Cytosolic DNA sensing by cGAS/STING promotes TRPV2-mediated Ca2+ release to protect stressed replication forks.

The protection of DNA replication forks under stress is essential for genome maintenance and cancer suppression. One mechanism of fork protection involves an elevation in intracellular Ca2+ ([Ca2+]i), which in turn activates CaMKK2 and AMPK to prevent uncontrolled fork processing by Exo1. How replication stress triggers [Ca2+]i elevation is unclear. Here, we report a role of cytosolic self-DNA (cytosDNA) and the ion channel TRPV2 in [Ca2+]i induction and fork protection. Replication stress leads to the generation of ssDNA and dsDNA species that, upon translocation into cytoplasm, trigger the activation of the sensor protein cGAS and the production of cGAMP. The subsequent binding of cGAMP to STING causes its dissociation from TRPV2, leading to TRPV2 derepression and Ca2+ release from the ER, which in turn activates the downstream signaling cascade to prevent fork degradation. This Ca2+-dependent genome protection pathway is also activated in response to replication stress caused by oncogene activation.

Chromatin as a metabolic organelle: Integrating the cellular flow of carbon with gene expression.

Hsieh et al. (2022) reveal that carbon starvation elicits an unexpected compensatory reallocation of histone acetylation to establish an adaptive gene expression program, demonstrating how chromatin may integrate cellular carbon flow via histone acetylation with gene regulation.

Iron regulatory protein 2 contributes to antimicrobial immunity by preserving lysosomal function in macrophages.

Colorectal cancer and Crohn's disease patients develop pyogenic liver abscesses due to failures of immune cells to fight off bacterial infections. Here, we show that mice lacking iron regulatory protein 2 (Irp2), globally (Irp2-/-) or myeloid cell lineage (Lysozyme 2 promoter-driven, LysM)-specifically (Irp2ΔLysM), are highly susceptible to liver abscesses when the intestinal tissue was injured with dextran sodium sulfate treatment. Further studies demonstrated that Irp2 is required for lysosomal acidification and biogenesis, both of which are crucial for bacterial clearance. In Irp2-deficient liver tissue or macrophages, the nuclear location of transcription factor EB (Tfeb) was remarkably reduced, leading to the downregulation of Tfeb target genes that encode critical components for lysosomal biogenesis. Tfeb mislocalization was reversed by hypoxia-inducible factor 2 inhibitor PT2385 and, independently, through inhibition of lactic acid production. These experimental findings were confirmed clinically in patients with Crohn's disease and through bioinformatic searches in databases from Crohn's disease or ulcerative colitis biopsies showing loss of IRP2 and transcription factor EB (TFEB)-dependent lysosomal gene expression. Overall, our study highlights a mechanism whereby Irp2 supports nuclear translocation of Tfeb and lysosomal function, preserving macrophage antimicrobial activity and protecting the liver against invading bacteria during intestinal inflammation.

The role of histone H3 leucine 126 in fine-tuning the copper reductase activity of nucleosomes.

The copper reductase activity of histone H3 suggests undiscovered characteristics within the protein. Here, we investigated the function of leucine 126 (H3L126), which occupies an axial position relative to the copper binding. Typically found as methionine or leucine in copper-binding proteins, the axial ligand influences the reduction potential of the bound ion, modulating its tendency to accept or yield electrons. We found that mutation of H3L126 to methionine (H3L126M) enhanced the enzymatic activity of native yeast nucleosomes in vitro and increased intracellular levels of Cu1+, leading to improved copper-dependent activities including mitochondrial respiration and growth in oxidative media with low copper. Conversely, H3L126 to histidine (H3L126H) mutation decreased nucleosome's enzymatic activity and adversely affected copper-dependent activities in vivo. Our findings demonstrate that H3L126 fine-tunes the copper reductase activity of nucleosomes and highlights the utility of nucleosome enzymatic activity as a novel paradigm to uncover previously unnoticed features of histones.

NCOA4 requires a [3Fe-4S] to sense and maintain the iron homeostasis.

NCOA4 is a selective cargo receptor for ferritinophagy, the autophagic turnover of ferritin (FTH), a process critical for regulating intracellular iron bioavailability. However, how ferritinophagy flux is controlled through NCOA4 in iron-dependent processes needs to be better understood. Here, we show that the C-terminal FTH-binding domain of NCOA4 harbors a [3Fe-4S]-binding site with a stoichiometry of approximately one labile [3Fe-4S] cluster per NCOA4 monomer. By analyzing the interaction between NCOA4 and HERC2 ubiquitin ligase or NCOA4 and FTH, we demonstrate that NCOA4 regulates ferritinophagy by sensing the intracellular iron-sulfur cluster levels. Under iron-repletion conditions, HERC2 recognizes and recruits holo-NCOA4 as a substrate for polyubiquitination and degradation, favoring ferritin iron storage. Under iron-depletion conditions, NCOA4 exists in the form of apo-protein and binds ferritin to promote the occurrence of ferritinophagy and release iron. Thus, we identify an iron-sulfur cluster [3Fe-4S] as a critical cofactor in determining the fate of NCOA4 in favoring iron storage in ferritin or iron release via ferritinophagy and provide a dual mechanism for selective interaction between HERC2 and [3Fe-4S]-NCOA4 for proteasomal degradation or between ferritin and apo-NCOA4 for ferritinophagy in the control of iron homeostasis.

Interaction of human dendritic cell receptor DEC205/CD205 with keratins.

DEC205 (CD205) is one of the major endocytic receptors on dendritic cells and has been widely used as a receptor target in immune therapies. It has been shown that DEC205 can recognize dead cells through keratins in a pH-dependent manner. However, the mechanism underlying the interaction between DEC205 and keratins remains unclear. Here we determine the crystal structures of an N-terminal fragment of human DEC205 (CysR∼CTLD3). The structural data show that DEC205 shares similar overall features with the other mannose receptor family members such as the mannose receptor and Endo180, but the individual domains of DEC205 in the crystal structure exhibit distinct structural features that may lead to specific ligand binding properties of the molecule. Among them, CTLD3 of DEC205 adopts a unique fold of CTLD, which may correlate with the binding of keratins. Furthermore, we examine the interaction of DEC205 with keratins by mutagenesis and biochemical assays based on the structural information and identify an XGGGX motif on keratins that can be recognized by DEC205, thereby providing insights into the interaction between DEC205 and keratins. Overall, these findings not only improve the understanding of the diverse ligand specificities of the mannose receptor family members at the molecular level but may also give clues for the interactions of keratins with their binding partners in the corresponding pathways.

Trappc1 intrinsically prevents ferroptosis of naive T cells to avoid spontaneous autoinflammatory disease in mice.

T lymphocytes are pivotal in adaptive immunity. The role of the trafficking protein particle complex (TRAPPC) in regulating T-cell development and homeostasis is unknown. Using CD4cre -Trappc1flox/flox (Trappc1 cKO) mice, we found that Trappc1 deficiency in T cells significantly decreased cell number of naive T cells in the periphery, whereas thymic T-cell development in Trappc1 cKO mice was identical as WT mice. In the culture assays and mouse models with adoptive transfer of the sorted WT (CD45.1+ CD45.2+ ) and Trappc1 cKO naive T cells (CD45.2+ ) to CD45.1+ syngeneic mice, Trappc1-deficient naive T cells showed significantly reduced survival ability compared with WT cells. RNA-seq and molecular studies showed that Trappc1 deficiency in naive T cells reduced protein transport from the endoplasmic reticulum to the Golgi apparatus, enhanced unfolded protein responses, increased P53 transcription, intracellular Ca2+ , Atf4-CHOP, oxidative phosphorylation, and lipid peroxide accumulation, and subsequently led to ferroptosis. Trappc1 deficiency in naive T cells increased ferroptosis-related damage-associated molecular pattern molecules like high mobility group box 1 or lipid oxidation products like prostaglandin E2, leukotriene B4, leukotriene C4, and leukotriene D4. Functionally, the culture supernatant of Trappc1 cKO naive T cells significantly promoted neutrophils to express inflammatory cytokines like TNFα and IL-6, which was rescued by lipid peroxidation inhibitor Acetylcysteine. Importantly, Trappc1 cKO mice spontaneously developed severe autoinflammatory disease 4 weeks after birth. Thus, intrinsic expression of Trappc1 in naive T cells plays an integral role in maintaining T-cell homeostasis to avoid proinflammatory naive T-cell death-caused autoinflammatory syndrome in mice. This study highlights the importance of the TRAPPC in T-cell biology.

CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins.

We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.

Cbx3 maintains lineage specificity during neural differentiation.

Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.

Assembly and recognition of keratins: A structural perspective.

Keratins are one of the major components of cytoskeletal network and assemble into fibrous structures named intermediate filaments (IFs), which are important for maintaining the mechanical properties of cells and tissues. Over the past decades, evidence has shown that the functions of keratins go beyond providing mechanical support for cells, they interact with multiple cellular components and are widely involved in the pathways of cell proliferation, differentiation, motility and death. However, the structural details of keratins and IFs are largely missing and many questions remain regarding the mechanisms of keratin assembly and recognition. Here we briefly review the current structural models and assembly of keratins as well as the interactions of keratins with the binding partners, which may provide a structural view for understanding the mechanisms of keratins in the biological activities and the related diseases.

Nerve growth factor promote osteogenic differentiation of dental pulp stem cells through MEK/ERK signalling pathways.

Nerve growth factor (NGF) and its receptor, tropomyosin receptor kinase A (TrkA), are known to play important roles in the immune and nervous system. However, the effects of NGF on the osteogenic differentiation of dental pulp stem cells (DPSCs) remain unclear. This study aimed to investigate the role of NGF on the osteogenic differentiation of DPSCs in vitro and the underlying mechanisms. DPSCs were cultured in osteogenic differentiation medium containing NGF (50 ng/mL) for 7 days. Then osteogenic-related genes and protein markers were analysed using qRT-PCR and Western blot, respectively. Furthermore, addition of NGF inhibitor and small interfering RNA (siRNA) transfection experiments were used to elucidate the molecular signalling pathway responsible for the process. NGF increased osteogenic differentiation of DPSCs significantly compared with DPSCs cultured in an osteogenic-inducing medium. The NGF inhibitor Ro 08-2750 (10 µM) and siRNA-mediated gene silencing of NGF receptor, TrkA and ERK signalling pathways inhibitor U0126 (10 µM) suppressed osteogenic-related genes and protein markers on DPSCs. Furthermore, our data revealed that NGF-upregulated osteogenic differentiation of DPSCs may be associated with the activation of MEK/ERK signalling pathways via TrkA. Collectively, NGF was capable of promoting osteogenic differentiation of DPSCs through MEK/ERK signalling pathways, which may enhance the DPSCs-mediated bone tissue regeneration.

Polymers from Plant Oils Linked by Siloxane Bonds for Programmed Depolymerization.

The increased production of plastics is leading to the accumulation of plastic waste and depletion of limited fossil fuel resources. In this context, we report a strategy to create polymers that can undergo controlled depolymerization by linking renewable feedstocks with siloxane bonds. α,ω-Diesters and α,ω-diols containing siloxane bonds were synthesized from an alkenoic ester derived from castor oil and then polymerized with varied monomers, including related biobased monomers. In addition, cyclic monomers derived from this alkenoic ester and hydrosiloxanes were prepared and cyclized to form a 26-membered macrolactone containing a siloxane unit. Sequential ring-opening polymerization of this macrolactone and lactide afforded an ABA triblock copolymer. This set of polymers containing siloxanes underwent programmed depolymerization into monomers in protic solvents or with hexamethyldisiloxane and an acid catalyst. Monomers afforded by the depolymerization of polyesters containing siloxane linkages were repolymerized to demonstrate circularity in select polymers. Evaluation of the environmental stability of these polymers toward enzymatic degradation showed that they undergo enzymatic hydrolysis by a fungal cutinase from Fusarium solani. Evaluation of soil microbial metabolism of monomers selectively labeled with 13C revealed differential metabolism of the main chain and side chain organic groups by soil microbes.

From Oxygen Redox to Sulfur Redox: A Paradigm for Li-Rich Layered Cathodes.

The utilization of anionic redox chemistry provides an opportunity to further improve the energy density of Li-ion batteries, particularly for Li-rich layered oxides. However, oxygen-based hosts still suffer from unfavorable structural rearrangement, including the oxygen release and transition metal (TM)-ion migration, in association with the tenuous framework rooted in the ionicity of the TM-O bonding. An intrinsic solution, by using a sulfur-based host with strong TM-S covalency, is proposed here to buffer the lattice distortion upon the highly activating sulfur redox process, and it achieves howling success in stabilizing the host frameworks. Experimental results demonstrate the prolonged preservation of the layered sulfur lattice, especially the honeycomb superlattice, during the Li+ extraction/insertion process in contrast to the large structural degeneration in Li-rich oxides. Moreover, the Li-rich sulfide cathodes exhibited a negligible overpotential of 0.08 V and a voltage drop of 0.13 mV/cycle, while maintaining a substantial reversible capacity upon cycling. These superior electrochemical performances can be unambiguously ascribed to the much shorter trajectories of sulfur in comparison to those of oxygen revealed by molecular dynamics simulations at a large scale (∼30 nm) and a long time scale (∼300 ps) via high-dimensional neural network potentials during the delithiation process. Our findings highlight the importance of stabilizing host frameworks and establish general guidance for designing Li-rich cathodes with durable anionic redox chemistry.

Regulating Oxygen Redox Chemistry through the Synergistic Effect of Transition-Metal Vacancy and Substitution Element for Layered Oxide Cathodes.

Reversible oxygen redox (OR) is considered as a paradigmatic avenue to boost the energy densities of layered oxide cathodes. However, its activation is largely coupled with the local coordination environment around oxygen, which is usually accompanied with irreversible oxygen release and unfavorable structure distortion. Herein, it is revealed that the synergistic effect of transition-metal (TM) vacancy and substitution element for modulating the OR activity and reversibility of layered Na0.67 MnO2 through multimodal operando synchrotron characterizations and electrochemical investigations. It is disclosed that TM vacancy can not only suppress the complicated phase transition but also stimulate the OR activity by creating nonbonding O 2p states via the Na─O─vacancy configurations. Notably, the substitution element plays a decisive role for regulating the reversibility of vacancy-boosted OR activity: the presence of strong Al─O bonds stabilizes the Mn-O motifs by sharing O with Al in the rigid Mn─O─Al frameworks, which mitigates TM migration and oxygen release induced by TM vacancy, leading to enhanced OR reversibility; while the introduction of weak Zn─O bonds exacerbates TM migration and irreversible oxygen release. This work clarifies the critical role of both TM vacancy and substitution element for regulating the OR chemistry, providing an effective avenue for designing high-performance cathodes employing anionic redox.

Reversible Oxygen Redox With Enhanced Structural Stability Through Covalency Modulation for Layered Oxide Cathodes.

P2-type Mn-based layered oxides have emerged as one of the most promising cathode materials for sodium-ion batteries owing to their advantages of facile preparation and high theoretical capacity. However, challenges such as phase transition and irreversible oxygen release during cycling often lead to rapid structural distortion and the formation of oxygen vacancies, ultimately resulting in rapid capacity decay. Herein, a covalency modulation strategy is adopted to address these challenges and successfully achieved a stable P2-type Mn-based layered oxide by introducing strong covalent Ni─O bonds. The robust Ni─O motif plays a crucial role in maintaining the rigidity of transition metal (TM) layered frameworks, which efficiently alleviates the structural distortion and degradation of the coordination environments of local TM sites, thereby achieving durable structural stiffness over extended cycles. In addition, the strong covalent Ni─O bonds can also stabilize the local oxygen environment, effectively suppressing the irreversible oxygen release. Benefiting from these advancements, the as-designed Na0.6Mg0.15Mn0.7Ni0.15O2 cathode displays a full solid-solution behavior with a low volume change of only 0.9% and an enhanced reversibility of lattice oxygen redox (OR) reaction. This investigation emphasizes the crucial role of covalency modulation in regulating OR chemistry and structural integrity to achieve high-energy-density Mn-based layered oxides.

Bias-aided DD-LMS equalizer for optical multipath-interference-impaired high-speed PAM4 transmission systems.

Multipath interference (MPI) noise induces drastic fluctuations in high-speed 4-level pulse amplitude modulation (PAM4) intensity modulation direct detection (IMDD) systems, severely degrading the transmission performance. Here, we propose a bias-aided decision-directed least mean square (DD-LMS) equalizer to eliminate the MPI noise. In the simulation, the proposed bias-aided DD-LMS equalizer could adeptly track and compensate the MPI-impaired PAM4 signal, markedly improving the bit error rate (BER) performance under different MPI levels and laser linewidths. Within a 112 Gbps PAM4 transmission system, the proposed equalizer achieves a MPI tolerance over 4 dB at the KP4-forward error correction (FEC) threshold (2.4 × 10-4), outperforming existing MPI suppression techniques.

Receiver in-phase and quadrature skew tolerant baud-rate timing recovery scheme for short-reach coherent optical interconnection.

A baud-rate sampling timing recovery (TR) scheme with receiver IQ skew tolerance is proposed and experimentally demonstrated. The proposed scheme performs independent TR for the in-phase and quadrature (IQ) tributary signals, thereby tracking the sampling phase error while naturally compensating for receiver IQ skew. The robustness of the IQ-independent TR to frequency offset (FO) and phase noise is theoretically analyzed. To address IQ misalignment caused by the IQ-independent TR, the use of pseudo-noise (PN) sequences for IQ frame synchronization is proposed. The proposed scheme achieves accurate timing recovery with hardware-efficient baud-rate sampling in the presence of receiver IQ skew, laying the foundation for stable performance of subsequent baud-rate equalization. The performance of the scheme is validated in a 56 GBaud polarization division multiplexed (PDM) 16QAM coherent experimental system. Experimental results demonstrate that the proposed scheme achieves similar BER performance to the modified Gardner + real-valued multiple-input multiple-output (RVMIMO) (@2 SPS) scheme. Moreover, the proposed scheme exhibits robustness to arbitrary IQ skew compared to the ABSPD + RVMIMO (@1 SPS) scheme.

Robust, wide-range, and precise transmitter IQ impairment monitoring scheme for coherent digital subcarrier multiplexing systems.

In this Letter, we present a robust, wide-range, and precise monitoring scheme for transmitter (Tx) impairments in coherent digital subcarrier multiplexing (DSCM) systems. The proposed scheme employs frequency-domain pilot tones (FPTs) to compensate for frequency offset (FO), polarization aliasing, and carrier phase noise, thus isolating Tx impairments from channel distortions. It then implements 4 × 4 real-valued MIMO to compensate for Tx impairments by equalizing symmetric subcarriers. Tx impairment monitoring is derived from the equalizer coefficients. By considering the phase shift caused by Tx impairments, a wide-range and precise monitoring of Tx impairments including IQ skew, IQ phase, and gain imbalances is achieved. We experimentally validated our approach using a 48-GBaud, four-subcarrier, dual-polarization coherent DSCM system. The results confirm the method's capability for a wide-range, robust, and precise Tx impairment monitoring in coherent DSCM systems, maintaining performance even in the presence of ultra-fast polarization variation.

Weight-adaptive joint mixed-precision quantization and pruning for neural network-based equalization in short-reach direct detection links.

Neural network (NN)-based equalizers have been widely applied for dealing with nonlinear impairments in intensity-modulated direct detection (IM/DD) systems due to their excellent performance. However, the computational complexity (CC) is a major concern that limits the real-time application of NN-based receivers. In this Letter, we propose, to our knowledge, a novel weight-adaptive joint mixed-precision quantization and pruning approach to reduce the CC of NN-based equalizers, where only integer arithmetic is taken into account instead of floating-point operations. The NN connections are either directly cutoff or represented by a proper number of quantization bits by weight partitioning, leading to a hybrid compressed sparse network that computes much faster and consumes less hardware resources. The proposed approach is verified in a 50-Gb/s 25-km pulse amplitude modulation (PAM)-4 IM/DD link using a directly modulated laser (DML) in the C-band. Compared with the traditional fully connected NN-based equalizer operated with standard floating-point arithmetic, about 80% memory can be saved at a minimum network size without degrading the system performance. Quantization is also shown to be more suitable to over-parameterized NN-based equalizers compared with NNs selected at a minimum size.

Multiplication-free and hardware-efficient baud-rate timing error detector for Nyquist and faster than Nyquist optical IM/DD systems.

Clock recovery (CR) algorithms that support higher baud rates and advanced modulation formats are crucial for short-distance optical interconnections, and it is desirable to push CR to operate at baud rate with minimal computing resources and power. In this Letter, we proposed a hardware-efficient and multiplication operation-free baud-rate timing error detector (TED) as a solution to meet these demands. Our approach involves employing both the absolute value of samples and the nonlinear sign operation to emphasize the clock tone, which is deteriorated by severe bandwidth limitation in Nyquist and faster than Nyquist (FTN) systems. Through experimental investigations based on a transceiver system with a 3 dB bandwidth of 30 GHz, the proposed baud-rate TED exhibits excellent performance. The proposed scheme successfully achieves clock synchronization of the received signals with the transmitted signals, including 50 GBaud PAM4/8, 80 GBaud PAM4, and up to 120 GBaud PAM4 FTN signals. To the best of our knowledge, the CR based on the proposed baud-rate TED is the most optimal solution for ultrahigh-speed short-reach IM/DD transmission, comprehensively considering the timing jitter, bit error rate (BER), and implementation complexity.