Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.

Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful strategy to dissect gene regulatory networks in development and disease.

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.

Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.

Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo.

Measuring cellular and tissue mechanics inside intact living organisms is essential for interrogating the roles of force in physiological and disease processes. Current agents for studying the mechanobiology of intact, living organisms are limited by poor light penetration and material stability. Magnetomotive ultrasound is an emerging modality for real-time in vivo imaging of tissue mechanics. Nonetheless, it has poor sensitivity and spatiotemporal resolution. Here we describe magneto-gas vesicles (MGVs), protein nanostructures based on gas vesicles and magnetic nanoparticles that produce differential ultrasound signals in response to varying mechanical properties of surrounding tissues. These hybrid nanomaterials significantly improve signal strength and detection sensitivity. Furthermore, MGVs enable non-invasive, long-term and quantitative measurements of mechanical properties within three-dimensional tissues and in vivo fibrosis models. Using MGVs as novel contrast agents, we demonstrate their potential for non-invasive imaging of tissue elasticity, offering insights into mechanobiology and its application to disease diagnosis and treatment.

MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.

DNA double-strand break (DSB) repair via homologous recombination is initiated by end resection. The extent of DNA end resection determines the choice of the DSB repair pathway. Nucleases for end resection have been extensively studied. However, it is still unclear how the potential DNA structures generated by the initial short resection by MRE11-RAD50-NBS1 are recognized and recruit proteins, such as EXO1, to DSB sites to facilitate long-range resection. We found that the MSH2-MSH3 mismatch repair complex is recruited to DSB sites through interaction with the chromatin remodeling protein SMARCAD1. MSH2-MSH3 facilitates the recruitment of EXO1 for long-range resection and enhances its enzymatic activity. MSH2-MSH3 also inhibits access of POLθ, which promotes polymerase theta-mediated end-joining (TMEJ). Collectively, we present a direct role of MSH2-MSH3 in the initial stages of DSB repair by promoting end resection and influencing the DSB repair pathway by favoring homologous recombination over TMEJ.

Precision targeting tumor cells using cancer-specific InDel mutations with CRISPR-Cas9.

An ideal cancer therapeutic strategy involves the selective killing of cancer cells without affecting the surrounding normal cells. However, researchers have failed to develop such methods for achieving selective cancer cell death because of shared features between cancerous and normal cells. In this study, we have developed a therapeutic strategy called the cancer-specific insertions-deletions (InDels) attacker (CINDELA) to selectively induce cancer cell death using the CRISPR-Cas system. CINDELA utilizes a previously unexplored idea of introducing CRISPR-mediated DNA double-strand breaks (DSBs) in a cancer-specific fashion to facilitate specific cell death. In particular, CINDELA targets multiple InDels with CRISPR-Cas9 to produce many DNA DSBs that result in cancer-specific cell death. As a proof of concept, we demonstrate here that CINDELA selectively kills human cancer cell lines, xenograft human tumors in mice, patient-derived glioblastoma, and lung patient-driven xenograft tumors without affecting healthy human cells or altering mouse growth.

Ferritin Nanoshuttle for Long-Lasting Self-Healing of Phenolic Hydrogels.

Herein, we highlight a novel finding that ferritin can play a crucial role in the "self-healing lifetime" of soft phenolic materials. Ferritin interacts with a catechol-functionalized polymer to form a self-healable and adhesive hydrogel bidirectionally by providing and retrieving Fe3+. As a result of its unique role as a nanoshuttle to store and release iron, ferritin significantly increases the self-healing lifetime of the hydrogel compared with that afforded by catechol-Fe3+ coordination through direct Fe3+ addition without ferritin. Ferritin also induces stable oxidative coupling between catechol moieties following metal coordination, which contributes to double cross-linking networks of catechol-catechol adducts and catechol-Fe3+ coordination. Thus, ferritin-mediated cross-linking can provide phenolic hydrogels with the advantages of hydrogels prepared by both metal coordination and oxidative coupling, thereby overcoming the limitations of the current cross-linking methods of phenolic hydrogels and broadening their versatility in biomedical applications.

Multimodal Characterization of Cardiac Organoids Using Integrations of Pressure-Sensitive Transistor Arrays with Three-Dimensional Liquid Metal Electrodes.

Herein, we present an unconventional method for multimodal characterization of three-dimensional cardiac organoids. This method can monitor and control the mechanophysiological parameters of organoids within a single device. In this method, local pressure distributions of human-induced pluripotent stem-cell-derived cardiac organoids are visualized spatiotemporally by an active-matrix array of pressure-sensitive transistors. This array is integrated with three-dimensional electrodes formed by the high-resolution printing of liquid metal. These liquid-metal electrodes are inserted inside an organoid to form the intraorganoid interface for simultaneous electrophysiological recording and stimulation. The low mechanical modulus and low impedance of the liquid-metal electrodes are compatible with organoids' soft biological tissue, which enables stable electric pacing at low thresholds. In contrast to conventional electrophysiological methods, this measurement of a cardiac organoid's beating pressures enabled simultaneous treatment of electrical therapeutics using a single device without any interference between the pressure signals and electrical pulses from pacing electrodes, even in wet organoid conditions.

pH-Universal Catechol-Amine Chemistry for Versatile Hyaluronic Acid Bioadhesives.

Catechol, a major mussel-inspired underwater adhesive moiety, has been used to develop functional adhesive hydrogels for biomedical applications. However, oxidative catechol chemistry for interpolymer crosslinking and adhesion is exclusively effective under alkaline conditions, with limited applications in non-alkaline conditions. To overcome this limitation, pH-universal catechol-amine chemistry to recapitulate naturally occurring biochemical events induced by pH variation in the mussel foot is suggested. Aldehyde moieties are introduced to hyaluronic acid (HA) by partial oxidation, which enables dual-mode catechol tethering to the HA via both stable amide and reactive secondary amine bonds. Because of the presence of additional reactive amine groups, the resultant aldehyde-modified HA conjugated with catechol (AH-CA) is effectively crosslinked in acidic and neutral pH conditions. The AH-CA hydrogel exhibits not only fast gelation via active crosslinking regardless of pH conditions, but also strong adhesion and excellent biocompatibility. The hydrogel enables rapid and robust wound sealing and hemostasis in neutral and alkaline conditions. The hydrogel also mediates effective therapeutic stem cell and drug delivery even in dynamic and harsh environments, such as a motile heart and acidic stomach. Therefore, the AH-CA hydrogel can serve as a versatile biomaterial in a wide range of pH conditions in vivo.

A Multimodal Approach to Huge Fibrous Dysplasia With Ocular Symptoms Using a Navigation System and Endoscope.

BACKGROUND: Fibrous dysplasia (FD) is a rare sporadic benign disease, which involves from single to several bones with unilateral distribution. Recently, image-based surgical navigation systems have played a significant role in surgical process on neurological and orthopedic operations. However, because an intraoral approach can visualize the field for maxillary surgery, there are few cases using endoscopes for excision of FD. Even though, a huge mass involving posterior side of maxillary sinus can be assisted with an endoscope to protect essential structures. To the best of our knowledge, this is the first report of plastic and reconstructive surgeons to perform the operation of a huge FD with both an endoscope and a navigation system. METHODS: Preoperative computed tomography scan and magnetic resonance imaging was performed for precise diagnosis and setting the navigation system (Medtronic Navigation, Louisville, CO). The main problem of the patient was exophthalmos and decreased visual acuity, the authors decided to remove the mass involving the intraorbital portion and sphenoidal portion. Moreover, the mass was extending to intracranium, cooperation with the department of neurosurgery and otolaryngology was planned. The tumor reached by the endoscope was resected as much as possible. During the excision of the sphenoidal portion by the head and neck surgeon of the department of otolaryngology, cerebrospinal fluid leakage was observed and repaired by the neurosurgeon. RESULTS: The exophthalmos measured by Hertel exophthalmometry was reduced only 1 mm, however, gross morphology of the patient was totally changed after the operation. Visual acuity of the right eye was improved from 0.3 to 0.9. The patient was followed up about 6 months and had a seizure event at 2 weeks after the surgery. Afterwards, the symptom has been well controlled by the medication. CONCLUSIONS: This multimodal approach offers a safe, rapid surgical aid in treating huge lesions involving orbital and intracranial area.

Core Extirpation and Zygoma Reduction: A New Surgical Approach for Fibrous Dysplasia of Zygomaticomaxillary Region.

INTRODUCTION: In case of zygomaticomaxillary fibrous dysplasia (FD), surgical treatment is often required due to visual disturbance, exophthalmos, and also necessary for cosmetic reasons. However, it is not easy to determine the timing and method of operation. The objective of our study is to define a new surgical option, for the treatment of FD of zygomaticomaxillary area. MATERIALS AND METHODS: Five patients affected by FD of their zygomaticomaxillary area who underwent surgery with a core extirpation were included in this study. A retrospective chart review and pre- and post-operative analysis of computed tomography scan were performed. RESULTS: All patients underwent core extirpation surgery and zygoma reduction was combined in 2 patients. All patients showed the cessation of the increase of external size postoperatively and results of the operation were well maintained over the follow-up period of 1 year. CONCLUSIONS: In this article, we present our experiences in the management of FD using the core extirpation with or without zygoma reduction, focusing on surgical indication, techniques, and results. Although there are limitations due to selective operative indication, the procedure can be usefully performed to prevent external growth and avoid repetitive surgery.

Vertical Nanowire Electrode Array for Enhanced Neurogenesis of Human Neural Stem Cells via Intracellular Electrical Stimulation.

Extracellular electrical stimulation (ES) can provide electrical potential from outside the cell membrane, but it is often ineffective due to interference from external factors such as culture medium resistance and membrane capacitance. To address this, we developed a vertical nanowire electrode array (VNEA) to directly provide intracellular electrical potential and current to cells through nanoelectrodes. Using this approach, the cell membrane resistivity and capacitance could be excluded, allowing effective ES. Human fetal neural stem cells (hfNSCs) were cultured on the VNEA for intracellular ES. Combining the structural properties of VNEA and VNEA-mediated ES, transient nanoscale perforation of the electrode was induced, promoting cell penetration and delivering current to the cell. Intracellular ES using VNEA improved the neuronal differentiation of hfNSCs more effectively than extracellular ES and facilitated electrophysiological functional maturation of hfNSCs because of the enhanced voltage-dependent ion-channel activity. The results demonstrate that VNEA with advanced nanoelectrodes serves as a highly effective culture and stimulation platform for stem-cell neurogenesis.

Polycaprolactone Mesh for Asian Rhinoplasty: Outcomes and Complications of Composite Septal Extension Graft Compared to Mesh-Only Graft.

Despite the great demand of aesthetic rhinoplasty in Asian population, it is difficult to obtain the lasting ideal tip projection along with lengthening of the nose due to the small and weak nasal septum. The shortage of available septal cartilage to work with is another major obstacle. A retrospective study was conducted between January 2017 and December 2019 in Seoul, Korea. A total of 774 patients underwent septorhinoplasty using polycaprolactone (PCL) mesh for the cosmetic enhancement of the nasal tip and the projection. Comparisons of aesthetic outcomes, patients' satisfaction surveys, and complications were performed between PCL mesh-only group and composite PCL group. Of all the patients, 97.5% of the patients in composite PCL group were rated more than 3 scores in aesthetic outcomes, whereas 90.4% in mesh-only group (p-value = 0.0002). About 96.7% of the patients with composite PCL rated their satisfaction level as more than satisfied, whereas 94.3% in mesh-only group (p-value = 0.0365). Overall, there were 17 patients in composite PCL group who exhibited complications including decreased tip projection, deviated nasal tip, mesh infection, and mesh exposure. However, there were two patients who had mesh injection in mesh-only group. Septorhinoplasty with septal extension graft using composite PCL graft provides robust support to the aesthetically modified projection and the lengthened nose without obvious complications on the nasal tip. Such technique allows surgeons to overcome the nature of Asian nose that is weak and small, and also provides satisfaction to patients who desire ideal tip projections and dramatic changes.

Biphasic Electrical Pulse by a Micropillar Electrode Array Enhances Maturation and Drug Response of Reprogrammed Cardiac Spheroids.

Direct reprogramming is an efficient strategy to produce cardiac lineage cells necessary for cardiac tissue engineering and drug testing for cardiac toxicity. However, functional maturation of reprogrammed cardiomyocytes, which is of great importance for their regenerative potential and drug response, still remains challenging. In this study, we propose a novel electrode platform to promote direct cardiac reprogramming and improve the functionality of reprogrammed cardiac cells. Nonviral cardiac reprogramming was improved via a three-dimensional spheroid culture of chemically induced cardiomyocytes exposed to a small-molecule cocktail. A micropillar electrode array providing biphasic electrical pulses mimicking the heartbeat further enhanced maturation and electrophysiological properties of reprogrammed cardiac spheroids, leading to proper responses and increased sensitivity to drugs. On the basis of our results, we conclude that our device may have a wider application in the generation of functional cardiac cells for regenerative medicine and screening of novel drugs.

Effects of a Catechol-Functionalized Hyaluronic Acid Patch Combined with Human Adipose-Derived Stem Cells in Diabetic Wound Healing.

INTRODUCTION: Chronic inflammation and impaired neovascularization play critical roles in delayed wound healing in diabetic patients. To overcome the limitations of current diabetic wound (DBW) management interventions, we investigated the effects of a catechol-functionalized hyaluronic acid (HA-CA) patch combined with adipose-derived mesenchymal stem cells (ADSCs) in DBW mouse models. METHODS: Diabetes in mice (C57BL/6, male) was induced by streptozotocin (50 mg/kg, >250 mg/dL). Mice were divided into four groups: control (DBW) group, ADSCs group, HA-CA group, and HA-CA + ADSCs group (n = 10 per group). Fluorescently labeled ADSCs (5 × 105 cells/100 µL) were transplanted into healthy tissues at the wound boundary or deposited at the HA-CA patch at the wound site. The wound area was visually examined. Collagen content, granulation tissue thickness and vascularity, cell apoptosis, and re-epithelialization were assessed. Angiogenesis was evaluated by immunohistochemistry, quantitative real-time polymerase chain reaction, and Western blot. RESULTS: DBW size was significantly smaller in the HA-CA + ADSCs group (8% ± 2%) compared with the control (16% ± 5%, p < 0.01) and ADSCs (24% ± 17%, p < 0.05) groups. In mice treated with HA-CA + ADSCs, the epidermis was regenerated, and skin thickness was restored. CD31 and von Willebrand factor-positive vessels were detected in mice treated with HA-CA + ADSCs. The mRNA and protein levels of VEGF, IGF-1, FGF-2, ANG-1, PIK, and AKT in the HA-CA + ADSCs group were the highest among all groups, although the Spred1 and ERK expression levels remained unchanged. CONCLUSIONS: The combination of HA-CA and ADSCs provided synergistic wound healing effects by maximizing paracrine signaling and angiogenesis via the PI3K/AKT pathway. Therefore, ADSC-loaded HA-CA might represent a novel strategy for the treatment of DBW.

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-µm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes.

CpG, 5'-C-phosphate-G-3', islands (CGIs) have long been known for their association with enhancers, silencers, and promoters, and for their epigenetic signatures. They are maintained in embryonic stem cells (ESCs) in a poised but inactive state via the formation of bivalent chromatin containing both active and repressive marks. CGIs also occur within coding sequences, where their functional role has remained obscure. Intragenic CGIs (iCGIs) are largely absent from housekeeping genes, but they are found in all genes associated with organ development and cell lineage control. In this paper, we investigated the epigenetic status of iCGIs and found that they too reside in bivalent chromatin in ESCs. Cell type-specific DNA methylation of iCGIs in differentiated cells was linked to the loss of both the H3K4me3 and H3K27me3 marks, and disruption of physical interaction with promoter regions, resulting in transcriptional activation of key regulators of differentiation such as PAXs, HOXs, and WNTs. The differential epigenetic modification of iCGIs appears to be mediated by cell type-specific transcription factors distinct from those bound by promoter, and these transcription factors may be involved in the hypermethylation of iCGIs upon cell differentiation. iCGIs thus play a key role in the cell type-specific regulation of transcription.

Magnetic Control of Axon Navigation in Reprogrammed Neurons.

While neural cell transplantation represents a promising therapy for neurodegenerative diseases, the formation of functional networks of transplanted cells with host neurons constitutes one of the challenging steps. Here, we introduce a magnetic guidance methodology that controls neurite growth signaling via magnetic nanoparticles (MNPs) conjugated with antibodies targeting the deleted in colorectal cancer (DCC) receptor (DCC-MNPs). Activation of the DCC receptors by clusterization and subsequent axonal growth of the induced neuronal (iN) cells was performed in a spatially controlled manner. In addition to the directionality of the magnetically controlled axon projection, axonal growth of the iN cells assisted the formation of functional connections with pre-existing primary neurons. Our results suggest magnetic guidance as a strategy for improving neuronal connectivity by spatially guiding the axonal projections of transplanted neural cells for synaptic interactions with the host tissue.

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.

Estimating Lifetime Duration of Diabetes by Age and Gender in the Korean Population Using a Markov Model.

BACKGROUND: Duration of type 2 diabetes is clinically important. Duration of morbidity is an independent and critical predictor of developing its complications. This study aims to explore an applicability of a Markov model to estimate the duration of diabetes in the Korean population. METHODS: We constructed the Markov model with two Markov states, diabetes and death, for estimation of duration of diabetes. The cycle of the Markov model was 1 year. Each diabetes onset by 5 years was considered from 30 to 85 years old or above. The endpoint of the Markov was 100 years old. Type 2 diabetes was operationally defined using the 10th revision of International Statistical Classification of Diseases and prescriptions of anti-diabetic drugs from the National Health Insurance Services-National Sample cohort. In each incident and existing prevalence cases, survival probabilities were obtained. Durations of diabetes from the Markov model were compared with those from the DisMod II program. Reductions of life expectancy due to diabetes were defined as differences of life expectancies between diabetic patients and the general public. Sensitivity analyses were also conducted using a cure rate and 95% confidence interval of survival probability. RESULTS: The duration of diabetes gradually decreased with incident age in both genders. In the early 30s, the duration was the largest at 48.9 and 41.9 years in women and men, respectively. In the average incident age group of type 2 diabetes, the late 50s, the reduction of life expectancy due to diabetes was estimated to be about two years in both genders. As annual cure probabilities increased, the durations of diabetes were reduced. CONCLUSION: This study estimated the duration of diabetes using a Markov model. The model seems to work well and diabetes could reduce life expectancy by about 2 years on average. This approach could be useful to estimate the duration of illness, calculate disability-adjusted life years, and conduct economic evaluation studies on interventions for diabetic patients.

Pore Diameter of Mesoporous Silica Modulates Oxidation of H2O2-Sensing Chromophore in a Porous Matrix.

Hydrogen peroxide (H2O2) is an attractive chemical because of its bleaching properties in paper and pulp industry and as a disinfectant in the food, water, and medical industries. However, it is important to monitor the residual H2O2 level after its usage and prevent any unintended health problems or chemical reactions. Most H2O2 sensors often utilize fluorophores or electrical circuitry that requires an additional irradiation or a digital display. To this end, this study presents a 3,3',5,5'-tetramethylbenzidine (TMB)/horseradish peroxidase (HRP)-loaded patch that alerts the presence of high H2O2 levels by generating a visible blue color. We hypothesized that water-insoluble TMB immobilized within mesoporous silica particles of proper pore diameter and structure would act as a colorimetric indicator through the H2O2-mediated oxidation within a cross-linked patch. We examined this hypothesis by immobilizing TMB molecules in mesoporous silica particles with 2 and 7 nm diameter cylindrical pores as well as on nonporous silica particles. Then, we loaded these TMB-silica particles and HRP in a porous alginate patch via sequential in situ cross-linking reaction and lyophilization. In the presence of 25-5000 µM H2O2, which simulate H2O2 concentrations found in residual disinfecting fluids, the patch loaded with TMB-mesoporous silica particles with 7 nm diameter pores generated a distinct blue color with varying intensities depending on the H2O2 concentration. The design principles demonstrated in this study should be applicable to a broad array of sensors to be integrated into a moldable, three-dimensional matrix.