the nanoformulation, triggered oxidative stress, activating the apoptosis cascade, promoting cell cycle arrest and damaging the mitochondrial membrane potential, collectively directing glioblastoma cell death. The suppression of the polycomb group of proteins in the glioblastoma upon ICG-Gen@CasNPs/NIR exposure revealed the involvement of the epigenetic repression complex machinery in the regulation. Furthermore, ICG-Gen@CasNPs/PDT/PTT directed ubiquitination and proteasomal degradation of EZH2 and BMI1 indicates the implication of the polycomb in conferring glioblastoma survival. The increased activation of the apoptotic pathways and the generation of cellular reactive oxygen species upon inhibiting the expression of EZH2 and BMI1 strengthen our observations. It is worth noting that ICG-Gen@CasNPs robustly accumulated in the brain after crossing the blood-brain barrier, which represents the eminent biocompatibility and means that the system is devoid of any nonspecific toxicity in vivo. Moreover, a superior anti-tumor effect was demonstrated on a three-dimensional glioma spheroid model. Thus, this combinatorial chemo/photodynamic therapy revealed that ICG-Gen@CasNPs mediated epigenetic regulation, which is a crucial molecular mechanism of GBM suppression.

Nanomelatonin triggers superior anticancer functionality in a human malignant glioblastoma cell line

Melatonin (MEL) has promising medicinal value as an anticancer agent in a variety of malignancies, but there are difficulties in achieving a therapeutic dose due to its short half-life, low bioavailability, poor solubility and extensive first-pass metabolism. In this study chitosan/tripolyphosphate (TPP) nanoparticles were prepared by an ionic gelation method to overcome the therapeutic challenges of melatonin and to improve its anticancer efficacy. Characterization of the melatonin-loaded chitosan (MEL-CS) nanoformulation was performed using transmission and scanning electron microscopies, dynamic light scattering, Fourier transform infrared spectroscopy, Raman spectroscopy and x-ray diffraction. In vitro release, cellular uptake and efficacy studies were tested for their enhanced anticancer potential in human U87MG glioblastoma cells. Confocal studies revealed higher cellular uptake of MEL-CS nanoparticles and enhanced anticancer efficacy in human malignant glioblastoma cancer cells than in healthy non-malignant human HEK293T cells in mono- and co-culture models. Our study has shown for the first time that MEL-CS nanocomposites are therapeutically more effective as compared to free MEL at inducing functional anticancer efficacy in the human brain tumour U87MG cell line.