Integrating spatial and single-cell transcriptomics reveals tumor heterogeneity and intercellular networks in colorectal cancer.

Single cell RNA sequencing (scRNA-seq), a powerful tool for studying the tumor microenvironment (TME), does not preserve/provide spatial information on tissue morphology and cellular interactions. To understand the crosstalk between diverse cellular components in proximity in the TME, we performed scRNA-seq coupled with spatial transcriptomic (ST) assay to profile 41,700 cells from three colorectal cancer (CRC) tumor-normal-blood pairs. Standalone scRNA-seq analyses revealed eight major cell populations, including B cells, T cells, Monocytes, NK cells, Epithelial cells, Fibroblasts, Mast cells, Endothelial cells. After the identification of malignant cells from epithelial cells, we observed seven subtypes of malignant cells that reflect heterogeneous status in tumor, including tumor_CAV1, tumor_ATF3_JUN | FOS, tumor_ZEB2, tumor_VIM, tumor_WSB1, tumor_LXN, and tumor_PGM1. By transferring the cellular annotations obtained by scRNA-seq to ST spots, we annotated four regions in a cryosection from CRC patients, including tumor, stroma, immune infiltration, and colon epithelium regions. Furthermore, we observed intensive intercellular interactions between stroma and tumor regions which were extremely proximal in the cryosection. In particular, one pair of ligands and receptors (C5AR1 and RPS19) was inferred to play key roles in the crosstalk of stroma and tumor regions. For the tumor region, a typical feature of TMSB4X-high expression was identified, which could be a potential marker of CRC. The stroma region was found to be characterized by VIM-high expression, suggesting it fostered a stromal niche in the TME. Collectively, single cell and spatial analysis in our study reveal the tumor heterogeneity and molecular interactions in CRC TME, which provides insights into the mechanisms underlying CRC progression and may contribute to the development of anticancer therapies targeting on non-tumor components, such as the extracellular matrix (ECM) in CRC. The typical genes we identified may facilitate to new molecular subtypes of CRC.

TGF-ß downstream of Smad3 and MAPK signaling antagonistically regulate the viability and partial epithelial-mesenchymal transition of liver progenitor cells.

BACKGROUND: Liver progenitor cells (LPCs) are a subpopulation of cells that contribute to liver regeneration, fibrosis and liver cancer initiation under different circumstances. RESULTS: By performing adenoviral-mediated transfection, CCK-8 analyses, F-actin staining, transwell analyses, luciferase reporter analyses and Western blotting, we observed that TGF-ß promoted cytostasis and partial epithelial-mesenchymal transition (EMT) in LPCs. In addition, we confirmed that TGF-ß activated the Smad and MAPK pathways, including the Erk, JNK and p38 MAPK signaling pathways, and revealed that TGFß-Smad signaling induced growth inhibition and partial EMT, whereas TGFß-MAPK signaling had the opposite effects on LPCs. We further found that the activity of Smad and MAPK signaling downstream of TGF-ß was mutually restricted in LPCs. Mechanistically, we found that TGF-ß activated Smad signaling through serine phosphorylation of both the C-terminal and linker regions of Smad2 and 3 in LPCs. Additionally, TGFß-MAPK signaling inhibited the phosphorylation of Smad3 but not Smad2 at the C-terminus, and it reinforced the linker phosphorylation of Smad3 at T179 and S213. We then found that overexpression of mutated Smad3 at linker phosphorylation sites intensifies TGF-ß-induced cytostasis and EMT, mimicking the effects of MAPK inhibition in LPCs, whereas mutation of Smad3 at the C-terminus caused LPCs to blunt TGF-ß-induced cytostasis and partial EMT. CONCLUSION: These results suggested that TGF-ß downstream of Smad3 and MAPK signaling were mutually antagonistic in regulating the viability and partial EMT of LPCs. This antagonism may help LPCs overcome the cytostatic effect of TGF-ß under fibrotic conditions and maintain partial EMT and progenitor phenotypes.

Spatial enrichment and genomic analyses reveal the link of NOMO1 with amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease with uncertain genetic predisposition in most sporadic cases. Spatial architecture of cell types and gene expression is the basis of cell-cell interactions, biological function and disease pathology, but is not well investigated in human motor cortex, a key ALS relevant brain region. Recent studies indicated single nucleus transcriptomic features of motor neuron vulnerability in ALS motor cortex. However, it remains largely unclear what is the brain regional vulnerability of ALS-associated genes, and what is the genetic link between region-specific genes and ALS risk. Here, we developed an entropy-weighted differential gene expression matrix-based tool (SpatialE) to identify the spatial enrichment of gene sets in spatial transcriptomics (ST). We benchmarked SpatialE against another enrichment tool (Multimodal Intersection Analysis, MIA) using ST data from both human and mouse brain tissues. To investigate regional vulnerability, we analyzed three human motor cortex and two dorsolateral prefrontal cortex tissues for spatial enrichment of ALS-associated genes. We also used Cell2location to estimate the abundance of cell types in ALS-related cortex layers. To dissect the link of regionally expressed genes and ALS risk, we performed burden analyses of rare loss-of-function (LOF) variants detected by whole-genome sequencing in ALS patients and controls, and then analyzed differential gene expression in the TargetALS RNA-seq dataset. SpatialE showed more accurate and specific spatial enrichment of regional cell type markers than MIA in both mouse brain and human dorsolateral prefrontal cortex. Spatial transcriptomic analyses of human motor cortex showed heterogenous cell types and spatial gene expression profiles. We found that 260 manually curated ALS-associated genes are significantly enriched in layer 5 (L5) motor cortex, with abundant expression of upper motor neurons and L5 excitatory neurons. Burden analyses of rare LOF variants in L5-associated genes nominated NOMO1 as a novel ALS-associated gene in a combined sample set of 6,814 ALS patients and 3,324 controls (P = 0.029). Gene expression analyses in central nervous system tissues revealed down-regulation of NOMO1 in ALS, which is consistent with a LOF disease mechanism. In conclusion, our integrated ST and genomic analyses identified regional brain vulnerability in ALS and the association of a L5 gene (NOMO1) with ALS risk.

Generation of a human iPSC line from a Parkinson's disease patient with a novel CHCHD2 mutation (p.R145Q).

Mutations in CHCHD2 have been reported to be associated with familial Parkinson's disease (PD). We generated a human induced pluripotent stem cell (hiPSC) line by reprogramming dermal fibroblasts from a PD patient harboring a novel CHCHD2 mutation (c.434G > A, p.R145Q). This line exhibited human embryonic stem cell (hESC)-like clonal morphology, expression of undifferentiated stem cell markers, a normal karyotype and trilineage differentiation capacity and thus the potential to serve as a model for further investigating the underlying molecular mechanisms of CHCHD2 function in PD.

Influence of shear strain on the electronic properties of monolayers MoS2, WS2, and MoS2/WS2 vdW heterostructure.

CONTEXT: This study investigates the dynamic stability of monolayers MoS2, WS2, and MoS2/WS2 van der Waals heterostructures (vdWHs) and the influence of shear strain on their electronic properties. The computational results of the binding energy and phonon dispersion demonstrate the excellent dynamic stability of MoS2/WS2 vdWHs. The MoS2/WS2 vdWH, with a type-II band alignment and an indirect bandgap, reduces electron-hole recombination, enhancing the efficiency and performance of optoelectronic devices. Under shear strain, the bandgap size and type of monolayers MoS2, WS2, and MoS2/WS2 vdWHs were effectively modulated, along with the interlayer charge redistribution in the MoS2/WS2 vdWHs. This work reveals the tunability of the electronic properties of monolayers MoS2, WS2, and MoS2/WS2 vdWHs under shear strain, offering new possibilities and solutions for developing optoelectronic devices, sensors, and related fields. METHODS: This work employed the CASTEP module within the Materials Studio software package for first-principles calculations. Ultrasoft pseudopotentials were employed during geometry optimizations to account for ion-electron interactions using the GGA-PBE functional for exchange-correlation potentials. The electronic configurations of the S, Mo, and W atoms were chosen as their typical arrangements: (3s2p4), (4s2p6d55s1), and (5s2p6d46s2), respectively. A vacuum layer of 20 Å was added to avoid interactions between the atomic layers. A cutoff energy of 500 eV was set for structural optimization and self-consistent calculations, with k-point grids of 6 × 6 × 1 and 9 × 9 × 1. During the structural optimization process, the energy convergence criterion was set to 1 × 10-5 eV, and the thresholds for interatomic forces and stresses were set to 0.01 eV/Å and 0.01 GPa, respectively. Grimmer's DFT-D2 correction accounted for the interlayer vdW interactions in the MoS2/WS2 vdWH, while the phonon dispersion was calculated using the linear response method.

Clinical features, disease progression, and nuclear imaging in ATXN2-related parkinsonism in a longitudinal cohort.

BACKGROUND: Spinocerebellar ataxia 2 (SCA2) with a low range of CAG repeat expansion of ATXN2 gene can present with predominant or isolated parkinsonism that closely resembles Parkinson's disease (PD). This study is aimed at comparing clinical features, disease progression, and nuclear imaging between ATXN2-related parkinsonism (ATXN2-P) and PD. METHODS: Three hundred and seventy-seven clinically diagnosed PD with family history were screened by multiplex ligation-dependent probe amplification, whole-exome sequencing or target sequencing, and dynamic mutation testing of 10 SCA subtypes. The baseline and longitudinal clinical features as well as the dual-tracer positron emission tomography (PET) imaging were compared between ATXN2-P and genetically undefined familial PD (GU-fPD). RESULTS: Fifteen ATXN2-P patients from 7 families and 50 randomly selected GU-fPD patients were evaluated. Significantly less resting tremor and more symmetric signs were observed in ATXN2-P than GU-fPD. No significant difference was found in motor progression and duration from onset to occurrence of fluctuation, dyskinesia, and recurrent falls between the two groups. Cognitive impairment and rapid-eye-movement sleep behavior disorder were more common in ATXN2-P. During follow-up, olfaction was relatively spared, and no obvious progression of cognition dysfunction evaluated by Mini-Mental State Examination scores was found in ATXN2-P. PET results of ATXN2-P demonstrated a symmetric, diffuse, and homogenous dopamine transporter loss of bilateral striatum and a glucose metabolism pattern inconsistent with that in PD. CONCLUSIONS: Symmetric motor signs and unique nuclear imaging might be the clues to distinguish ATXN2-P from GU-fPD.

Pt-Clusters-Equipped Antioxidase-Like Biocatalysts as Efficient ROS Scavengers for Treating Periodontitis.

Developing high-efficiency artificial biocatalysts for scavenging reactive oxygen species (ROS) is critical for treating inflammation diseases and promoting tissue regeneration. By mimicking the active sites in catalase, here, a Pt-clusters-equipped antioxidase-like biocatalysts (Pt─CN) with superior catalytic abilities for stem cell protection and periodontitis treatment are reported. Owing to the excellent effects of multiple Pt clusters, Pt─CN yields exceptional catalytic ROS-scavenging activities for multiple types of ROS. In vitro studies show that Pt─CN can effectively protect stem cell survival, adhesion, and differentiation in a high ROS levels microenvironment. Additionally, Pt─CN can reduce the M1/M2 ratio of macrophages when stimulated by lipopolysaccharide. In vivo treatment of mouse periodontitis further confirms the protection against bone loss and reduction in the inflammatory response. This study provides a basis for the application of biocatalysts with Pt catalytic center in macrophage polarization, stem cell protection, and periodontitis treatment, thus offering a new strategy for the design of high-performance artificial biocatalysts.

Exploring the degradation mechanism of nickel-copper-molybdenum hydrogen evolution catalysts during intermittent operation.

We investigate the dynamic degradation behaviors of a nickel-copper-molybdenum hydrogen evolution catalyst in a liquid and solid polymer electrolyte to figure out its endurance in a renewable energy-driven electrolyzer. A cathode current protection approach is proposed to achieve a durable electrolyzer during intermittent operation.

singleCellBase: a high-quality manually curated database of cell markers for single cell annotation across multiple species.

Annotating cells in the analysis of single-cell RNA-seq (scRNA-seq) data is one of the most challenging tasks that researchers are actively addressing. Manual cell annotation is generally considered the gold standard method, although it is labor intensive and independent of prior knowledge. At present, the relationship between high-quality, known marker genes and cell types is very limited, especially for a variety of species other than humans and mice. The singleCellBase is a manually curated resource of high-quality cell types and gene markers associations across multiple species. In details, it offers 9,158 entries spanning a total of 1,221 cell types and linking with 8,740 genes (cell markers), covering 464 diseases/status, and 165 types of tissues across 31 species. The singleCellBase provides a user-friendly interface to the scientific community to browse, search, download and submit records of marker genes and cell types. The resource providing ineluctable prior knowledge required by manual cell annotation, which is valuable to interpret scRNA-seq data and elucidate what cell type or cell state that a cell population represents.

Improved interpretation of 18F-florzolotau PET in progressive supranuclear palsy using a normalization-free deep-learning classifier.

While 18F-florzolotau tau PET is an emerging biomarker for progressive supranuclear palsy (PSP), its interpretation has been hindered by a lack of consensus on visual reading and potential biases in conventional semi-quantitative analysis. As clinical manifestations and regions of elevated 18F-florzolotau binding are highly overlapping in PSP and the Parkinsonian type of multiple system atrophy (MSA-P), developing a reliable discriminative classifier for 18F-florzolotau PET is urgently needed. Herein, we developed a normalization-free deep-learning (NFDL) model for 18F-florzolotau PET, which achieved significantly higher accuracy for both PSP and MSA-P compared to semi-quantitative classifiers. Regions driving the NFDL classifier's decision were consistent with disease-specific topographies. NFDL-guided radiomic features correlated with clinical severity of PSP. This suggests that the NFDL model has the potential for early and accurate differentiation of atypical parkinsonism and that it can be applied in various scenarios due to not requiring subjective interpretation, MR-dependent, and reference-based preprocessing.

Continuous On-Site H2O2 Electrosynthesis via Two-Electron Oxygen Reduction Enabled by an Oxygen-Doped Single-Cobalt Atom Catalyst with Nitrogen Coordination.

Single-Co atom catalysts are suggested as an efficient platinum metal group-free catalyst for promoting the oxygen reduction into water or hydrogen peroxide, while the relevance of the catalyst structure and selectivity is still ambiguous. Here, we propose a thermal evaporation method for modulating the chemical environment of single-Co atom catalysts and unveil the effect on the selectivity and activity. It discloses that nitrogen functional groups prefer to proceed the oxygen reduction via a 4e- pathway and notably improve the intrinsic activity, especially when being coordinated with the Co center, while oxygen doping tempts the electron delocalization around cobalt sites and decreases the binding force toward HOO* intermediates, thereby increasing the 2e- selectivity. Consequently, the well-designed oxygen-doped single-Co atom catalysts with nitrogen coordination deliver an impressive 2e- oxygen reduction performance, approaching the onset potential of 0.78 V vs RHE and selectivity of >90%. As an impressive cathode catalyst of an electrochemical flow cell, it generates H2O2 at a rate of 880 mmol gcat-1 h-1 and faradaic efficiency of 95.2%, in combination with an efficient nickel-iron oxygen evolution anode.

Hybridizing Ti3C2Tx Layers with Layered Double Hydroxide Nanosheets at the Molecular Level: A Smart Electrode Material for H2O2 Monitoring in Cancer Cells.

Vertically stacked artificial 2D superlattice hybrids fabricated through molecular-level hybridization in a controlled fashion play a vital role in scientific and technological fields, but developing an alternate assembly of 2D atomic layers with strong electrostatic interactions could be much more challenging. In this study, we have constructed an alternately stacked self-assembled superlattice composite through integration of CuMgAl layered double hydroxide (LDH) nanosheets having positive charge with negatively charged Ti3C2Tx layers using well-controlled liquid-phase co-feeding protocol and electrostatic attraction and investigated its electrochemical performance in sensing early cancer biomarkers, i.e., hydrogen peroxide (H2O2). The molecular-level CuMgAl LDH/Ti3C2Tx superlattice self-assembly possesses superb conductivity and electrocatalytic properties, which are significant for obtaining a high electrochemical sensing aptitude. Electron penetration in Ti3C2Tx layers and rapid ion diffusion along 2D galleries have shortened the diffusion path and enhanced the charge transferring efficacy. The electrode modified with the CuMgAl LDH/Ti3C2Tx superlattice has demonstrated admirable electrocatalytic abilities in H2O2 detection with a wide linear concentration range and low real-time limit of detection (LOD) of 0.1 nM with signal/noise ratio (S/N) = 3. Practically, an electrochemical sensing podium based on the CuMgAl LDH/Ti3C2Tx superlattice has been effectively applied in real-time in vitro tracking of H2O2 effluxes excreted from different live cancer cells and normal cells after being encouraged by stimulation. The results exhibit that molecular-level heteroassembly holds great potential in electrochemical sensors to detect promising biomarkers.

Autosomal dominant Parkinson's disease caused by the recently identified LRRK2 N1437D mutation in a Chinese family: Clinical features, imaging findings, and functional impact.

INTRODUCTION: Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of autosomal dominantly inherited Parkinson's disease (PD). Recently, a novel pathogenic variant (N1437D; c.4309A > G; NM_98578) in the LRRK2 gene has been identified in three Chinese families with PD. In this study, we describe a Chinese family with autosomal dominant PD that segregated with the N1437D mutation. A detailed clinical and neuroimaging characterization of the affected family members is reported. We also sought to investigate the functional mechanisms by which the detected mutation could cause PD. METHODS: We characterized the clinical and imaging phenotype of a Chinese pedigree with autosomal dominant PD. We searched for a disease-causing mutation by targeted sequencing and multiple ligation-dependent probe amplification. The functional impact of the mutation was investigated in terms of LRRK2 kinase activity, guanosine triphosphate (GTP) binding, and guanosine triphosphatase (GTPase) activity. RESULTS: The disease was found to co-segregate with the LRRK2 N1437D mutation. Patients in the pedigree exhibited typical parkinsonism (age at onset: 54.0 ± 5.9 years). One affected family member - who had evidence of abnormal tau accumulation in the occipital lobe on tau PET imaging - developed PD dementia at follow-up. The mutation markedly increased LRRK2 kinase activity and promoted GTP binding, without affecting GTPase activity. CONCLUSIONS: This study describes the functional impact of a recently identified LRRK2 mutation, N1437D, that causes autosomal dominant PD in the Chinese population. Further research is necessary to investigate the contribution of this mutation to PD in multiple Asian populations.

The genetic spectrum of a cohort of patients clinically diagnosed as Parkinson's disease in mainland China.

So far, over 20 causative genes of monogenic Parkinson's disease (PD) have been identified. Some causative genes of non-parkinsonian entities may also manifest with parkinsonism mimicking PD. This study aimed to investigate the genetic characteristics of clinically diagnosed PD with early onset age or family history. A total of 832 patients initially diagnosed with PD were enrolled, of which, 636 were classified into the early-onset group and 196 were classified into the familial late-onset group. The genetic testing included the multiplex ligation-dependent probe amplification and next generation sequencing (target sequencing or whole-exome sequencing). The dynamic variants of spinocerebellar ataxia were tested in probands with family history. In the early-onset group, 30.03% of patients (191/636) harbored pathogenic/likely pathogenic (P/LP) variants in known PD-related genes (CHCHD2, DJ-1, GBA (heterozygous), LRRK2, PINK1, PRKN, PLA2G6, SNCA and VPS35). Variants in PRKN were the most prevalent, accounting for 15.72% of the early-onset patients, followed by GBA (10.22%), and PLA2G6 (1.89%). And 2.52% (16/636) had P/LP variants in causative genes of other diseases (ATXN3, ATXN2, GCH1, TH, MAPT, GBA (homozygous)). In the familial late-onset group, 8.67% of patients (17/196) carried P/LP variants in known PD-related genes (GBA (heterozygous), HTRA2, SNCA) and 2.04% (4/196) had P/LP variants in other genes (ATXN2, PSEN1, DCTN1). Heterozygous GBA variants (7.14%) were the most common genetic cause found in familial late-onset patients. Genetic testing is of vital importance in differential diagnosis especially in early-onset and familial PD. Our findings may also provide some clues to the nomenclature of genetic movement disorders.

Manganese-Based Antioxidase-Inspired Biocatalysts with Axial Mn-N5 Sites and 2D d-π-Conjugated Networks for Rescuing Stem Cell Fate.

Constructing highly effective biocatalysts with controllable coordination geometry for eliminating reactive oxygen species (ROS) to address the current bottlenecks in stem-cell-based therapeutics remains challenging. Herein, inspired by the coordination structure of manganese-based antioxidase, we report a manganese-coordinated polyphthalocyanine-based biocatalyst (Mn-PcBC) with axial Mn-N5 sites and 2D d-π-conjugated networks that serves as an artificial antioxidase to rescue stem cell fate. Owing to the unique chemical and electronic structures, Mn-PcBC displays efficient, multifaceted, and robust ROS-scavenging activities, including elimination of H2 O2 and O2 ⋅- . Consequently, Mn-PcBC efficiently rescues the bioactivity and functionality of stem cells in high-ROS-level microenvironments by protecting the transcription of osteogenesis-related genes. This study offers essential insight into the crucial functions of axially coordinated Mn-N5 sites in ROS scavenging and suggests new strategies to create efficient artificial antioxidases for stem-cell therapies.

Association between Respiratory Function and Motor Function in Different Stages of Parkinson's Disease.

INTRODUCTION: Respiratory dysfunction in patients with Parkinson's disease (PD) could present in the early stage and worsen in the late stages. These changes could be a factor affecting the ability of daily living and quality of life of patients with PD. The primary objective of this study was to assess the respiratory function and its association with motor function in patients with different stages of PD. METHODS: This was a cross-sectional study conducted at the Huashan Hospital of Fudan University in Shanghai, China. The study included 65 patients diagnosed with PD (the Hoehn and Yahr scale between 1 and 4) and 20 healthy individuals of similar age, gender, weight, and height. The ventilatory function was assessed using the spirometry. Motor function was evaluated using subscale III of the United Parkinson's disease rating scale (UPDRS-III). After confirming the normality of data distribution, we performed one-way ANOVA with a Tukey's post hoc test. RESULTS: Compared with the healthy individuals, there was no statistical significance in forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), and forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) in the H&Y 1 group and H&Y 2 group (p > 0.05) but reduced peak expiratory flow (PEF) in the H&Y 2 group (p = 0.002). Reduced FVC, FEV1, and PEF was seen in the H&Y 3 group (p = 0.002, p = 0.001, and p = 0.0001, respectively). Reduced FVC, FEV1, PEF, and FEF25-75% was seen in the H&Y 4 group (p = 0.001, p = 0.0001, p = 0.0001, and p = 0.025, respectively). The correlation analysis revealed that there was a significant negative correlation between FVC and UPDRS-III scores (r = -0.248, p = 0.046), disease duration (r = -0.276, p = 0.026), H&Y scale (r = -0.415, p = 0.001). FEV1 was negatively correlated with UPDRS-III scores (r = -0.277, p = 0.025), disease duration (r = -0.291, p = 0.019), H&Y scale (r = -0.434, p = 0.0001). FEF25-75% was negatively correlated with disease duration (r = -0.247, p = 0.047), H&Y scale (r = -0.278, p = 0.025). CONCLUSION: Our findings revealed that respiratory impairment is present in moderate and advanced PD patients, and directly related to the severity of the disease. It is important to conduct respiratory function test in the clinical practice.

Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.).

Auxin response factor (ARF) is an important transcription factor that regulates the expression of auxin-responsive genes by direct binding to their promoters, which play a central role in plant growth, development, and response to abiotic stresses. The availability of the entire Coix (Coix lacryma-jobi L.) genome sequence provides an opportunity to investigate the characteristics and evolutionary history of the ARF gene family in this medicine and food homology plant for the first time. In this study, a total of 27 ClARF genes were identified based on the genome-wide sequence of Coix. Twenty-four of the 27 ClARF genes were unevenly distributed on 8 chromosomes except Chr 4 and 10, and the remaining three genes (ClARF25-27) were not assigned to any chromosome. Most of the ClARF proteins were predicted to be localized to the nucleus, except ClARF24, which was localized to both the plasma membrane and nucleus. Twenty-seven ClARFs were clustered into six subgroups based on the phylogenetic analysis. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the ClARF gene family. Synteny analysis showed that purifying selection might have been a primary driving force in the development of the ARF gene family in Coix and other investigated cereal plants. The prediction of the cis element of the promoter showed that 27 ClARF genes contain several stress response elements, suggesting that ClARFs might be involved in the abiotic stress response. Expression profile analysis shows that 27 ClARF genes were all expressed in the root, shoot, leaf, kernel, glume, and male flower of Coix with varying expression levels. Furthermore, qRT-PCR analyses revealed that the majority of ClARFs members were upregulated or downregulated in response to hormone treatment and abiotic stress. The current study expands our understanding of the functional roles of ClARFs in stress responses and provides basic information for the ClARF genes.

Single-cell analysis of peripheral blood from high-altitude pulmonary hypertension patients identifies a distinct monocyte phenotype.

Immune and inflammatory responses have an important function in the pathophysiology of pulmonary hypertension (PH). However, little is known about the immune landscape in peripheral circulation in patients with high-altitude pulmonary hypertension (HAPH). We apply single-cell transcriptomics to characterize the monocytes that are significantly enriched in the peripheral blood mononuclear cells (PBMC) of HAPH patients. We discover an increase in C1 (non-classical) and C2 (intermediate) monocytes in PBMCs and a decrease in hypoxia-inducible transcription factor-1α (HIF-1α) in all monocyte subsets associated with HAPH. In addition, we demonstrate that similar immune adaptations may exist in HAPH and PH. Overall, we characterize an immune cell atlas of the peripheral blood in HAPH patients. Our data provide evidence that specific monocyte subsets and HIF-1α downregulation might be implicated in the pathogenesis of HAPH.

Optimized Cingulate Island Sign in Discriminating Dementia With Lewy Bodies From Alzheimer Disease.

PURPOSE: This study aimed to optimize the analysis of cingulate island sign (CIS) to improve its diagnostic accuracy in discriminating dementia with Lewy bodies (DLB) from Alzheimer disease (AD). PATIENTS AND METHODS: Patients with DLB (n = 80), AD (n = 75), and normal controls (n = 22) with 18 F-FDG PET imaging were enrolled in this study. Sixty-two DLB patients also underwent dopaminergic PET scans. The optimized/conventional CIS ratios and metabolism in associated brain regions were evaluated by diagnostic accuracy among groups and correlation with cognitive/dopaminergic dysfunction. RESULTS: In discriminating DLB from AD, the optimized CIS ratio calculated by dorsal posterior cingulate cortex (PCC)/lateral occipital lobe metabolism achieved the highest specificity, sensitivity, and accuracy at 0.907, 0.750, and 0.825, respectively. The metabolism of dorsal-PCC positively correlated with cognitive impairment in DLB patients cross-sectionally and longitudinally ( P < 0.001, r = 0.601; P = 0.044, r = 0.645), and also correlated with dopaminergic impairment in the caudate ( P = 0.048, r = 0.315). CONCLUSIONS: Optimized CIS ratios of incorporated metabolic activity of dorsal-PCC and occipital subregions are clinically useful for differentiating DLB from AD, in which dorsal-PCC metabolism may provide an objective biomarker to reflect the severity of cognitive impairment in DLB.