Differential Modulation Research Articles

Living biodrugs and how tissue source influences mesenchymal stem cell therapeutics for heart failure

In this editorial we comment on the article by Safwan M et al . We especially focused on the cardiac function restoration by the use of mesenchymal stem cells (MSCs) therapy for heart failure (HF), which has emerged as a new treatment approach as “Living Biodrugs”. HF remains a significant clinical challenge due to the heart’s inability to pump blood effectively, despite advancements in medical and device-based therapies. MSCs have emerged as a promising therapeutic approach, offering benefits beyond traditional treatments through their ability to modulate inflammation, reduce fibrosis, and promote endogenous tissue regeneration. MSCs can be derived from various tissues, including bone marrow and umbilical cord. Umbilical cord-derived MSCs exhibit superior expansion capabilities, making them an attractive option for HF therapy. Conversely, bone marrow-derived MSCs have been extensively studied for their potential to improve cardiac function but face challenges related to cell retention and delivery. Future research is focusing on optimizing MSC sources, enhancing differentiation and immune modulation, and improving delivery methods to overcome current limitations.

3D‐Printed In Situ Growth of Bilayer MOF Hydrogels for Accelerated Osteochondral Defect Repair

AbstractRepairing osteochondral (OC) defect presents a significant challenge due to the intricate structural requirements and the unpredictable differentiation pathways of bone marrow mesenchymal stem cells (BMSCs). To address this challenge, a novel biomimetic OC hydrogel scaffold is developed that features a structure of soft and hard components. This scaffold incorporates bilayer metal–organic frameworks (MOFs), specifically ZIF‐67 in the upper layer and ZIF‐8 in the lower layer, achieved through an in situ printing process. This configuration enables the spatial and temporal modulation of BMSC differentiation by controlling the release of Co2⁺ and Zn2⁺. The results demonstrate that the bilayer MOF hydrogels significantly outperform hydrogels that either lack MOFs or contain a single type of MOF in enhancing repair outcomes in rabbit models of knee OC defects. The improved regenerative efficacy is attributed to the distinct chondrogenic and osteogenic differentiation cues provided by the bilayer MOFs, effectively guiding BMSCs toward enhanced tissue regeneration. This customizable biomimetic OC hydrogel scaffold not only opens new avenues for innovative therapeutic strategies but also holds great promise for widespread clinical applications.

The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana

As sessile organisms, the plant immune system plays a vital role in protecting plants from the widespread pathogens in the environment. The Arabidopsis thaliana (Arabidopsis) receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE1 (BIK1) acts as a central regulator during plant immunity. As such, not only the BIK1 protein accumulation but also the attenuation is tightly regulated to ensure effective immune responses. Recent studies have highlighted the critical roles of ubiquitination in maintaining BIK1 homeostasis. Here, we review the latest advances in the ubiquitination of BIK1 in plant immunity, which is mediated by ubiquitin ligases PUB25/26, RHA3A/B, RGLG1/2, and PUB4. Additionally, we summarize and discuss the sites and types of BIK1 ubiquitination. Collectively, these analyses not only illustrate that the differential modifications on BIK1 by multiple ubiquitin ligases hold a crucial position in plant immunity but also provide a good example for future studies on ubiquitin-mediated modifications in plants.

Intraosseous Delivery of Mesenchymal Stem Cells for the Treatment of Bone and Hematological Diseases

Mesenchymal stem cells are used most in regenerative medicine due to their capacities in differentiation and immune modulation. The intraosseous injection of MSC into the bone has been recommended because of expected outcomes for retention, bioavailability, and enhanced therapeutic efficacy, particularly in conditions involving the bone, such as osteoporosis and osteonecrosis. A review of the intraosseous delivery of mesenchymal stem cells in comparison with intravenous and intra-arterial delivery methods will be subjected to critical examination. This delivery mode fares better regarding paracrine signaling and immunomodulation attributes, which are the cornerstone of tissue regeneration and inflammation reduction. The local complications and technical challenges still apply with this method. This study was more focused on further research soon to be conducted to further elucidate long-term safety and efficacy of intraosseous mesenchymal stem cell therapy. Though much has been achieved with very impressive progress in this field, it is worth noting that more studies need to be put into place so that this technique can be established as a routine approach, especially with further research in biomaterials, gene therapy, and personalized medicine.

Untangling the role of tau in sex hormone responsive cancers: lessons learnt from Alzheimer's disease.

Tubulin associated unit has been extensively studied in neurodegenerative diseases including Alzheimer's disease (AD), whereby its hyperphosphorylation and accumulation contributes to disease pathogenesis. Tau is abundantly expressed in the central nervous system but is also present in non-neuronal tissues and in tumours including sex hormone responsive cancers such as breast and prostate. Curiously, hormonal effects on tau also exist in an AD context from numerous studies on menopause, hormone replacement therapy, and androgen deprivation therapy. Despite sharing some risk factors, most importantly advancing age, there are numerous reports from population studies of, currently poorly explained inverse associations between cancer and Alzheimer's disease. We previously reviewed important components of the phosphoinositide-3-kinase/protein kinase B (PI3K/Akt) signalling pathway and their differential modulation in relation to the two diseases. Similarly, receptor tyrosine kinases, estrogen receptor and androgen receptor have all been implicated in the pathogenesis of both cancer and AD. In this review, we focus on tau and its effects in hormone responsive cancer in terms of development, progression, and treatment and in relation to sex hormones and PI3K/Akt signalling molecules including IRS-1, PTEN, Pin1, and p53.

Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during navigation in familiar and novel environments.

Neuromodulatory inputs to the hippocampus play pivotal roles in modulating synaptic plasticity, shaping neuronal activity, and influencing learning and memory. Recently, it has been shown that the main sources of catecholamines to the hippocampus, ventral tegmental area (VTA) and locus coeruleus (LC), may have overlapping release of neurotransmitters and effects on the hippocampus. Therefore, to dissect the impacts of both VTA and LC circuits on hippocampal function, a thorough examination of how these pathways might differentially operate during behavior and learning is necessary. We therefore utilized two-photon microscopy to functionally image the activity of VTA and LC axons within the CA1 region of the dorsal hippocampus in head-fixed male mice navigating linear paths within virtual reality (VR) environments. We found that within familiar environments some VTA axons and the vast majority of LC axons showed a correlation with the animals' running speed. However, as mice approached previously learned rewarded locations, a large majority of VTA axons exhibited a gradual ramping-up of activity, peaking at the reward location. In contrast, LC axons displayed a pre-movement signal predictive of the animal's transition from immobility to movement. Interestingly, a marked divergence emerged following a switch from the familiar to novel VR environments. Many LC axons showed large increases in activity that remained elevated for over a minute, while the previously observed VTA axon ramping-to-reward dynamics disappeared during the same period. In conclusion, these findings highlight distinct roles of VTA and LC catecholaminergic inputs in the dorsal CA1 hippocampal region. These inputs encode unique information, with reward information in VTA inputs and novelty and kinematic information in LC inputs, likely contributing to differential modulation of hippocampal activity during behavior and learning.

Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during navigation in familiar and novel environments

Neuromodulatory inputs to the hippocampus play pivotal roles in modulating synaptic plasticity, shaping neuronal activity, and influencing learning and memory. Recently, it has been shown that the main sources of catecholamines to the hippocampus, ventral tegmental area (VTA) and locus coeruleus (LC), may have overlapping release of neurotransmitters and effects on the hippocampus. Therefore, to dissect the impacts of both VTA and LC circuits on hippocampal function, a thorough examination of how these pathways might differentially operate during behavior and learning is necessary. We therefore utilized two-photon microscopy to functionally image the activity of VTA and LC axons within the CA1 region of the dorsal hippocampus in head-fixed male mice navigating linear paths within virtual reality (VR) environments. We found that within familiar environments some VTA axons and the vast majority of LC axons showed a correlation with the animals’ running speed. However, as mice approached previously learned rewarded locations, a large majority of VTA axons exhibited a gradual ramping-up of activity, peaking at the reward location. In contrast, LC axons displayed a pre-movement signal predictive of the animal’s transition from immobility to movement. Interestingly, a marked divergence emerged following a switch from the familiar to novel VR environments. Many LC axons showed large increases in activity that remained elevated for over a minute, while the previously observed VTA axon ramping-to-reward dynamics disappeared during the same period. In conclusion, these findings highlight distinct roles of VTA and LC catecholaminergic inputs in the dorsal CA1 hippocampal region. These inputs encode unique information, with reward information in VTA inputs and novelty and kinematic information in LC inputs, likely contributing to differential modulation of hippocampal activity during behavior and learning.

Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt-Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica).

Salinity stress induces ionic and osmotic imbalances in rice plants that in turn negatively affect the photosynthesis rate, resulting in growth retardation and yield penalty. Efforts have, therefore, been carried out to understand the mechanism of salt tolerance, however, the complexity of biological processes at proteome levels remains a major challenge. Here, we performed a comparative proteome and phosphoproteome profiling of microsome enriched fractions of salt-tolerant (cv. IR73; indica) and salt-susceptible (cv. Dongjin/DJ; japonica) rice varieties. This approach led to the identification of 5856 proteins, of which 473 and 484 proteins showed differential modulation between DJ and IR73 sample sets, respectively. The phosphoproteome analysis led to the identification of a total of 10,873 phosphopeptides of which 2929 and 3049 phosphopeptides showed significant differences in DJ and IR73 sample sets, respectively. The integration of proteome and phosphoproteome data showed activation of ABA and Ca2+ signaling components exclusively in the salt-tolerant variety IR73 in response to salinity stress. Taken together, our results highlight the changes at proteome and phosphoproteome levels and provide a mechanistic understanding of salinity stress tolerance in rice.

FedGen: Personalized federated learning with data generation for enhanced model customization and class imbalance

Federated learning has emerged as a prominent solution for the collaborative training of machine learning models without exchanging local data. However, existing approaches often impose rigid constraints on model heterogeneity, limiting the ability of clients to customize unique models and increasing the vulnerability of models to potential attacks. This paper presents FedGen, a novel personalized federated learning framework based on generative adversarial networks (GANs). FedGen shifts the focus from training task-specific models to generating data, especially for minority classes with imbalanced data. With FedGen, clients can gain knowledge from others by training generators, while maintaining a heterogeneous local model and avoiding sharing model information with other participants. Moreover, to address challenges arising from imbalanced data, we propose AT-GAN, a novel generative model incorporating pseudo augmentation and differentiable augmentation modules to foster healthy competition between the generator and discriminator. To evaluate the effectiveness of our approach, we conduct extensive experiments on real-world tabular datasets. The experimental results demonstrate that FedGen significantly enhances the performance of local models, achieving improvements of up to 11.92% in F1 score and up to 9.14% in MCC score compared to existing methods.

Differential modulation of polycomb-associated histone marks by cBAF, pBAF, and gBAF complexes.

Chromatin regulators alter the physical properties of chromatin to make it more or less permissive to transcription by modulating another protein's access to a specific DNA sequence through changes in nucleosome occupancy or histone modifications at a particular locus. Mammalian SWI/SNF complexes are a group of ATPase-dependent chromatin remodelers. In mouse embryonic stem cells, there are three primary forms of mSWI/SNF: canonical BAF (cBAF), polybromo-associated BAF (pBAF), and GLTSCR-associated BAF (gBAF). Nkx2-9 is bivalent, meaning nucleosomes at the locus have active and repressive modifications. In this study, we used unique BAF subunits to recruit each of the three complexes to Nkx2-9 using dCas9-mediated inducible recruitment (FIRE-Cas9). We show that recruitment of cBAF complexes leads to a significant loss of the polycomb repressive-2 H3K27me3 histone mark and polycomb repressive-1 and repressive-2 complex proteins, whereas gBAF and pBAF do not. Moreover, nucleosome occupancy alone cannot explain the loss of these marks. Our results demonstrate that cBAF has a unique role in the direct opposition of polycomb-associated histone modifications that gBAF and pBAF do not share.

Differential contributions of fetal mononuclear phagocytes to Zika virus neuroinvasion versus neuroprotection during congenital infection.

Fetal immune cell functions during congenital infections are poorly understood. Zika virus (ZIKV) can vertically transmit from mother to fetus, causing nervous system infection and congenital ZIKV syndrome (CZS). We identified differential functional roles for fetal monocyte/macrophage cell types and microglia in ZIKV dissemination versus clearance using mouse models. Trafficking of ZIKV-infected primitive macrophages from the yolk sac allowed initial fetal virus inoculation, while recruited monocytes promoted non-productive neuroinflammation. Conversely, brain-resident differentiated microglia were protective, limiting infection and neuronal death. Single-cell RNA sequencing identified transcriptional profiles linked to the protective versus detrimental contributions of mononuclear phagocyte subsets. In human brain organoids, microglia also promoted neuroprotective transcriptional changes and infection clearance. Thus, microglia are protective before birth, contrasting with the disease-enhancing roles of primitive macrophages and monocytes. Differential modulation of myeloid cell phenotypes by genetically divergent ZIKVs underscores the potential of immune cells to regulate diverse outcomes during fetal infections.

Elucidation of pineapple softening based on cell wall polysaccharides degradation during storage

The degradation of cell wall polysaccharides in pineapple fruit during softening was investigated in the present study. Two pectin fractions and two hemicellulose fractions were extracted from the cell wall materials of ‘Comte de Paris’ pineapple fruit at five softening stages, and their compositional changes were subsequently analyzed. The process of softening of the fruit corresponded to an increase in the water-soluble pectin (WSP) and 1 M KOH-soluble hemicellulose (HC1) fractions, and a decrease in the acid-soluble pectin (ASP) fraction, which suggested the solubilization and conversion of cellular wall components. However, the content of 4 M KOH-soluble hemicellulose (HC2) decreased and then returned to the initial level. Furthermore, WSP, ASP, and HC1 showed an increment in the content of low molecular weight polymers while a decline in the high molecular weight polymers throughout softening, and not significant change in the contents of different molecular polymers of HC2 was observed. Moreover, the galacturonic acid (GalA) content in the main chain of WSP was maintained at a relatively constant level, but the major branch monosaccharide galactose (Gal) in WSP decreased. Different from WSP, the molar percentages of Gal and GalA in ASP decreased. The Gal or Arabinose (Ara) in HC1 exhibited a gradual decline while the molar percentages of xylose (Xyl) and glucose (Glu) in the main chain increased. These suggested that the main chain of ASP degraded while the branched chains of ASP, WSP and HC1 depolymerized during pineapple softening. Overall, fruit softening of ‘Comte de Paris’ pineapple was found to be the result of differential modification of pectin and hemicellulose.

Environmental Stress Drives Transgenerational Epigenetic Inheritance Through miR-212/132 Expression Upregulation

This is a research proposal on environmental induced transgenerational epigenetic inheritance. This work focus on pressure on food supply lead to a modification in miR-212/132 expression that result in an increased feeding of mice, and is inherited by the transfer of the miRNAs from hippocampus to sperm. Experiments including behavior tests, miRNA differential expression, gene knock-out, and nucleotide modification are proposed to prove the hypothesis. Once carried out, the research is going to help expand the understanding of transgenerational epigenetic inheritance, explore the cause of inherited obesity susceptibility, and contribute to public health.

Differential modulations of theta and beta oscillations by audiovisual congruency in letter-speech sound integration.

The integration of visual letters and speech sounds is a crucial part of learning to read. Previous studies investigating this integration have revealed a modulation by audiovisual (AV) congruency, commonly known as the congruency effect. To investigate the cortical oscillations of the congruency effects across different oscillatory frequency bands, we conducted a Japanese priming task in which a visual letter was followed by a speech sound. We analyzed the power and phase properties of oscillatory activities in the theta and beta bands between congruent and incongruent letter-speech sound (L-SS) pairs. Our results revealed stronger theta-band (5-7Hz) power in the congruent condition and cross-modal phase resetting within the auditory cortex, accompanied by enhanced inter-trial phase coherence (ITPC) in the auditory-related areas in response to the congruent condition. The observed congruency effect of theta-band power may reflect increased neural activities in the left auditory region during L-SS integration. Additionally, theta ITPC findings suggest that visual letters amplify neuronal responses to the following corresponding auditory stimulus, which may reflect the differential cross-modal influences in the primary auditory cortex. In contrast, decreased beta-band (20-35 Hz) oscillatory power was observed in the right centroparietal regions for the congruent condition. The reduced beta power seems to be unrelated to the processing of AV integration, but may be interpreted as the brain response to predicting auditory sounds during language processing. Our data provide valuable insights by indicating that oscillations in different frequency bands contribute to the disparate aspects of L-SS integration.

Differential modulation of hormonal pathways by strigolactone and karrikin signaling

Differential modulation of hormonal pathways by strigolactone and karrikin signaling

Integrated analysis of muscle lncRNA and mRNA of Chinese indigenous breed Ningxiang pig in four developmental stages.

Meat and its derivatives serve as crucial sources of protein, vitamins, minerals, and other essential nutrients for humans. Pork stands as China's primary animal-derived food product consumed widely across diverse dietary structures; evaluating intramuscular fat content becomes pivotal in assessing its quality standards. Nonetheless, the intricate molecular mechanisms governing intramuscular fat deposition remain elusive. Our study utilized sequencing technology to scrutinize longitudinal development stages within Ningxiang pig's longest dorsal muscles aiming to unravel these underlying mechanisms. In three distinct comparisons (30d vs. 90d, 90d vs. 150d and 150d vs. 210d) there were 578, 1,000 and 3,238 differentially expressed mRNA, along with 16, 158 and 85 lncRNAs were identified. STEM analysis unveiled six enriched model profiles for lncRNAs while seven such profiles emerged for mRNAs; notably, multiple shared model profiles existed between both RNA types. Enriched analysis highlighted numerous genes from mRNA profile8 and lncRNA profile7 significantly associated with pathways linked to fat deposition. Weight Gene Co-Expression Network Analysis (WGCNA) revealed that differential expression modules (DMEs) & differential expression lncRNAs primarily clustered within cyan, dark slate blue and pale turquoise modules. Furthermore, target genes PKD2 (MSTRG21592.MTRSG8859 and MTRSG18175), COL5A1 (MTRSG9969 and MTRSG180) and SOX13 (MTRSG21592 and MTRSG9088) as core components all intricately tied into processes related to fat deposition. This study lays the groundwork for deeper exploration into the molecular mechanisms underlying LDM fat deposition traits, and it also presents candidate genes for future molecular marker-assisted breeding.

DNA methylation profiles of transgenerational rat hyperactivity primed by silver nanoparticles: Comparison with valproate model rats of autism

There is an increasing body of evidence suggesting that a single exposure to certain chemicals can have transgenerational effects, with the underlying mechanism believed to be epigenetic. However, it remains largely unknown whether psychiatric conditions like ADHD or autism, induced by environmental chemicals, can be inherited across generations. Pregnant rats were purchased from a commercial breeder. On the 7th day of gestation (E7), they were divided into two groups: one group was orally exposed to silver nanoparticles (AgNP; 4 mg/kg), while the control group received vehicle alone. The subsequent generation (F1) underwent spontaneous motor activity (SMA) measurements at 8–11 weeks of age. For breeding at 26 weeks of age, rats with higher SMA were selected from hyperactive litters, while untreated rats were randomly selected. This process was continued for four generations in both groups. The AgNP-primed rats at 4th generation displayed significantly higher SMA, 1.8 times greater than that of untreated rats. Intraperitoneal injection of valproic acid (150 mg/kg), an epigenetic modifier to 5-day-old rats causes adult hyperactivity (1.4-fold), suggesting that epigenetic modification contributes to rat hyperactivity. Global DNA methylation profiles in the mesencephalon were positively correlated in both groups of hyperactive rats. Furthermore, there were 7–8 common genes showing both hypermethylation and hypomethylation, which are involved in neuronal development, neuronal function, transcriptional activity, DNA binding activity, cell differentiation, ubiquitination processes, or histone modification, including Pax 6 and Mecp 2. Thus, it is most likely that rats retain hyperactivity through mesencephalic DNA methylation status across transgeneration.

Mapping the epigenomic landscape of post-traumatic stress disorder in human cortical neurons.

The study conducted a comprehensive genome-wide analysis of differential 5mC and 5hmC modifications at both CpG and non-CpG sites in postmortem orbitofrontal neurons from 25 PTSD cases and 13 healthy controls. It was observed that PTSD patients exhibit a greater number of differential 5hmC sites compared to 5mC sites. Specifically, individuals with PTSD tend to show hyper-5mC/5hmC at CpG sites, particularly within CpG islands and promoter regions, and hypo-5mC/5hmC at non-CpG sites, especially within intragenic regions. Functional enrichment analysis indicated distinct yet interconnected roles for 5mC and 5hmC in PTSD. The 5mC marks primarily regulate cell-cell adhesion processes, whereas 5hmC marks are involved in embryonic morphogenesis and cell fate commitment. By integrating published PTSD findings from central and peripheral tissues through multi-omics approaches, several biological mechanisms were prioritized, including developmental processes, HPA axis regulation, and immune responses. Based on the consistent enrichment in developmental processes, we hypothesize that if epigenetic changes occur during early developmental stages, they may increase the risk of developing PTSD following trauma exposure. Conversely, if these epigenetic changes occur in adulthood, they may influence neuronal apoptosis and survival mechanisms.

Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder.

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Past molecular studies of AUD used underpowered single cell analysis or bulk homogenates of postmortem brain tissue, which obscures gene expression changes in specific cell types. Here we performed single nuclei RNA-sequencing analysis of 73 post-mortem samples from individuals with AUD (N=36, Nnuclei= 248,873) and neurotypical controls (N=37, Nnuclei= 210,573) in both sexes across two institutional sites. We identified 32 clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glia. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and co-expression modules linked to AUD. Analysis for cell type-specific enrichment of aggregate genetic risk for AUD identified subtypes of glial and neuronal cell types as potential key players not only affected by but causally linked to the progression of AUD. Most of the enrichments for genetic risk for AUD were in glial cell types. These results highlight the importance of cell-type specific molecular changes in AUD and offer opportunities to identify novel targets for treatment.

Adipose-Derived Mesenchymal Stem Cells from Arthritis Patients: Differential Modulation of CD4⁺ T Cell Activation and Cytokine Production.

BACKGROUND Adipose-derived stem cells (ASCs) from intra-articular adipose tissue of osteoarthritis (OA) and rheumatoid arthritis (RA) patients similarly regulate the proliferation of activated CD4⁺ T lymphocytes and exhibit comparable differentiation potential. This study aimed to assess the impact of ASCs from RA patients on CD4⁺ T cell activation and differentiation into Th17 and T regulatory (Treg) cells. MATERIAL AND METHODS Intra-articular adipose tissue samples were obtained from patients with RA and OA, who underwent knee replacement surgery. ASCs were isolated and cultured either with isolated CD4⁺ cells or with peripheral blood mononuclear cells. After culture, CD4⁺ T cell phenotype was evaluated by flow cytometry, and cytokine concentrations in culture supernatants were analyzed via ELISA. Blocking experiments were conducted to identify the soluble agents responsible for the immunomodulatory effects of ASCs. RESULTS RA- and OA-derived ASCs effectively modulated CD25 and CD69 expression on CD4⁺ cells. RA-derived ASCs failed to induce Tregs, decreased HLA-DR expression, and increased IL-35 production. RA- and OA-derived ASCs reduced TNF and IFN-γ production but increased IL-17 production. The immunomodulatory activities of ASCs were linked to the kynurenine pathway and prostaglandin E2. CONCLUSIONS This study indicates that ASCs modulate the phenotype of CD4⁺ T cells and influence the production of both pro-inflammatory and anti-inflammatory cytokines. However, ASCs from RA patients appear to have impaired immunomodulatory abilities, raising concerns about their therapeutic potential. Further research is needed to enhance our understanding of ASCs biology and their therapeutic utility.