Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids.

BACKGROUND: Fragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses. RESULTS: We established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats. CONCLUSIONS: In conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.

An integrative approach for exploring the nature of fibroepithelial neoplasms.

BACKGROUND: Malignant phyllodes tumour (MPT) is a rare breast malignancy with epithelial and mesenchymal features. Currently, there are no appropriate research models or effective targeted therapeutic approaches for MPT. METHODS: We collected fresh frozen tissues from nine patients with MPT and performed whole-exome and RNA sequencing. Additionally, we established patient-derived xenograft (PDX) models from patients with MPT and tested the efficacy of targeting dysregulated pathways in MPT using the PDX model from one MPT. RESULTS: MPT has unique molecular characteristics when compared to breast cancers of epithelial origin and can be classified into two groups. The PDX model derived from one patient with MPT showed that the mouse epithelial component increased during tumour growth. Moreover, targeted inhibition of platelet-derived growth factor receptor (PDGFR) and phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) by imatinib mesylate and PKI-587 showed in vivo tumour suppression effects. CONCLUSIONS: This study revealed the molecular profiles of MPT that can lead to molecular classification and potential targeted therapy, and suggested that the MPT PDX model can be a useful tool for studying the pathogenesis of fibroepithelial neoplasms and for preclinical drug screening to find new therapeutic strategies for MPT.

Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data.

BACKGROUND: Although single-cell RNA sequencing of xenograft samples has been widely used, no comprehensive bioinformatics pipeline is available for human and mouse mixed single-cell analyses. Considering the numerous homologous genes across the human and mouse genomes, misalignment errors should be evaluated, and a new algorithm is required. We assessed the extents and effects of misalignment errors and exonic multi-mapping events when using human and mouse combined reference data and developed a new bioinformatics pipeline with expression-based species deconvolution to minimize errors. We also evaluated false-positive signals presumed to originate from ambient RNA of the other species and address the importance to computationally remove them. RESULT: Error when using combined reference account for an average of 0.78% of total reads, but such reads were concentrated to few genes that were greatly affected. Human and mouse mixed single-cell data, analyzed using our pipeline, clustered well with unmixed data and showed higher k-nearest-neighbor batch effect test and Local Inverse Simpson's Index scores than those derived from Cell Ranger (10 × Genomics). We also applied our pipeline to multispecies multisample single-cell library containing breast cancer xenograft tissue and successfully identified all samples using genomic array and expression. Moreover, diverse cell types in the tumor microenvironment were well captured. CONCLUSION: We present our bioinformatics pipeline for mixed human and mouse single-cell data, which can also be applied to pooled libraries to obtain cost-effective single-cell data. We also address misalignment, multi-mapping error, and ambient RNA as a major consideration points when analyzing multispecies single-cell data.

A Real-Time Wearable Physiological Monitoring System for Home-Based Healthcare Applications.

The acquisition of physiological data are essential to efficiently predict and treat cardiac patients before a heart attack occurs and effectively expedite motor recovery after a stroke. This goal can be achieved by using wearable wireless sensor network platforms for real-time healthcare monitoring. In this paper, we present a wireless physiological signal acquisition device and a smartphone-based software platform for real-time data processing and monitor and cloud server access for everyday ECG/EMG signal monitoring. The device is implemented in a compact size (diameter: 30 mm, thickness: 4.5 mm) where the biopotential is measured and wirelessly transmitted to a smartphone or a laptop for real-time monitoring, data recording and analysis. Adaptive digital filtering is applied to eliminate any interference noise that can occur during a regular at-home environment, while minimizing the data process time. The accuracy of ECG and EMG signal coverage is assessed using Bland-Altman analysis by comparing with a reference physiological signal acquisition instrument (RHS2116 Stim/Recording System, Intan). Signal coverage of R-R peak intervals showed almost identical outcome between this proposed work and the RHS2116, showing a mean difference in heart rate of 0.15 ± 4.65 bpm and a Wilcoxon's p value of 0.133. A 24 h continuous recording session of ECG and EMG is conducted to demonstrate the robustness and stability of the device based on extended time wearability on a daily routine.

Naphthalene Benzimidazole Based Neutral Ir(III) Emitters for Deep Red Organic Light-Emitting Diodes.

Rigid naphthalene benzimidazole (NBI) based ligands (L1 and L2) are synthesized and utilized to make deep red phosphorescent cyclometalated iridium(III) complexes ([Ir(NBI)2(PyPzCF3)] (1) and [Ir(DPANBI)2(PyPzCF3)] (2)). Complexes 1 and 2 are prepared from the reaction of L1/L2 with the aid of ancillary ligands (PyPzCF3, 2-(3-(trifluoromethyl)-1H-pyrazol-5-yl)pyridine) in a two step method. The complexes are characterized by analytical and spectroscopic methods, as well as X-ray diffraction for 1. These complexes show a strong emission in the range of 635-700 nm that extends up to the near-infrared region (800 nm). The introduction of the diphenylamino (DPA) donor group on the naphthalene unit leads to a further red-shift in the emission. The complexes exhibit radiative quantum efficiency (ΦPL) of 0.27-0.29 in poly(methylmethacrylate) film and relatively short phosphorescence decay lifetimes (τ = 1.1-3.5 µs). The structural, electronic, and optical properties are investigated with the support of density functional theory (DFT) and time-dependent-DFT calculations. The calculation results indicate that the lowest-lying triplet (T1) excited state of 1 has a mixed metal-to-ligand charge transfer (3MLCT) and ligand-centered (3LC) character, while 2 shows a dominant 3LC character. Deep red-emitting organic light-emitting diodes fabricated using 1 as a dopant display a maximum external quantum efficiency of 10.9% with the CIE color coordinates of (0.690, 0.294), with an emission centered at 644 and 700 nm. Similarly, the emitter 2 also shows a maximum external quantum efficiency of 6.9% with emissions at 657 and 722 nm.

Ping-Pong Free Advanced and Energy Efficient Sensor Relocation for IoT-Sensory Network.

With the growing interest in big data technology, mobile IoT devices play an essential role in data collection. Generally, IoT sensor nodes are randomly distributed to areas where data cannot be easily collected. Subsequently, when data collection is impossible (i.e., sensing holes occurrence situation) due to improper placement of sensors or energy exhaustion of sensors, the sensors should be relocated. The cluster header in the sensing hole sends requests to neighboring cluster headers for the sensors to be relocated. However, it can be possible that sensors in the specific cluster zones near the sensing hole are continuously requested to move. With this knowledge, there can be a ping-pong problem, where the cluster headers in the neighboring sensing holes repeatedly request the movement of the sensors in the counterpart sensing hole. In this paper, we first proposed the near-uniform selection and movement scheme of the sensors to be relocated. By this scheme, the energy consumption of the sensors can be equalized, and the sensing capability can be extended. Thus the network lifetime can be extended. Next, the proposed relocation protocol resolves a ping-pong problem using queues with request scheduling. Another crucial contribution of this paper is that performance was analyzed using the fully-customed OMNeT++ simulator to reflect actual environmental conditions, not under over-simplified artificial network conditions. The proposed relocation protocol demonstrates a uniform and energy-efficient movement with ping-pong free capability.

Energy and Distance-Aware Hopping Sensor Relocation for Wireless Sensor Networks.

Recent advances in big data technology collecting and analyzing large amounts of valuable data have attracted a lot of attention. When the information in non-reachable areas is required, IoT wireless sensor network technologies have to be applied. Sensors fundamentally have energy limitations, and it is almost impossible to replace energy-depleted sensors that have been deployed in an inaccessible region. Therefore, moving healthy sensors into the sensing hole will recover the faulty sensor area. In rough surfaces, hopping sensors would be more appropriate than wheel-driven mobile sensors. Sensor relocation algorithms to recover sensing holes have been researched variously in the past. However, the majority of studies to date have been inadequate in reality, since they are nothing but theoretical studies which assume that all the topology in the network is known and then computes the shortest path based on the nonrealistic backing up knowledge-The topology information. In this paper, we first propose a distributed hopping sensor relocation protocol. The possibility of movement of the hopping sensor is also considered to recover sensing holes and is not limited to applying the shortest path strategy. Finally, a performance analysis using OMNeT++ has demonstrated the solidification of the excellence of the proposed protocol.

Stretchable OLEDs based on a hidden active area for high fill factor and resolution compensation.

Stretchable organic light-emitting diodes (OLEDs) have emerged as promising optoelectronic devices with exceptional degree of freedom in form factors. However, stretching OLEDs often results in a reduction in the geometrical fill factor (FF), that is the ratio of an active area to the total area, thereby limiting their potential for a broad range of applications. To overcome these challenges, we propose a three-dimensional (3D) architecture adopting a hidden active area that serves a dual role as both an emitting area and an interconnector. For this purpose, an ultrathin OLED is first attached to a 3D rigid island array structure through quadaxial stretching for precise, deformation-free alignment. A portion of the ultrathin OLED is concealed by letting it 'fold in' between the adjacent islands in the initial, non-stretched condition and gradually surfaces to the top upon stretching. This design enables the proposed stretchable OLEDs to exhibit a relatively high FF not only in the initial state but also after substantial deformation corresponding to a 30% biaxial system strain. Moreover, passive-matrix OLED displays that utilize this architecture are shown to be configurable for compensation of post-stretch resolution loss, demonstrating the efficacy of the proposed approach in realizing the full potential of stretchable OLEDs.

Brain hypothyroidism silences the immune response of microglia in Alzheimer's disease animal model.

Thyroid hormone (TH) imbalance is linked to the pathophysiology of reversible dementia and Alzheimer's disease (AD). It is unclear whether tissue hypothyroidism occurs in the AD brain and how it affects on AD pathology. We find that decreased iodothyronine deiodinase 2 is correlated with hippocampal hypothyroidism in early AD model mice before TH alterations in the blood. TH deficiency leads to spontaneous activation of microglia in wild-type mice under nonstimulated conditions, resulting in lowered innate immune responses of microglia in response to inflammatory stimuli or amyloid-ß. In AD model mice, TH deficiency aggravates AD pathology by reducing the disease-associated microglia population and microglial phagocytosis. We find that TH deficiency reduces microglial ecto-5'-nucleotidase (CD73) and inhibition of CD73 leads to impaired innate immune responses in microglia. Our findings reveal that TH shapes microglial responses to inflammatory stimuli including amyloid-ß, and brain hypothyroidism in early AD model mice aggravates AD pathology by microglial dysfunction.

Heteroleptic Ir(III)-based near-infrared organic light-emitting diodes with high radiance capacity.

Near-infrared organic light-emitting diodes (NIR OLEDs) with heavy metals are regularly reported due to the advantages of their various applications in healthcare services, veil authentication, and night vision displays. For commercial applications, it is necessary to look at radiance capacity (RC) instead of radiance because of power consumption. However, recent papers still reported only simple high radiance performance and do not look at device from the point of view of RC. To overcome this hurdle, we designed Ir(III)-based heteroleptic NIR materials with two types of auxiliary ligand. The proposed emitters achieve a highly oriented horizontal dipole ratio (Ir(mCPDTiq)2tmd, complex 1: 80%, Ir(mCPDTiq)2acac, complex 2: 81%) with a short radiative lifetime (1: 386 ns, 2: 323 ns). The device also shows an extremely low turn-on voltage (Von) of 2.2 V and a high RC of 720 mW/sr/m2/V. The results on the Von and RC of the device is demonstrated an outstanding performance among the Ir(III)-based NIR OLEDs with a similar emission peak.

AKR1C2 Promotes Metastasis and Regulates the Molecular Features of Luminal Androgen Receptor Subtype in Triple Negative Breast Cancer Cells.

PURPOSE: Patients with triple-negative breast cancer (TNBC) have an increased risk of distant metastasis compared to those with other subtypes. In this study, we aimed to identify the genes associated with distant metastasis in TNBC and their underlying mechanisms. METHODS: We established patient-derived xenograft (PDX) models using surgically resected breast cancer tissues from 31 patients with TNBC. Among these, 15 patients subsequently developed distant metastases. Candidate metastasis-associated genes were identified using RNA sequencing. In vitro wound healing, proliferation, migration, and invasion assays and in vivo tumor xenograft and metastasis assays were performed to determine the functional importance of aldo-keto reductase family 1 member C2 (AKR1C2). Additionally, we used the METABRIC dataset to investigate the potential role of AKR1C2 in regulating TNBC subtypes and their downstream signaling activities. RESULTS: RNA sequencing of primary and PDX tumors showed that genes involved in steroid hormone biosynthesis, including AKR1C2, were significantly upregulated in patients who subsequently developed metastasis. In vitro and in vivo assays showed that silencing of AKR1C2 resulted in reduced cell proliferation, migration, invasion, tumor growth, and incidence of lung metastasis. AKR1C2 was upregulated in the luminal androgen receptor (LAR) subtype of TNBC in the METABRIC dataset, and AKR1C2 silencing resulted in the downregulation of LAR classifier genes in TNBC cell lines. The androgen receptor (AR) gene was a downstream mediator of AKR1C2-associated phenotypes in TNBC cells. AKR1C2 expression was associated with gene expression pathways that regulate AR expression, including JAK-STAT signaling or interleukin 6 (IL-6). The levels of phospho-signal transducer and activator of transcription and IL-6, along with secreted IL-6, were significantly downregulated in AKR1C2-silenced TNBC cells. CONCLUSION: Our data indicate that AKR1C2 is an important regulator of cancer growth and metastasis in TNBC and may be a critical determinant of LAR subtype features.

Toward highly efficient deep-blue OLEDs: Tailoring the multiresonance-induced TADF molecules for suppressed excimer formation and near-unity horizontal dipole ratio.

Boron-based compounds exhibiting a multiresonance thermally activated delayed fluorescence are regarded promising as a narrowband blue emitter desired for efficient displays with wide color gamut. However, their planar nature makes them prone to concentration-induced excimer formation that broadens the emission spectrum, making it hard to increase the emitter concentration without raising CIE y coordinate. To overcome this bottleneck, we here propose o-Tol-ν-DABNA-Me, wherein sterically hindered peripheral phenyl groups are introduced to reduce intermolecular interactions, leading to excimer formation and thus making the pure narrowband emission character far less sensitive to concentration. With this approach, we demonstrate deep-blue OLEDs with y of 0.12 and full width at half maximum of 18 nm, with maximum external quantum efficiency (EQE) of ca. 33%. Adopting a hyperfluorescent architecture, the OLED performance is further enhanced to EQE of 35.4%, with mitigated efficiency roll-off, illustrating the immense potential of the proposed method for energy-efficient deep-blue OLEDs.

OLED catheters for inner-body phototherapy: A case of type 2 diabetes mellitus improved via duodenal photobiomodulation.

Phototherapeutics has shown promise in treating various diseases without surgical or drug interventions. However, it is challenging to use it in inner-body applications due to the limited light penetration depth through the skin. Therefore, we propose an organic light-emitting diode (OLED) catheter as an effective photobiomodulation (PBM) platform useful for tubular organs such as duodenums. A fully encapsulated highly flexible OLED is mounted over a round columnar structure, producing axially uniform illumination without local hotspots. The biocompatible and airtight OLED catheter can operate in aqueous environments for extended periods, meeting the essential requirements for inner-body medical applications. In a diabetic Goto-Kakizaki (GK) rat model, the red OLED catheter delivering 798 mJ of energy is shown to reduce hyperglycemia and insulin resistance compared to the sham group. Results are further supported by the subdued liver fibrosis, illustrating the immense potential of the OLED-catheter-based internal PBM for the treatment of type 2 diabetes and other diseases yet to be identified.

Triple-Negative Breast Cancer-Derived Extracellular Vesicles Promote a Hepatic Premetastatic Niche via a Cascade of Microenvironment Remodeling.

Patients with triple-negative breast cancer (TNBC) often develop metastases in visceral organs including the liver, but the detailed molecular mechanisms of TNBC liver metastasis is not clearly understood. In this study, we tried to dissect the process of premetastatic niche formation in the liver by using patient-derived xenograft (PDX) models of TNBC with different metastatic propensity. RNA sequencing of TNBC PDX models that successfully metastasized to liver showed upregulation of the Cx3cr1 gene in the liver microenvironment. In syngeneic breast cancer models, the Cx3cr1 upregulation in liver preceded the development of cancer cell metastasis and was the result of recruitment of CX3CR1-expressing macrophages. The recruitment was induced by the CX3CL1 production from the liver endothelial cells and this CX3CL1-CX3CR1 signaling in the premetastatic niche resulted in upregulation of MMP9 that promoted macrophage migration and cancer cell invasion. In addition, our data suggest that the extracellular vesicles derived from the breast cancer cells induced the TNFα expression in liver, which leads to the CX3CL1 upregulation. Lastly, the plasma CX3CL1 levels in 155 patients with breast cancer were significantly associated with development of liver metastasis. IMPLICATIONS: Our data provides previously unknown cascades regarding the molecular education of premetastatic niche in liver for TNBC.

A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung.

We present an in-depth single-cell atlas of in vitro multiculture systems on human primary airway epithelium derived from normal and diseased lungs of 27 individual donors. Our large-scale single-cell profiling identified new cell states and differentiation trajectories of rare airway epithelial cell types in human distal lungs. By integrating single-cell datasets of human lung tissues, we discovered immune-primed subsets enriched in lungs and organoids derived from patients with chronic respiratory disease. To demonstrate the full potential of our platform, we further illustrate transcriptomic responses to various respiratory virus infections in vitro airway models. Our work constitutes a single-cell roadmap for the cellular and molecular characteristics of human primary lung cells in vitro and their relevance to human tissues in vivo.

Vertical sleeve gastrectomy induces distinctive transcriptomic responses in liver, fat and muscle.

Vertical sleeve gastrectomy (VSG) is the most commonly performed bariatric/metabolic surgery, exhibiting a high rate of diabetes remission in humans. To elucidate the molecular mechanisms of VSG, we performed transcriptomic analysis of the liver, fat, and muscle in VSG mice. C57BL/6 mice fed a high-fat diet were randomly assigned to sham or VSG surgery. The sham-operated mice were fed ad libitum (sham group) or pair-fed (sham-PF group) matching their food intake to the VSG-operated mice. Comparative transcriptomic analysis of the liver, fat, and muscle using RNA sequencing was performed. VSG reduced body weight and improved glucose tolerance compared to the sham group, but not more than the sham-PF group. Improvement in fatty liver and adipose tissue inflammation was comparable between VSG and sham-PF. However, global gene expression profiles showed distinctive changes in the liver, fat, and muscle of the VSG group compared to both the sham or sham-PF groups. The liver showed the most prominent gene expression changes. Immune response-related pathways were commonly upregulated in the three organs of the VSG group compared to the sham or sham-PF. VSG induces organ-specific gene expression changes in the liver, fat, and muscle, which may play critical roles in metabolic improvements after VSG.

Blue TADF Emitters Based on B-Heterotriangulene Acceptors for Highly Efficient OLEDs with Reduced Efficiency Roll-Off.

The design of robust boron acceptors plays a key role in the development of boron-based thermally activated delayed fluorescence (TADF) emitters for the realization of efficient and stable blue organic light-emitting diodes (OLEDs). Herein, we report a set of donor (D)-acceptor (A)-type blue TADF compounds (1-3) comprising triply bridged triarylboryl acceptors, the so-called B-heterotriangulenes, which differ depending on the identity of one of the bridging groups: methylene (1), dimethylmethylene (2), or oxo (3). The X-ray crystal structures of 2 and 3 reveal a highly twisted D-A connectivity and a completely planar geometry for the B-heterotriangulene rings. All compounds exhibit blue emissions with the unitary photoluminescence quantum yields and small singlet-triplet energy splitting (<0.1 eV) in their doped host films. The compounds exhibit a fast reverse intersystem crossing rate (kRISC ≈ 106 s-1) with short-lived delayed fluorescence (τd ≈ 2 µs), which is found to be promoted by the strong spin-orbit coupling between the local triplet excited state (3LE, T2) and singlet (S1) states. Using compounds 1-3 as the emitters, highly efficient blue TADF-OLEDs are realized. The devices based on the emitters with B-heterotriangulenes exhibit better performances than the device incorporating a singly bridged reference emitter over the whole luminance range. Notably, the device based on the fully dimethylmethylene-bridged emitter (2) achieves the highest maximum external quantum efficiency (EQE) of 28.2% and the lowest efficiency roll-off, maintaining a high EQE value of 21.2% at 1000 cd/m2.

Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts.

Gastric cancer (GC) is commonly treated by chemotherapy using 5-fluorouracil (5-FU) derivatives and platinum combination, but predictive biomarker remains lacking. We develop patient-derived xenografts (PDXs) from 31 GC patients and treat with a combination of 5-FU and oxaliplatin, to determine biomarkers associated with responsiveness. When the PDXs are defined as either responders or non-responders according to tumor volume change after treatment, the responsiveness of PDXs is significantly consistent with the respective clinical outcomes of the patients. An integrative genomic and transcriptomic analysis of PDXs reveals that pathways associated with cell-to-cell and cell-to-extracellular matrix interactions enriched among the non-responders in both cancer cells and the tumor microenvironment (TME). We develop a 30-gene prediction model to determine the responsiveness to 5-FU and oxaliplatin-based chemotherapy and confirm the significant poor survival outcomes among cases classified as non-responder-like in three independent GC cohorts. Our study may inform clinical decision-making when designing treatment strategies.

Wearable Robotic Glove Design Using Surface-Mounted Actuators.

We propose a novel wearable robotic glove or exo-glove design scalable to the variation of the hand kinematics. While most of the traditional robot hand is driven by rotating the joint directly with a rigid body, our exo-glove deforms a robotic finger's skin and, thus, the hand skeleton joints. Multiple tendons woven on the exo-glove's surface can make multi-DOF finger joint motions. We allocated tendons to mimic a hand's intrinsic and extrinsic muscles. Thus, a robotic hand actuated with the exo-glove can perform natural finger motions, including abduction/adduction and flexion/extension of finger joints. Moreover, additional tendons for the thumb enable power grips and the robotic hand's human-like motion. The proposed design approach places all the actuators on the surface without directly actuating any of the hand skeleton's joint. Therefore, a random hand skeleton can work as a robotic hand by putting the wearable robotic glove on it. Thus, the proposed model provides a high degree of freedom on choosing hand skeletons. We expect the aforementioned biomimetic features of our proposed method will benefit not only traditional robotic hands design but also the design of prosthetic hands and robot power-assisted hand glove.

Publisher Correction: Effect of Cutaneous Feedback on the Perception of Virtual Object Weight during Manipulation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.