Extracellular architecture of the SYG-1/SYG-2 adhesion complex instructs synaptogenesis.

SYG-1 and SYG-2 are multipurpose cell adhesion molecules (CAMs) that have evolved across all major animal taxa to participate in diverse physiological functions, ranging from synapse formation to formation of the kidney filtration barrier. In the crystal structures of several SYG-1 and SYG-2 orthologs and their complexes, we find that SYG-1 orthologs homodimerize through a common, bispecific interface that similarly mediates an unusual orthogonal docking geometry in the heterophilic SYG-1/SYG-2 complex. C. elegans SYG-1's specification of proper synapse formation in vivo closely correlates with the heterophilic complex affinity, which appears to be tuned for optimal function. Furthermore, replacement of the interacting domains of SYG-1 and SYG-2 with those from CAM complexes that assume alternative docking geometries or the introduction of segmental flexibility compromised synaptic function. These results suggest that SYG extracellular complexes do not simply act as "molecular velcro" and that their distinct structural features are important in instructing synaptogenesis. PAPERFLICK:

The Coding Logic of Interoception.

Interoception, the ability to precisely and timely sense internal body signals, is critical for life. The interoceptive system monitors a large variety of mechanical, chemical, hormonal, and pathological cues using specialized organ cells, organ innervating neurons, and brain sensory neurons. It is important for maintaining body homeostasis, providing motivational drives, and regulating autonomic, cognitive, and behavioral functions. However, compared to external sensory systems, our knowledge about how diverse body signals are coded at a system level is quite limited. In this review, we focus on the unique features of interoceptive signals and the organization of the interoceptive system, with the goal of better understanding the coding logic of interoception.

RETICULON-LIKE PROTEIN B2 is a proviral factor co-opted for the biogenesis of viral replication organelles in plants.

Endomembrane remodeling to form a viral replication complex (VRC) is crucial for a virus to establish infection in a host. Although the composition and function of VRCs have been intensively studied, host factors involved in the assembly of VRCs for plant RNA viruses have not been fully explored. TurboID-based proximity labeling (PL) has emerged as a robust tool for probing molecular interactions in planta. However, few studies have employed the TurboID-based PL technique for investigating plant virus replication. Here, we used Beet black scorch virus (BBSV), an endoplasmic reticulum (ER)-replicating virus, as a model and systematically investigated the composition of BBSV VRCs in Nicotiana benthamiana by fusing the TurboID enzyme to viral replication protein p23. Among the 185 identified p23-proximal proteins, the reticulon family of proteins showed high reproducibility in the mass spectrometry data sets. We focused on RETICULON-LIKE PROTEIN B2 (RTNLB2) and demonstrated its proviral functions in BBSV replication. We showed that RTNLB2 binds to p23, induces ER membrane curvature, and constricts ER tubules to facilitate the assembly of BBSV VRCs. Our comprehensive proximal interactome analysis of BBSV VRCs provides a resource for understanding plant viral replication and offers additional insights into the formation of membrane scaffolds for viral RNA synthesis.

Cyclin-G-associated kinase GAK/dAux regulates autophagy initiation via ULK1/Atg1 in glia.

Autophagy is a major means for the elimination of protein inclusions in neurons in neurodegenerative diseases such as Parkinson's disease (PD). Yet, the mechanism of autophagy in the other brain cell type, glia, is less well characterized and remains largely unknown. Here, we present evidence that the PD risk factor, Cyclin-G-associated kinase (GAK)/Drosophila homolog Auxilin (dAux), is a component in glial autophagy. The lack of GAK/dAux increases the autophagosome number and size in adult fly glia and mouse microglia, and generally up-regulates levels of components in the initiation and PI3K class III complexes. GAK/dAux interacts with the master initiation regulator UNC-51like autophagy activating kinase 1/Atg1 via its uncoating domain and regulates the trafficking of Atg1 and Atg9 to autophagosomes, hence controlling the onset of glial autophagy. On the other hand, lack of GAK/dAux impairs the autophagic flux and blocks substrate degradation, suggesting that GAK/dAux might play additional roles. Importantly, dAux contributes to PD-like symptoms including dopaminergic neurodegeneration and locomotor function in flies. Our findings identify an autophagy factor in glia; considering the pivotal role of glia under pathological conditions, targeting glial autophagy is potentially a therapeutic strategy for PD.

A versatile fluorescence-quenched substrate for quantitative measurement of glucocerebrosidase activity within live cells.

Loss of activity of the lysosomal glycosidase ß-glucocerebrosidase (GCase) causes the lysosomal storage disease Gaucher disease (GD) and has emerged as the greatest genetic risk factor for the development of both Parkinson disease (PD) and dementia with Lewy bodies. There is significant interest into how GCase dysfunction contributes to these diseases, however, progress toward a full understanding is complicated by presence of endogenous cellular factors that influence lysosomal GCase activity. Indeed, such factors are thought to contribute to the high degree of variable penetrance of GBA mutations among patients. Robust methods to quantitatively measure GCase activity within lysosomes are therefore needed to advance research in this area, as well as to develop clinical assays to monitor disease progression and assess GCase-directed therapeutics. Here, we report a selective fluorescence-quenched substrate, LysoFQ-GBA, which enables measuring endogenous levels of lysosomal GCase activity within living cells. LysoFQ-GBA is a sensitive tool for studying chemical or genetic perturbations of GCase activity using either fluorescence microscopy or flow cytometry. We validate the quantitative nature of measurements made with LysoFQ-GBA using various cell types and demonstrate that it accurately reports on both target engagement by GCase inhibitors and the GBA allele status of cells. Furthermore, through comparisons of GD, PD, and control patient-derived tissues, we show there is a close correlation in the lysosomal GCase activity within monocytes, neuronal progenitor cells, and neurons. Accordingly, analysis of clinical blood samples using LysoFQ-GBA may provide a surrogate marker of lysosomal GCase activity in neuronal tissue.

Ion-Sieve-Confined Synthesis of Size-Tunable Ru for Electrochemical Hydrogen Evolution.

The controllable and low-cost synthesis of nanometal particles is highly desired in scientific and industrial research. Herein, size-tunable Ru nanoparticles were synthesized by using a novel ion-sieve-confined reduction method. The H2TiO3 ion-sieve was used to adsorb Ru3+ into the hydroxyl-enriched porous [TiO3]2- layers. The confined environment of the interlayer space facilitates Ru-Ru collision and bonding during annealing, achieving a precise reduction from Ru3+ to Ru0 without additional reductants. Owing to the confinement effect, Ru0 nanoparticles are uniformly embedded in the pores on the surface of the postannealed TiO2 matrix (Ru@TiO2). Ru@TiO2 exhibited a lower overpotential than Pt/C (57 vs 87 mV at 10 mA cm-2) for the HER in 0.1 M KOH solution. The confinement-induced reduction of metal ions was also preliminarily proved in ion-exchanged zeolites, which provides facile and abundant approaches for the size-controllable synthesis of nanometal catalysts with high catalytic activity.

Natriuretic peptide receptor-C perturbs mitochondrial respiration in white adipose tissue.

Natriuretic peptide receptor-C (NPR-C) is highly expressed in adipose tissues and regulates obesity-related diseases; however, the detailed mechanism remains unknown. In this research, we aimed to explore the potential role of NPR-C in cold exposure and high-fat/high-sugar (HF/HS) diet-induced metabolic changes, especially in regulating white adipose tissue (WAT) mitochondrial function. Our findings showed that NPR-C expression, especially in epididymal WAT (eWAT), was reduced after cold exposure. Global Npr3 (gene encoding NPR-C protein) deficiency led to reduced body weight, increased WAT browning, thermogenesis, and enhanced expression of genes related to mitochondrial biogenesis. RNA-sequencing of eWAT showed that Npr3 deficiency enhanced the expression of mitochondrial respiratory chain complex genes and promoted mitochondrial oxidative phosphorylation in response to cold exposure. In addition, Npr3 KO mice were able to resist obesity induced by HF/HS diet. Npr3 knockdown in stromal vascular fraction (SVF)-induced white adipocytes promoted the expression of proliferator-activated receptor gamma coactivator 1α (PGC1α), uncoupling protein one (UCP1), and mitochondrial respiratory chain complexes. Mechanistically, NPR-C inhibited cGMP and calcium signaling in an NPR-B-dependent manner but suppressed cAMP signaling in an NPR-B-independent manner. Moreover, Npr3 knockdown induced browning via AKT and p38 pathway activation, which were attenuated by Npr2 knockdown. Importantly, treatment with the NPR-C-specific antagonist, AP-811, decreased WAT mass and increased PGC-1α, UCP1, and mitochondrial complex expression. Our findings reveal that NPR-C deficiency enhances mitochondrial function and energy expenditure in white adipose tissue, contributing to improved metabolic health and resistance to obesity.

Genome-wide identification and expressional analysis of carotenoid cleavage oxygenase (CCO) gene family in Betula platyphylla under abiotic stress.

BACKGROUND: Carotenoid cleavage oxygenases (CCOs) are a group of enzymes that catalyze the oxidative cleavage of carotenoid molecules. These enzymes widely exist in plants, fungi, and certain bacteria, and are involved in various biological processes. It would be of great importance and necessity to identify CCO members in birch and characterize their responses upon abiotic stresses. RESULTS: A total of 16 BpCCOs, including 8 BpCCDs and 8 BpNCEDs were identified in birch, and phylogenetic tree analysis showed that they could be classified into six subgroups. Collinearity analysis revealed that BpCCOs have the largest number of homologous genes in Gossypium hirsutum and also have more homologous genes in other dicotyledons. In addition, promoter analysis revealed that the promoter regions of BpCCOs contained many abiotic stress-related and hormone-responsive elements. The results of qRT-PCR showed that most of the BpCCOs were able to respond significantly to ABA, PEG, salt and cold stresses. Finally, the prediction of the interacting proteins of BpCCOs by STRING revealed several proteins that may interact with BpCCOs and be involved in plant growth and development/abiotic stress processes, such as HEC1 (bHLH), ATABA1, ATVAMP714, etc. CONCLUSION: In this study, the CCO members were identified in birch in a genome-wide scale. These results indicate that BpCCO genes may play important roles in the abiotic stress responses of birch plants.

Genome-wide identification and expression analysis of the ADH gene family under diverse stresses in tobacco (Nicotiana tabacum L.).

BACKGROUND: Alcohol dehydrogenases (ADHs) are the crucial enzymes that can convert ethanol into acetaldehyde. In tobacco, members of ADH gene family are involved in various stresses tolerance reactions, lipid metabolism and pathways related to plant development. It will be of great application significance to analyze the ADH gene family and expression profile under various stresses in tobacco. RESULTS: A total of 53 ADH genes were identified in tobacco (Nicotiana tabacum L.) genome and were grouped into 6 subfamilies based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were highly conserved among the NtADH genes, especially the members within the same subfamily. A total of 5 gene pairs of tandem duplication, and 3 gene pairs of segmental duplication were identified based on the analysis of gene duplication events. Cis-regulatory elements of the NtADH promoters participated in cell development, plant hormones, environmental stress, and light responsiveness. The analysis of expression profile showed that NtADH genes were widely expressed in topping stress and leaf senescence. However, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 13 NtADH genes displayed their differential expression pattern in response to the bacterial pathogen Ralstonia solanacearum L. INFECTION: Metabolomics analysis revealed that NtADH genes were primarily associated with carbohydrate metabolism, and moreover, four NtADH genes (NtADH20/24/48/51) were notably involved in the pathway of alpha-linolenic acid metabolism which related to the up-regulation of 9-hydroxy-12-oxo-10(E), 15(Z)-octadecadienoic acid and 9-hydroxy-12-oxo-15(Z)-octadecenoic acid. CONCLUSION: The genome-wide identification, evolutionary analysis, expression profiling, and exploration of related metabolites and metabolic pathways associated with NtADH genes have yielded valuable insights into the roles of these genes in response to various stresses. Our results could provide a basis for functional analysis of NtADH gene family under stressful conditions.

Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

BACKGROUND: The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS: A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION: The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.

Ultralow Thermal Conductivity of a Chalcogenide System Pt3Bi4Q9 (Q = S, Se) Driven by the Hierarchy of Rigid [Pt6Q12]12- Clusters Embedded in Soft Bi-Q Sublattice.

Knowledge of structure-property relationships in solids with intrinsic low thermal conductivity is crucial for fields such as thermoelectrics, thermal barrier coatings, and refractories. Herein, we propose a new "rigidness in softness" structural scheme for intrinsic low lattice thermal conductivity (κL), which embeds rigid clusters into the soft matrix to induce large lattice anharmonicity, and accordingly discover a new series of chalcogenides Pt3Bi4Q9 (Q = S, Se). Pt3Bi4S9-xSex (x = 3, 6) achieved an intrinsic ultralow κL down to 0.39 W/(m K) at 773 K, which is considerably low among the Bi chalcogenide thermoelectric materials. Pt3Bi4Q9 contains the rigid cubic [Pt6Q12]12- clusters embedded in the soft Bi-Q sublattice, involving multiple bonding interactions and vibration hierarchy. The hierarchical structure yields a large lattice anharmonicity with high Grüneisen parameters (γ) 1.97 of Pt3Bi4Q9, as verified by the effective scatter of low-lying optical phonons toward heat-carrying acoustic phonons. Consequently, the rigid-soft coupling significantly inhibits heat propagation, exhibiting low acoustic phonon frequencies (∼25 cm-1) and Debye temperatures (ΘD = 170.4 K) in Pt3Bi4Se9. Owing to the suppressed κL and considerable power factor (PF), the ZT value of Pt3Bi4S6Se3 can reach 0.56 at 773 K without heavy carrier doping, which is competitive among the pristine Bi chalcogenides. Theoretical calculations predicted a large potential for performance improvement via proper doping, indicating the great potential of this structure type for promising thermoelectric materials.

Exciton Localization Modulated by Ultradeep Moiré Potential in Twisted Bilayer γ-Graphdiyne.

Twisted moiré superlattice is featured with its moiré potential energy, the depth of which renders an effective approach to strengthening the exciton-exciton interaction and exciton localization toward high-performance quantum photonic devices. However, it remains as a long-standing challenge to further push the limit of moiré potential depth. Herein, owing to the pz orbital induced band edge states enabled by the unique sp-C in bilayer γ-graphdiyne (GDY), an ultradeep moiré potential of ∼289 meV is yielded. After being twisted into the hole-to-hole layer stacking configuration, the interlayer coupling is substantially intensified to augment the lattice potential of bilayer GDY up to 475%. The presence of lateral constrained moiré potential shifts the spatial distribution of electrons and holes in excitons from the regular alternating mode to their respective separated and localized mode. According to the well-established wave function distribution of electrons contained in excitons, the AA-stacked site is identified to serve for exciton localization. This work extends the materials systems available for moiré superlattice design further to serial carbon allotropes featured with benzene ring-alkyne chain coupling, unlocking tremendous potential for twistronic-based quantum device applications.

Screening and anti-angiogenesis activity of Chiloscyllium plagiosum anti-human VEGFR2 single-domain antibody.

Recently, the incidence of malignant tumors is on the rise and searching for new treatments on it has become the research priority. Blocking the vascular endothelial growth factor (VEGF) and its receptor (VEGFR) is one of the treatment strategies that used in the development of specific anti-angiogenic drugs. The deficiencies in tissue penetration and affinity maturation become the weakness of these drugs in anti-tumors applications. The single heavy chain antibody found in Chiloscyllium plagiosum, which has a low molecular weight and superior tissue penetration of variable region (variable new antigen receptor, VNARs), was considered to have the high antigen-binding activity and stability. This type of antibody has a simple structure that can be prokaryoticaly expressed, which makes it easily to produce new antiangiogenic target drugs. Specific anti-IgNAR rabbit multiple antibodies have been used to assess the level of VNARs in sharks and have shown a significant enrichment of IgNAR after triple immunization. An anti-VEGFR2 phage library was used for the targeted VNARs screening, and five candidate VNARs sequences were subsequently obtained by phage screening, followed by combined screening with the transcriptome library, and analysis of conserved regions along with 3D modelling matched the VNAR profile. ELISA and cell-based assays showed that two of the VNARs, VNAR-A6, and VNAR-E3, had a superior antigen affinity and anti-angiogenic activity thereby being able to inhibit human Umbilical Vein Endothelial Cells proliferation and migration. The anti-VEGFR2 VNARs derived from the immunized C. plagiosum and screened by phage library, which provide the new research ideas and specific approaches for the development of new drugs. The anti-VEGFR2 VNARs are capable for blocking the VEGF-VEGFR pathway, which of these may contribute to expanding the use of anti-angiogenic drugs.

Constructing maps between distinct cell fates and parametric conditions by systematic perturbations.

MOTIVATION: Cell fate transitions are common in many developmental processes. Therefore, identifying the mechanisms behind them is crucial. Traditionally, due to complexity of networks and existence of plenty of kinetic parameters, dynamical analysis of biomolecular networks can only be performed by simultaneously perturbing a small number of parameters. Although many efforts have focused on how cell states change under specific perturbations, conversely, how to infer parametric conditions underlying distinct cell fates by systematic perturbations is less clear and needs to be further investigated. RESULTS: In this article, we present a general computational method by integrating systematic perturbations, unsupervised clustering, principal component analysis, and fitting analysis. The method can be used to to construct maps between distinct cell fates and parametric conditions by systematic perturbations. In particular, there are no needs of accurate parameter measurements and occurrence of bifurcations to establish the maps. To validate feasibility and inference performance of the method, we use toggle switch, inner cell mass, and epithelial mesenchymal transition as model systems to show how the maps are constructed and how system parameters encode essential information on cell fates. The maps tell us how systematic perturbations drive cell fate decisions and transitions, and allow us to purposefully predict, manipulate, and even control cell states. The approach is especially helpful in understanding crucial roles of certain parameter combinations during fate transitions. We hope that the approach can provide us valuable information on parametric or perturbation conditions so some specific targets, e.g. directional differentiation, can be realized. AVAILABILITY AND IMPLEMENTATION: No public data are used. The data we used are generated by randomly chosen values of model parameters in certain ranges, and the corresponding parameters are already attached in supplementary materials.

Atom-based optical polarization modulator.

In this work, we employ 87Rb atoms as rotation media to manipulate the polarization of optical fields in both magnetic and magnetic-free environments. Employing the nonlinear magneto-optical rotation mechanism, we achieve a state-of-the-art magneto-optical rotation coefficient of 1.74×108 rad⋅T-1⋅m-1 which is four orders of magnitude higher than commonly employed materials. Additionally, in a magnetic-free environment, we achieve all-optical cross-polarization modulation between the pump and probe light via Rb atoms. The nonlinear magneto-optical rotation configuration introduces inventive techniques for a new type of magneto-optical modulator while the all-optical configuration paves the way for exploring photonic integrated circuit (PIC) devices free from disruptions caused by electrical or magnetic crosstalk.

Translation and validation of a simplified Chinese version of the psychosocial assessment tool.

BACKGROUND: The Psychosocial Assessment Tool (PAT2.0) is widely used to assess psychosocial risk in families of children with cancer. Our study aims to apply PAT2.0 to Chinese patients and assess the reliability, content validity, and construct validity of the Chinese version. METHODS: A total of 161 participants completed the study, each with only one child diagnosed with cancer. Psychometric evaluations, including internal consistency, score distribution, test-retest reliability, and construct validity, were conducted. RESULTS: Cronbach's alpha values ranged from 0.732 to 0.843, indicating good internal consistency. Additionally, intraclass correlation coefficient values ranged from 0.869 to 0.984, indicating excellent test-retest reliability. The Simplified Chinese version of PAT2.0 demonstrated high construct validity in factor analyses and correlations with the General Functioning Subscale of the Family Assessment Device. CONCLUSION: The translation process of the Chinese version of PAT2.0 was successful, proving its applicability for psychosocial evaluation and interventions in families of children with cancer in China.

BeEAM vs. BEAM: evaluating conditioning regimens for autologous stem cell transplantation in patients with relapsed or refractory DLBCL.

PURPOSE: To evaluate whether BeEAM is an alternative to BEAM for autologous stem cell transplantation (ASCT) in patients with relapsed or refractory diffuse large B-cell lymphoma (DLBCL). METHODS: Data of 60 patients with relapsed or refractory DLBCL who underwent ASCT from January 2018 to June 2023 in our center, including 30 patients in the BeEAM group and 30 patients in the BEAM group, were retrospectively analyzed. The time to hematopoietic reconstitution, treatment-related adverse events, number of hospitalization days, hospitalization cost, and survival benefit were compared between the two groups. RESULTS: The clinical characteristics of the patients did not significantly differ between the two groups. The median number of reinfused CD34 + cells was 5.06 × 106/kg and 5.17 × 106/kg in the BeEAM and BEAM groups, respectively, which did not significantly different (p = 0.8829). In the BeEAM and BEAM groups, the median time to neutrophil implantation was 10.2 and 10.27 days, respectively (p = 0.8253), and the median time to platelet implantation was 13.23 and 12.87 days, respectively (p = 0.7671). In the BeEAM and BEAM groups, the median hospitalization duration was 30.37 and 30.57 days, respectively (p = 0.9060), and the median hospitalization cost was RMB 83,425 and RMB 96,235, respectively (p = 0.0560). The hospitalization cost was lower in the BeEAM group. The most common hematologic adverse events were grade ≥ 3 neutropenia and thrombocytopenia, whose incidences were similar in the two groups. The most common non-hematologic adverse events were ≤ grade 2 and the incidences of these events did not significantly differ between the two groups. Median overall survival was not reached in either group, with predicted 5-year overall survival of 72.5% and 60% in the BeEAM and BEAM groups, respectively (p = 0.5872). Five-year progression-free survival was 25% and 20% in the BeEAM and BEAM groups, respectively (p = 0.6804). CONCLUSION: As a conditioning regimen for relapsed or refractory DLBCL, BeEAM has a desirable safety profile and is well tolerated, and its hematopoietic reconstitution time, number of hospitalization days, and survival benefit are not inferior to those of BEAM. BeEAM has a lower hospitalization cost and is an alternative to BEAM.

Hypomethylating agents (HMAs) show benefit in AML rather than in intermediate/high-risk MDS based on genetic mutations in epigenetic modification (EMMs): from a retrospective study.

Since HMAs were recommended for treatments in AML and MDS, we wondered whether HMAs could provide similar benefit to AML and intermediate/high-risk MDS under the direction of next-generation sequencing. Here we retrospectively analyzed the prognosis of 176 AML and 128 intermediate/high-risk MDS patients treated with HMAs or non-HMA regimens. For AML, HMAs regimen was related to better CR rate compared with non-HMA regimen in elder cohort, while the situation was the opposite in younger cohort. In consolidation phase, EMM (+) patients could benefit from HMAs regimen. Relapsed AML patients receiving HMAs regimen rather than non-HMA regimen had better post-relapse survival. Multivariate analysis identified HMA regimen as an independent prognostic factor for OS in EMM (+) cohort. For intermediate/high-risk MDS patients not undergoing HSCT, however, HMA regimen showed no survival advantage in EMM (+) cohort and was conversely associated with shorter survival in EMM (-) cohort compared with non-HMA regimen. And among those undergoing HSCT, HMA prior to HSCT predicted poor prognosis compared with upfront HSCT regardless of the existence of EMMs. Therefore, HMAs had better therapeutic value in AML rather than in intermediate/high-risk MDS based on EMMs.

Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis.

One of the most significant challenges in biology is to elucidate the roles of various regulatory interactions in cell fate decision and transition. However, it remains to be fully clarified how they cooperate and determine fate transition. Here, a general framework based on statistical analysis and bifurcation theory is proposed to identify crucial regulatory interactions and how they play decisive roles in fate transition. More exactly, specific feedback loops determine occurrence of bifurcations by which cell fate transition can be realized. While regulatory interactions in the feedback loops determine the direction of transition. In addition, two-parameter bifurcation analysis further provides detailed understanding of how the fate transition based on statistical analysis occurs. Statistical analysis can also be used to reveal synergistic combinatorial perturbations by which fate transition can be more efficiently realized. The integrative analysis approach can be used to identify critical regulatory interactions in cell fate transition and reveal how specific cell fate transition occurs. To verify feasibility of the approach, the epithelial to mesenchymal transition (EMT) network is chosen as an illustrative example. In agreement with experimental observations, the approach reveals some critical regulatory interactions and underlying mechanisms in cell fate determination and transitions between three states. The approach can also be applied to analyze other regulatory networks related to cell fate decision and transition.

Epigenetic and integrative cross-omics analyses of cerebral white matter hyperintensities on MRI.

Cerebral white matter hyperintensities on MRI are markers of cerebral small vessel disease, a major risk factor for dementia and stroke. Despite the successful identification of multiple genetic variants associated with this highly heritable condition, its genetic architecture remains incompletely understood. More specifically, the role of DNA methylation has received little attention. We investigated the association between white matter hyperintensity burden and DNA methylation in blood at ∼450 000 cytosine-phosphate-guanine (CpG) sites in 9732 middle-aged to older adults from 14 community-based studies. Single CpG and region-based association analyses were carried out. Functional annotation and integrative cross-omics analyses were performed to identify novel genes underlying the relationship between DNA methylation and white matter hyperintensities. We identified 12 single CpG and 46 region-based DNA methylation associations with white matter hyperintensity burden. Our top discovery single CpG, cg24202936 (P = 7.6 × 10-8), was associated with F2 expression in blood (P = 6.4 × 10-5) and co-localized with FOLH1 expression in brain (posterior probability = 0.75). Our top differentially methylated regions were in PRMT1 and in CCDC144NL-AS1, which were also represented in single CpG associations (cg17417856 and cg06809326, respectively). Through Mendelian randomization analyses cg06809326 was putatively associated with white matter hyperintensity burden (P = 0.03) and expression of CCDC144NL-AS1 possibly mediated this association. Differentially methylated region analysis, joint epigenetic association analysis and multi-omics co-localization analysis consistently identified a role of DNA methylation near SH3PXD2A, a locus previously identified in genome-wide association studies of white matter hyperintensities. Gene set enrichment analyses revealed functions of the identified DNA methylation loci in the blood-brain barrier and in the immune response. Integrative cross-omics analysis identified 19 key regulatory genes in two networks related to extracellular matrix organization, and lipid and lipoprotein metabolism. A drug-repositioning analysis indicated antihyperlipidaemic agents, more specifically peroxisome proliferator-activated receptor-alpha, as possible target drugs for white matter hyperintensities. Our epigenome-wide association study and integrative cross-omics analyses implicate novel genes influencing white matter hyperintensity burden, which converged on pathways related to the immune response and to a compromised blood-brain barrier possibly due to disrupted cell-cell and cell-extracellular matrix interactions. The results also suggest that antihyperlipidaemic therapy may contribute to lowering risk for white matter hyperintensities possibly through protection against blood-brain barrier disruption.