Differential Activation Research Articles

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical outcomes. Current in silico approaches dovetail differential abundance, biostatistics, and machine learning, but often overlook non-linear proteomic dynamics, like post-translational modifications, and provide limited biological interpretability beyond feature ranking. We introduce APNet, a novel computational pipeline that combines differential activity analysis based on SJARACNe co-expression networks with PASNet, a biologically-informed sparse deep learning model, to perform explainable predictions for COVID-19 severity. The APNet driver-pathway network ingests SJARACNe co-regulation and classification weights to aid result interpretation and hypothesis generation. APNet outperforms alternative models in patient classification across three COVID-19 proteomic datasets, identifying predictive drivers and pathways, including some confirmed in single-cell omics and highlighting under-explored biomarker circuitries in COVID-19. APNet's R, Python scripts and Cytoscape methodologies are available at https://github.com/BiodataAnalysisGroup/APNet. Supplementary information can be accessed in Zenodo (10.5281/zenodo.14680520).

Terminal differentiation and persistence of effector regulatory T cells essential for preventing intestinal inflammation.

Regulatory T (Treg) cells are a specialized CD4+ T cell lineage with essential anti-inflammatory functions. Analysis of Treg cell adaptations to non-lymphoid tissues that enable their specialized immunosuppressive and tissue-supportive functions raises questions about the underlying mechanisms of these adaptations and whether they represent stable differentiation or reversible activation states. Here, we characterize distinct colonic effector Treg cell transcriptional programs. Attenuated T cell receptor (TCR) signaling and acquisition of substantial TCR-independent functionality seems to facilitate the terminal differentiation of a population of colonic effector Treg cells that are distinguished by stable expression of the immunomodulatory cytokine IL-10. Functional studies show that this subset of effector Treg cells, but not their expression of IL-10, is indispensable for colonic health. These findings identify core features of the terminal differentiation of effector Treg cells in non-lymphoid tissues and their function.

Measurement of differential activation by heart-rate-variability for youth MDD discrimination.

Major depression disorder (MDD) is a common illness that severely limits psychosocial functioning and diminishes quality of life, particularly in young adults. Thus, it is imperial to identify MDD youth patients efficiently. This study aims to determine whether differential activation (DA) oriented recognizers can work efficiently. This study collected heart rate variability (HRV) data and demographic information from 50 youth patients diagnosed with MDD and 53 healthy control participants. We developed six datasets, comprising baseline, stress, rest, differential activation period, Difference values between rest and stress period and combined dataset. From the provided data sets, we have developed machine learning models and also deep learning models. We then proceed to compare the performance metrics. Models that utilized DA period and integration data sets exhibited superior performance compared to others. The deep learning model based on Long Short-Term Memory model we developed demonstrated the highest performance among all the models in each data set. Specifically, in the integration dataset, the model attained a mean cross-validation accuracy of 0.806 (95% Confidential Interval (CI) 0.785-0.827), with a mean Area under Receiver Operating Characteristic Curve of 0.805 (95% CI 0.784-0.826) and a mean Area under the Precision-Recall Curve of 0.863 (95% CI 0.848-0.878). The combination of DA theory and HRV record provides a new insight and also an efficient way for youth MDD identification.

Neural processes of emotional conflict detection and prediction of posttraumatic stress disorder symptom clusters in traumatic injury survivors.

Given the prevalence and significant burden of posttraumatic stress disorder (PTSD), identifying early predictors of symptom development following trauma is critical. PTSD is a heterogeneous disorder comprised of distinct symptom clusters-reexperiencing, avoidance, negative mood, and hyperarousal-that contribute to the broad range of possible symptom profiles. Affective and attentional regulation processes, such as emotional conflict detection, are impaired in individuals with PTSD; however, the neural mechanisms underlying these alterations and their predictive utility for the development of PTSD symptoms remain unclear. Traumatic injury survivors (N = 49) without traumatic brain injury were recruited from the emergency department of an urban, Level-1 trauma center. Within 1 month of trauma exposure, participants completed a well-characterized emotional conflict task during a functional magnetic resonance imaging scan. Participants returned 6-month later for a clinical assessment of PTSD symptoms. Using a region-of-interest mask derived from whole-brain voxelwise analyses during emotional conflict detection (vs. no emotional conflict detection) we examined whether differential neural activity predicted 6-month PTSD symptom cluster severity. Greater activation of the right middle frontal gyrus during emotional conflict detection prospectively predicted lower PTSD avoidance symptom severity 6 months later (above and beyond the effects of self-reported baseline PTSD and depressive symptoms, previous traumatic life events, racial discrimination, age, sex, and injury severity). Neural processes of emotion conflict detection measured in the early aftermath of a potentially traumatic event are useful as predictors for the development of PTSD symptoms. (PsycInfo Database Record (c) 2025 APA, all rights reserved).

The differential physiological responses to heat stress in the scleractinian coral Pocillopora damicornis are affected by its energy reserve.

The scleractinian corals conduct various responses upon heat stress such as bleaching and tissue loss, and colonies from the same coral species can conduct differential physiological activities with the biochemical basis unknown. In the present study, factors that influence the heat stress responses in coral Pocillopora damicornis were investigated. It was observed that P. damicornis conducted three differential physiological responses under heat treatment including tissue loss, bleaching, and polyp bailout. During heat response process, coral colonies conducting tissue loss had significantly higher total antioxidant capacity (T-AOC) level, while the bleached coral colonies exhibited higher caspase-3 activation level. Moreover, the stress response varied based on the energy reserve status. Colonies with higher lipid and sugar reserves were more likely to bleach, while those with lower reserves tended to undergo polyp bailout. We demonstrate that energy reserves influence the heat response patterns of P. damicornis. Colonies with higher lipid and sugar reserves may survive longer under heat stress, suggesting that these energy reserves contribute to their heat resistance. This study suggests that colonies with higher energy reserves prior to thermal stress may have greater thermal resistance, indicating that long-term environmental stressors that deplete energy reserves could increase susceptibility to thermal stress.

Tideglusib enhances ALP activity and upregulates RANKL expression in Osteoblast-macrophage Co-cultures within a 3D collagen scaffold.

Tideglusib (Tx) is known for its osteogenic potential, yet its effects on the interplay between osteoblasts and M1 macrophages remain underexplored. This in vitro study aimed to isolate and evaluate both the individual and combined roles of M1 macrophages and osteoblasts in macrophage differentiation and osteoblast function, specifically focusing on how these interactions influence protein expression of osteogenesis and osteoclastogenesis in the presence or absence of Tx. Osteoblast and macrophage cells were co-cultured in direct contact for 24 and 48 h, with or without the presence of Tx. ALP activity, the expression of inflammatory-related genes using RT-qPCR, and histological analyses were performed. Co-culturing osteoblasts and M1 macrophages with Tx increased alkaline phosphatase production, indicative of enhanced osteoblast activity. Histological assessments revealed that Tx treatment contributed to the stability and maintenance of cell morphology within the scaffold, suggesting a supportive environment for cell viability and function. Tx significantly reduced the expression of pro-inflammatory markers, such as TNF-α and IL-1β, in the co-culture at both 24 and 48 h Tx also effectively inhibited osteoclastogenic differentiation in macrophages, thereby diminishing their pro-inflammatory phenotype. Tx increased ALP activity and produced a significant up-regulation of RANKL expression, indicating enhanced osteoblast differentiation and osteoclast activation. Tx mitigates macrophage-driven inflammation. Tx may enhance bone regeneration by modulating inflammatory responses and preserving cell integrity.

Tumor Cell Spatial Organization Directs EGFR/RAS/RAF Pathway Primary Therapy Resistance through YAP Signaling.

Non-small cell lung cancers (NSCLC) harboring common mutations in EGFR and KRAS characteristically respond transiently to targeted therapies against those mutations, but invariably, tumors recur and progress. Resistance often emerges through mutations in the therapeutic target or activation of alternative signaling pathways. Mechanisms of acute tumor cell resistance to initial EGFR (EGFRi) or KRASG12C (G12Ci) pathway inhibition remain poorly understood. Our study reveals that acute response to EGFR/RAS/RAF-pathway inhibition is spatial and culture context specific. In vivo, EGFR mutant tumor xenografts shrink by > 90% following acute EGFRi therapy, and residual tumor cells are associated with dense stroma and have increased nuclear YAP. Interestingly, in vitro EGFRi induced cell cycle arrest in NSCLC cells grown in monolayer, while 3D spheroids preferentially die upon inhibitor treatment. We find differential YAP nuclear localization and activity, driven by the distinct culture conditions, as a common resistance mechanism for selective EGFR/KRAS/BRAF pathway therapies. Forced expression of the YAPS127A mutant partially protects cells from EGFR-mediated cell death in spheroid culture. These studies identify YAP activation in monolayer culture as a non-genetic mechanism of acute EGFR/KRAS/BRAF therapy resistance, highlighting that monolayer vs spheroid cell culture systems can model distinct stages of patient cancer progression.

Differential Neuronal Activation of Nociceptive Pathways in Neuropathic Pain After Spinal Cord Injury

Neuropathic pain, a prevalent complication following spinal cord injury (SCI), severely impairs the life quality of patients. No ideal treatment exists due to incomplete knowledge on underlying neural processes. To explore the SCI-induced effect on nociceptive circuits, the protein expression of c-Fos was analyzed as an indicator of neuronal activation in a rat contusion model exhibiting below-level pain. Additional stimuli were delivered to mimic the different peripheral sensory inputs in daily life. Following noxious rather than innocuous or no stimulation, a greater number of spinal dorsal horn (DH) neurons were activated after SCI, mainly in the deep DH. SCI facilitated the activation of excitatory but not inhibitory DH neurons. Moreover, excitatory interneurons expressing protein kinase C gamma (PKCγ) in laminae II–III, which are known to play a role in mechanical allodynia after peripheral nerve injury, responded in larger amounts to both innocuous and noxious stimulation following SCI. Accordingly, more spinal projection neurons in lamina I were activated. Within supraspinal nuclei processing pain, differentially enhanced activation in response to noxious stimulation was detected after SCI, with a significant increase in the locus coeruleus and medial thalamus, a slight increase in the periaqueductal gray and dorsal raphe, and no change in the lateral parabrachial nucleus or primary sensory cortex. These findings indicated differential hyperexcitability along the sensory neuroaxis following SCI, with a particular emphasis on the involvement of specific neuron subtypes, such as spinal PKCγ interneurons and locus coeruleus noradrenergic neurons, which may serve as crucial targets for potential therapies.Graphical Rats exhibiting pain like behavior after spinal cord injury showed increased engagement of specific subtypes of spinal excitatory neurons and enhanced activity in supraspinal nuclei. The figure was created using Figdraw 2.0.

Brain activation patterns and dopaminergic neuron activity in response to conspecific advertisement calls in reproductive vs. non-reproductive male plainfin midshipman fish (Porichthys notatus).

The plainfin midshipman fish (Porichthys notatus) relies on the production and reception of social acoustic signals for reproductive success. During spawning, male midshipman produce long duration advertisement calls to attract females, which use their auditory sense to locate and access calling males. While seasonal changes based on reproductive state in inner-ear auditory sensitivity and frequency encoding in midshipman is well documented, little is known about reproductive-state dependent changes in central auditory sensitivity and auditory neural responsiveness to conspecific advertisement calls. Previous research indicates that forebrain dopaminergic neurons are preferentially active in response to conspecific advertisement calls and during female auditory-driven behavior in the breeding season. These dopamine neurons project to both the inner ear and central auditory nuclei and contribute to regulation of inner-ear auditory sensitivity based on reproductive state. The present study tested the hypothesis that exposure to the male advertisement call would elicit differential activation in auditory brain nuclei and in the forebrain auditory-projecting dopaminergic nucleus in reproductive vs. non-reproductive male midshipman. Fish were collected during the spring reproductive and winter non-reproductive months and were exposed to a playback of the advertisement call or ambient noise (control). Immunohistochemistry identified activated neurons (pS6-ir; proxy for neural activation) in midbrain and forebrain auditory and dopaminergic nuclei. Our results revealed that in key auditory and dopaminergic areas, the greatest activation (most pS6-ir cells) occurred in reproductive males exposed to the advertisement call.

Analysis of TNS3-203 and LRRFIP1-211 Transcripts as Oral Cancer Biomarkers.

A recent pan-cancer transcriptome analysis indicated differential activity of alternative promoters of genes TNS3 and LRRFIP1 in head and neck squamous cell carcinoma compared to non-cancerous tissue. The promoters upregulated in head and neck squamous cell carcinoma regulate expression of transcripts TNS3-203 and LRRFIP1-211. Our aim was to investigate the biomarker potential of TNS3-203 and LRRFIP1-211 transcripts in oral cancer, the most common type of head and neck cancer. An in silico approach was used to characterize the promoters and transcripts of interest. Relative expression of TNS3-203 and LRRFIP1-211 transcripts was evaluated by qRT-PCR in a group of 46 oral cancer patients in samples of cancer and adjacent non-cancerous tissue. TNS3-203 was significantly overexpressed in oral cancer compared with matched non-cancerous tissue, so this transcript can potentially be used as a diagnostic biomarker. There were no differences in LRRFIP1-211 level between analyzed tissues. None of the investigated transcripts has prognostic potential in oral cancer. The results obtained indicate the diagnostic potential of TNS3-203, but not LRRFIP1-211 transcript and its role in oral carcinogenesis.

Effect of meta-Topolin on morphological, physiochemical, and molecular dynamics during in vitro regeneration of Salix tetrasperma Roxb.

An efficient in vitro propagation protocol has been established for a valuable medicinal plant, Salix tetrasperma using mature nodal explants. The investigation aimed to observe the influence of various combinations and concentrations of cytokinins (mT, BA, and Kn) and auxins (NAA, IAA, and IBA) on regeneration potential using the Murashige and Skoog (MS) medium. Among individual cytokinin treatments, 5.0 µM mT resulted highest response of 92% with maximum shoot number (11.6 ± 0.08) per explant and shoot length (4.5 ± 0.22 cm) after 12 weeks of culture. However, synergistic treatment of mT (5.0 µM) and NAA (0.5 µM) further improved proliferation with (21.3 ± 0.40) shoots per explant and (6.9 ± 0.13 cm) shoot length in 96% cultures after 12 weeks of incubation. Rooting from in vitro raised microshoots was achieved on ½ MS medium supplemented with various concentrations of low-dose auxins. The highest number of roots (10.4 ± 0.20) per shoot with mean root length (5.7 ± 0.11 cm) with maximum rooting frequency (97%) was observed in 0.5 µM IBA, after 4 weeks of culture. The rooted plantlets achieved a remarkable 86% survivability rate, when transferred to ex vitro conditions during acclimatization. Analysis of photosynthetic parameters and their characteristics during the acclimatization phase revealed a gradual decline in photosynthetic attributes during initial weeks; however, a significant improvement was noted as the growth proceeded. SEM analysis revealed the ultra-morphological structural differences between in vivo and in vitro derived leaves of S. tetrasperma. Moreover, DPPH assay observed differential antioxidant activity of in vitro raised plantlets throughout the acclimatization period. The GC-MS analysis from leaf extracts of donor plants and in vitro derived plantlets has revealed a broad spectrum of phytochemical compounds with significant pharmacological properties. No polymorphism in the banding pattern was found when the genetic fidelity of the regenerated plants was evaluated using SCoT primers, indicating the clonal stability of micropropagated plants. This study is the first to explore the use of mT in regeneration of S. tetrasperma, showing its more effectiveness than BA and Kn.

TNF/IFN-γ Co-Signaling Induces Differential Cellular Activation in COVID-19 Patients: Implications for Patient Outcomes

TNF and IFN-γ are key proinflammatory cytokines implicated in the pathophysiology of COVID-19. Toll-like receptor (TLR)7 and TLR8 are known to recognize SARS-CoV-2 and induce TNF and IFN-γ production. However, it is unclear whether TNF and IFN-γ levels are altered through TLR-dependent pathways and whether these pathways mediate disease severity during COVID-19. This study aimed to investigate the association between TNF/IFN-γ levels and immune cell activation to understand their role in disease severity better. We enrolled 150 COVID-19 patients, who were classified by their systemic TNF and IFN-γ levels (high (H) or normal–low (N-L)) as TNFHIFNγH, TNFHIFNγN-L, TNFN-LIFNγH, and TNFN-LIFNγN-L. Compared to patients with TNFN-LIFNγN-L, patients with TNFHIFNγH had high systemic levels of pro- and anti-inflammatory cytokines and cytotoxic molecules, and their T cells and monocytes expressed TNF receptor 1 (TNFR1). Patients with TNFHIFNγH presented the SNP rs3853839 to TLR7 and increased levels of MYD88, NFκB, and IRF7 (TLR signaling), FADD, and TRADD (TNFR1 signaling). Moreover, critical patients were observed in the four COVID-19 groups, but patients with TNFHIFNγH or TNFHIFNγN-L most required invasive mechanical ventilation. We concluded that increased TNF/IFN-γ levels are associated with hyperactive immune cells, whereas normal/low levels are associated with hypoactivity, suggesting a model to explain that the pathophysiology of critical COVID-19 may be mediated through different pathways depending on TNF and IFN-γ levels. These findings highlight the potential for exploring the modulation of TNF and IFN-γ as a therapeutic strategy in severe COVID-19.

Investigation on the Regulation Mechanisms of Viscosity–Temperature Characteristics of High Calcium–Iron Coal by Coal Blending

ABSTRACTEntrained‐flow bed gasification was an important way to realize clean coal conversion. However, the high calcium–iron coal ash had a low flow temperature, low viscosity, and strong fluctuations in viscosity, which severely affected the service life of the gasifier. It was necessary to regulate its ash fusion temperature and viscosity–temperature characteristics (AFV). In the paper, the AFV of Datong coal (DTC, a high calcium–iron coal) and its regulation mechanism were investigated by ash fusion temperature tester, high‐temperature viscometer, Raman spectrometer, differential scanning calorimetry, X‐ray diffractometer, FactSage software, and activation energy calculation. With the increasing Pingdingshan coal (PDS, a high silicon–aluminum coal) mass ratio, the AFV of DTC mixtures increased, and the viscosity fluctuation of DTC mixtures disappeared gradually. When PDS mass ratio is in the range of 18%–24%, the flow temperature and viscosity of DTC ash were 1375°C–1400°C and 18–22 Pa·s, respectively. The increasing PDS mass ratio, the formation of high melting point anorthite and its increasing content, the polymerization degree of DTC mixed ash increasing, and a gradual increase in activation energy as well as their corresponding crystallization behavior led to the increase in the AFV. The mineral transformations and the position variation in the ternary phase diagram of ash compositions with PDS addition by FactSage calculation also explained the variations in the viscosity–temperature characteristics.

Activity of Azole and Non-Azole Substances Against Aspergillus fumigatus in Clinical and Environmental Samples to Address Antimicrobial Resistance

Aspergillus fumigatus is a common fungus which has gained attention due to its resistance to azole compounds, substances used in both medical and agricultural settings. One of the genetic alterations responsible for this resistance is the mutation TR34/L98H in the cyp51A gene. The aim of this study was to understand the impact of azoles and non-azoles on Aspergillus fumigatus. By examining clinical samples, soil samples, and compost material, this research aims to provide insights into the susceptibility of these strains to antifungal substances. To deepen our understanding of the factors potentially involved in antifungal resistance, we combined in vitro studies of sixteen compounds against Aspergillus fumigatus with results from the sequencing of the cyp51 gene. We observed that compounds generally displayed a similar pattern activity against wild-type Aspergillus fumigatus. Non-azoles, except Pyrisoxazole and Amisulbrom, did not show any activity against Aspergillus fumigatus, while azole compounds displayed differential activity against the fungus, except for Tetraconazole. For the mutant strains, a generally similar activity was observed in both clinical and environmental samples, likely due to the same mutation in all the isolates. The implications of these findings may be relevant for better understanding the relationship between Aspergillus fumigatus and its ability to develop resistance to antifungal substances.

Deciphering the Neural Effects of Emotional, Motivational, and Cognitive Challenges on Inhibitory Control Processes.

Converging lines of research indicate that inhibitory control is likely to be compromised in contexts that place competing demands on emotional, motivational, and cognitive systems, potentially leading to damaging impulsive behavior. The objective of this study was to identify the neural impact of three challenging contexts that typically compromise self-regulation and weaken impulse control. Participants included 66 healthy adults (M/SDage = 29.82/10.21 years old, 63.6% female) who were free of psychiatric disorders and psychotropic medication use. Participants completed a set of novel Go/NoGo (GNG) paradigms in the scanner, which manipulated contextual factors to induce (i) aversive emotions, (ii) appetitive drive, or (iii) concurrent working memory load. Voxelwise analysis of neural activation during each of these tasks was compared to that of a neutral GNG task. Findings revealed differential inhibition-related activation in the aversive emotions and appetitive drive GNG tasks relative to the neutral task in frontal, parietal and temporal cortices, suggesting emotional and motivational contexts may suppress activation of these cortical regions during inhibitory control. In contrast, the GNG task with a concurrent working memory load showed widespread increased activation across the cortex compared to the neutral task, indicative of enhanced recruitment of executive control regions. Results suggest the neural circuitry recruited for inhibitory control varies depending on the concomitant emotional, motivational, and cognitive demands of a given context. This battery of GNG tasks can be used by researchers interested in studying unique patterns of neural activation associated with inhibitory control across three clinically relevant contexts that challenge self-regulation and confer risk for impulsive behavior.

Chemical tools to define and manipulate interferon-inducible Ubl protease USP18

Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating the interferon-inducible ubiquitin-like modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) that incorporate unnatural amino acids into the C-terminal tail of ISG15, enabling the selective detection of USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) such as USP5 and USP14. Combined with a ubiquitin-based DUB ABP, the USP18 ABP is employed in a chemoproteomics screening platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.

Differential activation of defense responses in cucumbers by adapted versus non-adapted lineages of the cotton-melon aphid.

The cotton-melon aphid, Aphis gossypii Glover, is a polyphagous pest damaging plants across over 100 families. It has multiple host-specialized lineages, including one colonizing Malvaceae (MA) and one colonizing Cucurbitaceae (CU). The mechanisms underlying these host relationships remain unknown. Here, we compared defensive compounds, gene expressions and aphid susceptibility of cucumbers (Cucumis sativus L.) that were infested with both lineages for up to 14 days. Total jasmonic acid (JA) remained constant in CU-infested cucumbers while increased to a maximum of 19.11 folds at 1 dpi (days post infestation) in MA-infested cucumbers. Total salicylic acid (SA) increased to a maximum of 4.42 folds at 7 dpi in MA-infested cucumbers while increased to a maximum of 2.83 folds at 14 dpi in CU-infested cucumbers. Reactive oxygen species were constantly higher in MA-infested cucumbers than CU-infested cucumbers at each time point. Genes involved in defense signaling, for example, MAPKs, PR-1s, and WRKY, and genes involved in JA and SA biosynthesis, were largely up-regulated in MA-infested cucumbers compared with CU-infested ones. Both lineages exhibited more stylet probing, less phloem ingestion, higher mortality, and less reproduction on MA-infested cucumbers compared with CU-infested ones. MA lineage aphids elicited stronger defenses in cucumbers than the CU lineage aphids. A lack of salivary effectors specific to cucumbers most likely prevents MA lineage aphids from using cucumbers. Identifying lineage-specific elicitors or effectors is therefore expected to unveil the molecular mechanisms of host specificity of this aphid. © 2025 Society of Chemical Industry.

Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells.

Type 2 diabetes (T2D) is a common metabolic disorder characterized by dysregulation of glucose metabolism. Genome-wide association studies have defined hundreds of signals associated with T2D and related metabolic traits, predominantly in noncoding regions. While pancreatic islets have been a focal point given their central role in insulin production and glucose homeostasis, other metabolic tissues, including liver, adipose, and skeletal muscle, also contribute to T2D pathogenesis and risk. Here, we examined context-specific genetic regulation under basal and stimulated states. Using LHCN-M2 human skeletal muscle cells, we generated transcriptomic profiles and characterized regulatory activity of 327 metabolic trait-associated variants via a massively parallel reporter assay (MPRA). To identify condition-specific effects, we compared four different conditions: (1) undifferentiated, or (2) differentiated with basal media, (3) media supplemented with the AMP analog AICAR (to simulate exercise) or (4) media containing sodium palmitate (to induce insulin resistance). RNA-seq revealed these treatments extensively perturbed transcriptional regulation, with 498-3,686 genes showing significant differential expression between pairs of conditions. Among differentially expressed genes, we observed enrichment of relevant biological pathways including muscle differentiation (undifferentiated vs. differentiated), oxidoreductase activity (differentiated vs. AICAR), and glycogen binding (differentiated vs. palmitate). The results of our MPRA found broadly different levels of activity between all conditions. Our MPRA screen revealed a shared set of 7 variants with significant allelic activity across all conditions, along with a proportional number of variants showing condition-specific allelic bias and the total number of active oligos per condition. We found that a lead variant for serum triglyceride levels, rs490972, overlaps SP transcription factor motifs and has differential regulatory activity between conditions. Comparison of MPRA activity with paired gene expression data allowed us to predict that regulatory activity at this locus is mediated by SP1 transcription factor binding. While several of the MPRA variants have been previously characterized in other metabolic tissues, none have been studied in these stimulated states. Together, this work uncovers context-dependent transcriptomic and regulatory dynamics of T2D- and metabolic trait-associated variants in skeletal muscle cells, offering new insights into their functional roles in metabolic processes.

Inferring single-cell and spatial microRNA activity from transcriptomics data

The activity of miRNA varies across different cell populations and systems, as part of the mechanisms that distinguish cell types and roles in living organisms and in human health and disease. Typically, miRNA regulation drives changes in the composition and levels of protein-coding RNA and of lncRNA, with targets being down-regulated when miRNAs are active. The term “miRNA activity" is used to refer to this transcriptional effect of miRNAs. This study introduces miTEA-HiRes, a method designed to facilitate the evaluation of miRNA activity at high resolution. The method applies to single-cell transcriptomics, type-specific single-cell populations, and spatial transcriptomics data. By comparing different conditions, differential miRNA activity is inferred. For instance, miTEA-HiRes analysis of peripheral blood mononuclear cells comparing Multiple Sclerosis patients to control groups revealed differential activity of miR-20a-5p and others, consistent with the literature on miRNA underexpression in Multiple Sclerosis. We also show miR-519a-3p differential activity in specific cell populations.

Effects of functional strength training on pain, function, and lower extremity biomechanics in patients with patellofemoral pain syndrome: a randomized clinical trial

BackgroundPatellofemoral pain syndrome (PFPS) is a common disorder affecting the lower extremity. This study aimed to compare the effects of functional strength training (FST) and standard strength training (SST) in PFPS patients.MethodsForty college students (aged 18–30 years) with PFPS and no exercise habits were randomized into FST group (n = 20) and SST group (n = 20). FST group underwent six weeks of lower extremity training focused on functional adaptations, whereas SST group focus on lower extremity strength training. Function (Kujala Patellofemoral Scale, KPS), pain (visual analog scale, VAS), peak joint angles of hip, knee, and ankle, along with muscle activation (step-down test) of Vastus medialis, Vastus lateralis, Biceps femoris, Semitendinosus, Gluteus maximus, and Gluteus medius were assessed at baseline and after intervention.ResultsFST outperformed SST in pain reduction (p = 0.026) and function (p = 0.006) post-intervention. The FST group also showed increased hip flexion (p < 0.001), gluteus maximus activation (p < 0.001), and reduced knee valgus (p = 0.032), while SST group exhibited greater knee flexion (p = 0.008), and higher activation of the lateral femoral (p < 0.001) and semitendinosus (p < 0.001).ConclusionInterventions focused on functional adaptations result in differential kinematic and muscle activation changes that may result in greater improvements in pain and knee function than lower limb muscle strengthening alone.Trial registrationchictr.org.cn. NO: ChiCTR2400087664. Date 01/08/2024.