DOT1L/H3K79me2 represses HIV-1 reactivation via recruiting DCAF1.

DOT1L mediates the methylation of histone H3 at lysine 79 and, in turn, the transcriptional activation or repression in a context-dependent manner, yet the regulatory mechanisms and functions of DOT1L/H3K79me remain to be fully explored. Following peptide affinity purification and proteomic analysis, we identified that DCAF1-a component of the E3 ligase complex involved in HIV regulation-is associated with H3K79me2 and DOT1L. Interestingly, blocking the expression or catalytic activity of DOT1L or repressing the expression of DCAF1 significantly enhances the tumor necrosis factor alpha (TNF-α)/nuclear factor κB (NF-κB)-induced reactivation of the latent HIV-1 genome. Mechanistically, upon TNF-α/NF-κB activation, DCAF1 is recruited to the HIV-1 long terminal repeat (LTR) by DOT1L and H3K79me2. Recruited DCAF1 subsequently induces the ubiquitination of NF-κB and restricts its accumulation at the HIV-1 LTR. Altogether, our findings reveal a feedback modulation of HIV reactivation by DOT1L-mediated histone modification regulation and highlight the potential of targeting the DOT1L/DCAF1 axis as a therapeutic strategy for HIV treatment.

PRMT2 promotes HIV-1 latency by preventing nucleolar exit and phase separation of Tat into the Super Elongation Complex.

The HIV-1 Tat protein hijacks the Super Elongation Complex (SEC) to stimulate viral transcription and replication. However, the mechanisms underlying Tat activation and inactivation, which mediate HIV-1 productive and latent infection, respectively, remain incompletely understood. Here, through a targeted complementary DNA (cDNA) expression screening, we identify PRMT2 as a key suppressor of Tat activation, thus contributing to proviral latency in multiple cell line latency models and in HIV-1-infected patient CD4+ T cells. Our data reveal that the transcriptional activity of Tat is oppositely regulated by NPM1-mediated nucleolar retention and AFF4-induced phase separation in the nucleoplasm. PRMT2 preferentially methylates Tat arginine 52 (R52) to reinforce its nucleolar sequestration while simultaneously counteracting its incorporation into the SEC droplets, thereby leading to its functional inactivation to promote proviral latency. Thus, our studies unveil a central and unappreciated role for Tat methylation by PRMT2 in connecting its subnuclear distribution, liquid droplet formation, and transactivating function, which could be therapeutically targeted to eradicate latent viral reservoirs.

Enhancer decommissioning by MLL4 ablation elicits dsRNA-interferon signaling and GSDMD-mediated pyroptosis to potentiate anti-tumor immunity.

Enhancer deregulation is a well-established pro-tumorigenic mechanism but whether it plays a regulatory role in tumor immunity is largely unknown. Here, we demonstrate that tumor cell ablation of mixed-lineage leukemia 3 and 4 (MLL3 and MLL4, also known as KMT2C and KMT2D, respectively), two enhancer-associated histone H3 lysine 4 (H3K4) mono-methyltransferases, increases tumor immunogenicity and promotes anti-tumor T cell response. Mechanistically, MLL4 ablation attenuates the expression of RNA-induced silencing complex (RISC) and DNA methyltransferases through decommissioning enhancers/super-enhancers, which consequently lead to transcriptional reactivation of the double-stranded RNA (dsRNA)-interferon response and gasdermin D (GSDMD)-mediated pyroptosis, respectively. More importantly, we reveal that both the dsRNA-interferon signaling and GSDMD-mediated pyroptosis are of critical importance to the increased anti-tumor immunity and improved immunotherapeutic efficacy in MLL4-ablated tumors. Thus, our findings establish tumor cell enhancers as an additional layer of immune evasion mechanisms and suggest the potential of targeting enhancers or their upstream and/or downstream molecular pathways to overcome immunotherapeutic resistance in cancer patients.

From aniline to phenol: carbon-nitrogen bond activation via uranyl photoredox catalysis.

Carbon-nitrogen bond activation, via uranyl photoredox catalysis with water, enabled the conversion of 40 protogenetic anilines, 8 N-substituted anilines and 9 aniline-containing natural products/pharmaceuticals to the corresponding phenols in an ambient environment. A single-electron transfer process between a protonated aniline and uranyl catalyst, which was disclosed by radical quenching experiments and Stern-Volmer analysis, facilitated the following oxygen atom transfer process between the radical cation of protonated anilines and uranyl peroxide originating from water-splitting. 18O labeling and 15N tracking unambiguously depicted that the oxygen came from water and amino group left as ammonium salt. The 100-fold efficiency of the flow operation demonstrated the great potential of the conversion process for industrial synthetic application.

Sequential posterior interosseous artery perforator flap for reconstruction of dorsal hand defects.

Dorsal hand defects accompanied by exposure of bones and tendons remain a huge challenge for plastic surgeons. The pedicled perforator flaps have unique advantages in resurfacing the defects. This study aimed to investigate the clinical efficacy of the sequential posterior interosseous artery perforator flap for repairing dorsal hand defects. This study was composed of an anatomical study and clinical application. Anatomically, 30 adult upper limb specimens injected with red latex were dissected, the perforators from the branches of the posterior interosseous artery were observed in the dorsal forearm, and the sequential flap based on them was designed based on the anatomical characteristics. Clinically, nine cases of soft tissue defects on the dorsum of the hand were treated by this flap. Anatomically, the posterior interosseous artery divided into an ascending branch and a descending branch, and the descending branch traveled 1.0 ± 0.3 cm down to divide into the ulnar and radial terminal branches. The ulnar terminal branch presented constantly, and the radial terminal branch had an occurrence rate of 93.33%. Clinically, all flaps survived completely and possessed a soft texture and satisfactory appearance, as well as a nonbloated pedicle, and the donor region had a natural color and appearance with only a linear scar left behind. The sequential posterior interosseous artery perforator flap could become a useful option for repairing dorsal hand defects, as it has the advantages of being easy to perform without sacrificing the main vessels and avoiding donor area skin grafting.

Antecubital Fossa Perforator Flaps for Soft-Tissue Defect Repair of the Anterior Elbow: Anatomical Study and Clinical Application.

BACKGROUND: The antecubital fossa is a main perforator cluster region located beside the anterior elbow defect, rendering it crucial to harvest the perforator pedicled flaps for the anterior elbow defects. PATIENTS AND METHODS: A total of 30 preserved cadaveric forearms were dissected in order to describe the perforator anatomy in the antecubital fossa. For each perforator, the number, the site of origin, the diameter at its origin, and the trajectory were recorded. In addition, all the patients treated for anterior elbow defects using inferior cubital artery (ICA) perforator pedicled flaps between June 2013 and June 2018 were reviewed in this retrospective study. RESULTS: A total of 85 perforators were dissected in the antecubital fossa area from the 30 specimens. Among these, 65 perforators originated from the radial artery, 6 from the recurrent radial artery, 13 from the brachial artery, and 1 from the ulnar artery. Each forearm specimen had a constant and large ICA perforator. All perforators originated from source vessels 2-5 cm distal from the interepicondylar line and could be harvested as perforator pedicled flap for anterior elbow reconstruction. In the clinical study, 11 patients with anterior elbow defects were treated with ICA perforator pedicled flaps with satisfactory functional and aesthetic outcomes. CONCLUSION: The antecubital fossa has a constant and dominant ICA perforator and many other perforators. The pedicled antecubital fossa perforator flaps could be harvested flexibly with a reliable blood supply for anterior elbow reconstruction.

TmcA functions as a lysine 2-hydroxyisobutyryltransferase to regulate transcription.

Protein lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to play a critical role in the regulation of cellular processes. However, the mechanism and functional consequence of Khib in prokaryotes remain unclear. Here we report that TmcA, an RNA acetyltransferase, functions as a lysine 2-hydroxyisobutyryltransferase in the regulation of transcription. We show that TmcA can effectively catalyze Khib both in vitro and intracellularly, and that R502 is a key site for the Khib catalytic activity of TmcA. Using quantitative proteomics, we identified 467 endogenous candidates targeted by TmcA for Khib in Escherichia coli. Interestingly, we demonstrate that TmcA can specifically modulate the DNA-binding activity of H-NS, a nucleoid-associated protein, by catalysis of Khib at K121. Furthermore, this TmcA-targeted Khib regulates transcription of acid-resistance genes and enhances E. coli survival under acid stress. Our study reveals transcription regulation mediated by TmcA-catalyzed Khib for bacterial acid resistance.

Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche.

Tumor-initiating stem cells (TSCs) are critical for drug resistance and immune escape. However, the mutual regulations between TSC and tumor microenvironment (TME) remain unclear. Using DNA-label retaining, single-cell RNA sequencing (scRNA-seq), and other approaches, we investigated intestinal adenoma in response to chemoradiotherapy (CRT), thus identifying therapy-resistant TSCs (TrTSCs). We find bidirectional crosstalk between TSCs and TME using CellPhoneDB analysis. An intriguing finding is that TSCs shape TME into a landscape that favors TSCs for immunosuppression and propagation. Using adenoma-organoid co-cultures, niche-cell depletion, and lineaging tracing, we characterize a functional role of cyclooxygenase-2 (Cox-2)-dependent signaling, predominantly occurring between tumor-associated monocytes and macrophages (TAMMs) and TrTSCs. We show that TAMMs promote TrTSC proliferation through prostaglandin E2 (PGE2)-PTGER4(EP4) signaling, which enhances ß-catenin activity via AKT phosphorylation. Thus, our study shows that the bidirectional crosstalk between TrTSC and TME results in a pro-tumorigenic and immunosuppressive contexture.

Uranyl-Photocatalyzed Hydrolysis of Diaryl Ethers at Ambient Environment for the Directional Degradation of 4-O-5 Lignin.

Uranyl-photocatalyzed hydrolysis of diaryl ethers has been established to achieve two types of phenols at room temperature under normal pressure. The single electron transfer process was disclosed by a radical quenching experiment and Stern-Volmer analysis between diphenyl ether and uranyl cation catalyst, followed by oxygen atom transfer process between radical cation of diphenyl ether and uranyl peroxide species. The 18O-labeling experiment precisely demonstrates that the oxygen source is water. Further application in template substrates of 4-O-5 linkages from lignin and 30-fold efficiency of flow operation display the potential application for phenol recovery via an ecofriendly and low-energy consumption protocol.

Single-Cell Analysis of the Pan-Cancer Immune Microenvironment and scTIME Portal.

Single-cell sequencing opens a new era for the investigation of tumor immune microenvironments (TIME). However, at single-cell resolution, a pan-cancer analysis that addresses the identity and diversity of TIMEs is lacking. Here, we first built a pan-cancer single-cell reference of TIMEs with refined subcell types and recognized new cell type-specific transcription factors. We then presented a pan-cancer view of the common features of the TIME and compared the variation of each immune cell type across patients and tumor types in the aspects of abundance, cell states, and cell communications. We found that the abundance and the cell states of dysfunctional T cells were most variable, whereas those of regulatory T cells were relatively stable. A subset of tumor-associated macrophages (TAM), PLTP + C1QC + TAMs, may regulate the abundance of dysfunctional T cells through cytokine/chemokine signaling. The ligand-receptor communication network of TIMEs was tumor-type specific and dominated by the tumor-enriched immune cells. We additionally developed the single-cell TIME (scTIME) portal (http://scTIME.sklehabc.com) with the scTIME-specific analysis modules and a unified cell annotation. In addition to the immune cell compositions and correlation analysis using refined cell type classifications, the portal also provides cell-cell interaction and cell type-specific gene signature analysis. Our single-cell pan-cancer analysis and scTIME portal will provide more insights into the features of TIMEs, as well as the molecular and cellular mechanisms underlying immunotherapies.

Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates.

Vertebrates vary in their ability to regenerate, and the genetic mechanisms underlying such disparity remain elusive. Comparative epigenomic profiling and single-cell sequencing of two related teleost fish uncovered species-specific and evolutionarily conserved genomic responses to regeneration. The conserved response revealed several regeneration-responsive enhancers (RREs), including an element upstream to inhibin beta A (inhba), a known effector of vertebrate regeneration. This element activated expression in regenerating transgenic fish, and its genomic deletion perturbed caudal fin regeneration and abrogated cardiac regeneration altogether. The enhancer is present in mammals, shares functionally essential activator protein 1 (AP-1)-binding motifs, and responds to injury, but it cannot rescue regeneration in fish. This work suggests that changes in AP-1-enriched RREs are likely a crucial source of loss of regenerative capacities in vertebrates.

ß-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells.

Mouse embryonic stem cells (ESCs) cultured in defined medium resemble the pre-implantation epiblast in the ground state, with full developmental capacity including the germline. ß-Catenin is required to maintain ground state pluripotency in mouse ESCs, but its exact role is controversial. Here, we reveal a Tcf3-independent role of ß-catenin in restraining germline and somatic lineage differentiation genes. We show that ß-catenin binds target genes with E2F6 and forms a complex with E2F6 and HMGA2 or E2F6 and HP1γ. Our data indicate that these complexes help ß-catenin restrain and fine-tune germ cell and neural developmental potential. Overall, our data reveal a previously unappreciated role of ß-catenin in preserving lineage differentiation integrity in ground state ESCs.

Competition between PAF1 and MLL1/COMPASS confers the opposing function of LEDGF/p75 in HIV latency and proviral reactivation.

Transcriptional status determines the HIV replicative state in infected patients. However, the transcriptional mechanisms for proviral replication control remain unclear. In this study, we show that, apart from its function in HIV integration, LEDGF/p75 differentially regulates HIV transcription in latency and proviral reactivation. During latency, LEDGF/p75 suppresses proviral transcription via promoter-proximal pausing of RNA polymerase II (Pol II) by recruiting PAF1 complex to the provirus. Following latency reversal, MLL1 complex competitively displaces PAF1 from the provirus through casein kinase II (CKII)-dependent association with LEDGF/p75. Depleting or pharmacologically inhibiting CKII prevents PAF1 dissociation and abrogates the recruitment of both MLL1 and Super Elongation Complex (SEC) to the provirus, thereby impairing transcriptional reactivation for latency reversal. These findings, therefore, provide a mechanistic understanding of how LEDGF/p75 coordinates its distinct regulatory functions at different stages of the post-integrated HIV life cycles. Targeting these mechanisms may have a therapeutic potential to eradicate HIV infection.

The V-Y advancement flap based on the dorsal carpal perforators for dorsal metacarpal reconstruction: Anatomical and clinical study.

INTRODUCTION: Soft-tissue defects on the dorsal hand accompanied by exposed bone and tendon remain a challenge for plastic surgeons. The purpose of this study was to observe the morphological characteristics of the dorsal carpal perforators in the wrist and to design a V-Y advancement flap based on the dorsal carpal perforators. MATERIALS AND METHODS: Thirty cadaveric hand specimens were dissected to observe the origin, course, branches, and anastomoses of the dorsal carpal perforators, and a V-Y advancement flap was designed based on these perforators. Clinically, nine cases of dorsal hand defects were reconstructed with this flap. RESULTS: The dorsal carpal vascular network was formed by vascular anastomoses along the dorsal carpal branch of the radial artery, dorsal carpal branch of the anterior interosseous artery, ascending branch of the dorsal carpal perforator from the deep palmar arch, direct branch of the radial artery, dorsal carpal branch of the ulnar artery, posterior interosseous artery, and deep palmar branch of the ulnar artery; this network could be divided into a deep vascular network and superficial vascular network according to the anatomical plane. Among the perforators, the third and fourth perforators that pierce out bilaterally from the tendon of the extensor digitorium had a consistent occurrence rate (100%) with an outer diameter of 0.7 ± 0.3 mm and 0.6 ± 0.2 mm, respectively, and thus could be chosen as the vascular pedicle. In clinical applications, all flaps survived completely with excellent color and texture, a satisfactory appearance, and normal movement of the wrist joint. CONCLUSIONS: A V-Y advancement flap based on the dorsal carpal perforators can become a useful choice for the repair of dorsal metacarpal defects caused by trauma or dorsal metacarpal arterial flaps.

Anatomical basis and clinical application of the dorsal perforator flap based on the palmar artery in the first web.

PURPOSE: Soft-tissue defects of the thumb and index finger remain a challenge for plastic surgeons. Our purpose was to observe the morphological characteristics of the cutaneous vessels in the first web, to design a dorsal perforator flap based on the palmar artery in the first web and to propose its clinical application. METHODS: Thirty preserved hand specimens were dissected to observe the origin, course, branch and anastomosis of the dorsal perforators in the first web, and the dorsal perforator flap based on the palmar artery in the first web was designed. Clinically, seven cases of hand defects were reconstructed using this flap. RESULTS: The blood supply for the dorsum of the first web comprised the dorsal perforators from both the dorsal artery (the branch of the first dorsal metacarpal artery) and palmar artery (the radial palmar digital artery of the index finger and the ulnar palmar digital artery of the thumb). The first dorsal metacarpal artery constantly arose from the radial artery and was divided into the radial, ulnar and medial branches. The palmar artery sent out 1-2 perforators and formed a constant anastomosis with the medial branch of the first dorsal metacarpal artery to supply the dorsal skin of the first web. In clinical application, all the flaps survived completely without contracture of the first web or other complications and the donor regions all healed at the first stage. CONCLUSION: The dorsal perforator flap based on the palmar artery in the first web is useful to repair soft-tissue defects of the thumb, the proximal phalanx of the index finger and thenar region, leading to a satisfactory appearance and good functional and sensory recovery.

Anatomical Basis and Clinical Application of the First Metatarsal Proximal Perforator-Based Neurocutaneous Vascular Flap.

Forefoot defects caused by accidents are very common, but their reconstruction remains a substantial challenge for plastic surgeons. The purpose of this study is to determine the anatomical structure of the first metatarsal proximal perforator-based flap and to propose its clinical application. The study was divided into two parts: an anatomical study and a clinical application. Thirty preserved lower limbs injected with red latex were chosen for observation, and the following were recorded: the course and distribution of the medialis dorsalis pedis cutaneous nerve; the origin, course, branching and distribution of the first metatarsal proximal perforator; and the communication of the perforator and the dorsal medial vessels. Clinically, six cases of forefoot skin defects were reconstructed with the first metatarsal proximal perforator-based neurocutaneous vascular flap. The medialis dorsalis pedis cutaneous nerve mainly arose from the medial branch of the superficial peroneal nerve and proceeded forward for a distance of 2.5 ± 0.4 cm under the surface of the inferior extensor retinaculum; then, the nerve divided into the medial dorsal branch and the first and second dorsal metatarsal branches. The first metatarsal proximal perforator-based neurocutaneous vessels were multisegmented and multisourced, and the first branch was closely related to the operative procedure. In terms of the clinical application, all flaps of the six cases survived completely with good appearance, texture and elasticity. The first metatarsal proximal perforators present as constant. The first metatarsal proximal perforator-based neurocutaneous vascular flap may become a useful supplemental material for the reconstruction of forefoot defects. Clin. Anat., 33:653-660, 2020. © 2019 Wiley Periodicals, Inc.

Protein lysine de-2-hydroxyisobutyrylation by CobB in prokaryotes.

Lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to be an evolutionarily conserved histone mark. Here, we report that CobB serves as a lysine de-2-hydroxyisobutyrylation enzyme that regulates glycolysis and cell growth in prokaryotes. We identified the specific binding of CobB to Khib using a novel self-assembled multivalent photocrosslinking peptide probe and demonstrated that CobB can catalyze lysine de-2-hydroxyisobutyrylation both in vivo and in vitro. R58 of CobB is a critical site for its de-2-hydroxyisobutyrylase activity. Using a quantitative proteomics approach, we identified 99 endogenous substrates that are targeted by CobB for de-2-hydroxyisobutyrylation. We further demonstrated that CobB can regulate the catalytic activities of enolase (ENO) by removing K343hib and K326ac of ENO simultaneously, which account for changes of bacterial growth. In brief, our study dissects a Khib-mediated molecular mechanism that is catalyzed by CobB for the regulation of the activity of metabolic enzymes as well as the cell growth of bacteria.

Diagnosis of osteoarticular tuberculosis via metagenomic next-generation sequencing: A case report.

Osteoarticular tuberculosis (OAT) may cause severe complications and disability. Due to its indolent nature, OAT is difficult to diagnose in the early stages. Diagnosis by conventional culture is time-consuming and insensitive, and polymerase chain reaction-based molecular diagnostic methods are incapable of excluding co-infections. Metagenomic next-generation sequencing (mNGS) may identify a broad spectrum of microorganisms, including Mycobacterium, bacteria and fungi, in clinical specimens. Therefore, the diagnosis of OAT may be rapidly performed using mNGS. The present study reports on a case of OAT. The patient presented with right knee swelling and pain for 1 year; his C-reactive protein levels and erythrocyte sedimentation rate were markedly elevated. Although multiple pre-operative cultures were negative, mNGS was finally used to successfully detect the underlying pathogen. The result was confirmed by other molecular biology methods and Mycobacterium culture. Anti-tuberculosis therapy was administered accordingly and the patient finally recovered. In conclusion mNGS, with the ability to detect Mycobacterium and other microorganisms in a single assay, is an emerging approach for rapidly and accurately diagnosing OAT. This method may provide significant support to guide physicians in selecting the appropriate pharmacotherapy and surgical treatments.

Selective Late-Stage Oxygenation of Sulfides with Ground-State Oxygen by Uranyl Photocatalysis.

Oxygenation is a fundamental transformation in synthesis. Herein, we describe the selective late-stage oxygenation of sulfur-containing complex molecules with ground-state oxygen under ambient conditions. The high oxidation potential of the active uranyl cation (UO22+ ) enabled the efficient synthesis of sulfones. The ligand-to-metal charge transfer process (LMCT) from O 2p to U 5f within the O=U=O group, which generates a UV center and an oxygen radical, is assumed to be affected by the solvent and additives, and can be tuned to promote selective sulfoxidation. This tunable strategy enabled the batch synthesis of 32 pharmaceuticals and analogues by late-stage oxygenation in an atom- and step-efficient manner.

Recent advances in understanding intestinal stem cell regulation.

Intestinal homeostasis and regeneration are driven by intestinal stem cells (ISCs) lying in the crypt. In addition to the actively cycling ISCs that maintain daily homeostasis, accumulating evidence supports the existence of other pools of stem/progenitor cells with the capacity to repair damaged tissue and facilitate rapid restoration of intestinal integrity after injuries. Appropriate control of ISCs and other populations of intestinal epithelial cells with stem cell activity is essential for intestinal homeostasis and regeneration while their deregulation is implicated in colorectal tumorigenesis. In this review, we will summarize the recent findings about ISC identity and cellular plasticity in intestine, discuss regulatory mechanisms that control ISCs for intestinal homeostasis and regeneration, and put a particular emphasis on extrinsic niche-derived signaling and intrinsic epigenetic regulation. Moreover, we highlight several fundamental questions about the precise mechanisms conferring robust capacity for intestine to maintain physiological homeostasis and repair injuries.