Functional Interaction Research Articles

Crosstalk interactions between transcription factors ERRα and PPARα assist PPARα-mediated gene expression

ObjectiveThe peroxisome proliferator-activated receptor α (PPARα) is a transcription factor driving target genes involved in fatty acid β-oxidation. To what extent various PPARα interacting proteins may assist its function as a transcription factor is incompletely understood. An ORFeome-wide unbiased mammalian protein-protein interaction trap (MAPPIT) using PPARα as bait revealed a PPARα-ligand-dependent interaction with the orphan nuclear receptor estrogen-related receptor α (ERRα). The goal of this study was to characterize the nature of the interaction in depth and to explore whether it was of physiological relevance. MethodsWe used orthogonal protein-protein interaction assays and pharmacological inhibitors of ERRα in various systems to confirm a functional interaction and study the impact of crosstalk mechanisms. To characterize the interaction surfaces and contact points we applied a random mutagenesis screen and structural overlays. We pinpointed the extent of reciprocal ligand effects of both nuclear receptors via coregulator peptide recruitment assays. On PPARα targets revealed from a genome-wide transcriptome analysis, we performed an ERRα chromatin immunoprecipitation analysis on both fast and fed mouse livers. ResultsRandom mutagenesis scanning of PPARα’s ligand-binding domain and coregulator profiling experiments supported the involvement of (a) bridging coregulator(s), while recapitulation of the interaction in vitro indicated the possibility of a trimeric interaction with RXRα. The PPARα·ERRα interaction depends on 3 C-terminal residues within helix 12 of ERRα and is strengthened by both PGC1α and serum deprivation. Pharmacological inhibition of ERRα decreased the interaction of ERRα to ligand-activated PPARα and revealed a transcriptome in line with enhanced mRNA expression of prototypical PPARα target genes, suggesting a role for ERRα as a transcriptional repressor. Strikingly, on other PPARα targets, including the isolated PDK4 enhancer, ERRα behaved oppositely. Chromatin immunoprecipitation analyses demonstrate a PPARα ligand-dependent ERRα recruitment onto chromatin at PPARα-binding regions, which is lost following ERRα inhibition in fed mouse livers. ConclusionOur data support the coexistence of multiple layers of transcriptional crosstalk mechanisms between PPARα and ERRα, which may serve to finetune the activity of PPARα as a nutrient-sensing transcription factor.

‘Quantum of information’ functionality as a measure of subjectivity beyond the capabilities of deep learning

The potential of conscious artificial intelligence (AI), with its functional systems that surpass automation and rely on elements of understanding, is a beacon of hope in the AI revolution. The shift from automation to conscious AI, once replaced with machine understanding, offers a future where AI can comprehend without needing to experience, thereby revolutionizing the field of AI. In this context, the proposed Dynamic Organicity Theory of consciousness (DOT) stands out as a promising and novel approach for building artificial consciousness that is more like the brain with physiological nonlocality and diachronicity of self-referential causal closure. However, deep learning algorithms utilize "black box" techniques such as “dirty hooks” to make the algorithms operational by discovering arbitrary functions from a trained set of dirty data rather than prioritizing models of consciousness that accurately represent intentionality as intentions-in-action. The limitations of the “black box” approach in deep learning algorithms present a significant challenge as quantum information biology, or intrinsic information, is associated with subjective physicalism and cannot be predicted with Turing computation. This paper suggests that deep learning algorithms effectively decode labeled datasets but not dirty data due to unlearnable noise, and encoding intrinsic information is beyond the capabilities of deep learning. New models based on DOT are necessary to decode intrinsic information by understanding meaning and reducing uncertainty. The process of “encoding” entails functional interactions as evolving informational holons, forming informational channels in functionality space of time consciousness. The “quantum of information” functionality is the motivity of (negentropic) action as change in functionality through thermodynamic constraints that reduce informational redundancy (also referred to as intentionality) in informational pathways. It denotes a measure of epistemic subjectivity towards machine understanding beyond the capabilities of deep learning.

Ultra‐Small Au Nanoclusters with Tailored Photoluminescence Properties using Modified Thiol Ligands: A Computational and Experimental Demonstration

AbstractAu nanoclusters with tailored photoluminescence can be obtained through controlled nanoparticle ligand interface chemistry. The present work reports molecular gold nanoclusters with tuneable photoluminescence emission from 600 to 700 nm using N,N′,N″‐trialkyl (11‐mercaptoundecyl)ammonium chloride ligands as capping‐agents. The tunability within red spectral region is regulated through specific interface chemistry between gold nanoclusters of molecular range and functional groups of the quaternary ammonium head over N,N′,N″‐trialkyl(11‐mercaptoundecyl)ammonium chloride. Combined understanding obtained from the spectroscopy, microscopy, and density functional theory studies demonstrate that the functional group specific electronic interactions at the interfaces steer the emission characteristics of “molecular” Au nanoparticles. The study clearly identifies that bulkier functional groups, i.e., triethyl, tripropyl, tributyl, and dimethyl benzene over N+ (of thiol ligand) through their steric effects minimize the particle size giving rise to tunable photoluminescence emission in red spectral region. However, the red shift seen in the emission Au nanoclusters with N‐(11‐mercaptoundecyl)‐N,N′‐dimethylbenzenammonium chloride ligand in contradiction to particle size effect is computationally proved to be due to the delocalization of electron density from benzene aromatic ring to N+ of ammonium head leading to a reduction in the HOMO‐LUMO energy gap.

In silico identification and targeting of key genes involved in renal cell carcinoma metastasis

Metastasis is a challenge in the management of renal cell carcinoma (RCC). The clinical implications of RCC metastasis are significant, with patients experiencing a poorer response to treatment and a reduced life expectancy. Currently, there is no curative treatment for RCC metastasis, and systemic chemotherapy and immunotherapy remain mainstay therapies. However, emerging evidence suggests that targeted therapies may provide promising treatment options for improving the prognosis and quality of life of patients with metastatic RCC. The current study aimed to investigate the underlying molecular mechanisms of RCC metastasis and identify key therapeutic targets using computational approaches. Also, a library of FDA approved drugs was screened against the target genes to obtain potential inhibitors that can be used in therapies. Differential gene expression analysis followed by functional enrichment and protein-protein interaction analyses led to the identification of CCND2 and MMP9 as key genes involved in multiple process in the metastatic tumors in case of both clear cell and papillary cell renal carcinoma. Docking studies revealed good binding of drugs mysoline and ethisterone with CCND2 and canrenone and evodiamine with MMP9. Molecular Dynamics simulations showed stable and strong binding of these drugs with CCND2, but the identified drugs failed to have stable interactions with MMP9. Hence, our study reveals mysoline and ethisterone to be potential inhibitors that target CCND2 to control metastasis of RCC.

#2695 A Polycystin-1-Bicaudal C1 complex regulates focal adhesion function through integrin beta-1, F-actin organisation and local translation in HKE cells

Abstract Background and Aims Variants in Bicc1, result in a recessive murine PKD phenotype (bpk, jcpk) by uncertain mechanisms. In a recent study, we reported genetic and biochemical evidence of novel interactions between PKD1, PKD2 and BICC1 in Xenopus, mouse and man suggesting that BICC1 is a modifier of the ADPKD phenotype (submitted). In this study, our major aim was to investigate the molecular mechanisms underlying cystogenesis that result from loss of the normal interaction between the PKD1 protein, Polycystin-1 (PC1), a cell surface receptor and Bicaudal C1 (BICC1), an RNA-binding protein. Methods Isogenic PKD1 and BICC1 CRISP-Cas9 KO cells were generated from a conditionally-immortalised wild-type human proximal tubular line (UCL93); RNA-seq was performed in PKD1 and BICC1 KO cells to identify commonly altered genes and pathways; MS pull-down was conducted in HEK293 cells with BICC1-HA to identify BICC1 interacting proteins; cellular phenotypes in normal and KO cells were assessed through adhesion and migration assays, alongside Traction Force Microscopy (TFM); proximal ligation assays (PLA) to confirm protein-protein interactions; single-molecule FISH (smFISH) to localize mRNA transcripts; puromycin labeling with a proximity ligation assay (Puro-PLA) to detect sites of translation of specific mRNAs. Results Consistent with a functional interaction, loss of PC1 resulted in lower BICC1 levels and vice-versa in single KO (SKO) cells. In migrating cells, BICC1 was expressed at the leading edge where it co-localised with β1-integrin (ITGB1) by PLA, suggesting enrichment at focal adhesion sites (FA). BICC1 KO cells had no cilia phenotype but instead displayed striking disorganization of stress fibres and aster-like structures, features which could be completely rescued by lentiviral Bicc1-HA re-expression. Gene set enrichment and pathway analysis confirmed that F-actin organization and actin-associated proteins (AAP) were commonly dysregulated in SKO cells. BICC1 was also found to interact ITGB1, several components of an integrin-associated complex and proteins involved in actin turnover by MS pull-down. Both SKO cells showed major abnormalities of cell attachment, detachment and directional migration indicative of functional alterations in cell-matrix and cell-cell adhesion. We confirmed that FA structure and function were altered by reduced co-localisation of several AAPs (including TNS1 and FBLIM1) and by TFM. BICC1 directly interacted with F-actin and FBLIM1 in pull-down assays and with FBLIM1 by RNA-IP. Finally, we found evidence of FBLIM1 mRNA by smFISH and of local FBLIM1 translation (Puro-PLA) at FA sites in wild-type cells, both of which were markedly reduced in SKO cells. Conclusion Our data reveal the key roles for actin dynamics and local translation as novel mechanisms regulated by PC1 and BICC1 in the pathogenesis of ADPKD. We demonstrate that BICC1 and PC1 are co-regulated, forming a PC1-BICC1 complex critical for maintaining the structural integrity and function of FAs in normal kidney epithelial cells. Loss of this interaction results in major alterations in cell adhesion, migration and stress fibre organisation, features typical of the ADPKD cellular phenotype. BICC1 plays a dual role in this process via protein-protein interactions with ITGB1, F-actin and other AAPs, and through protein-RNA interactions regulating the local translation of key AAPs (FBLIM1) at FA sites.

#2423 Molecular classification of lupus nephritis based on immune pathway profiling—correlations with histological class and clinical manifestations

Abstract Background and Aims The ISN/RPS 2003 classification is the current gold standard histopathological classification for lupus nephritis (LN), and has important roles in guiding treatment and predicting prognosis. The classification system, largely based on light microscopy features, does not inform the underlying immunological aberrations. A classification based on molecular typing of immune-related pathways may better stratify LN patients and help select treatments that target specific immune cascades. Method The normalized expression matrix and clinical data were extracted from Gene Expression Omnibus database, Human Cell Atlas (Hacohen-Human-CELseq2) and Nephroseq. Four chip datasets (GSE127797, 32591, 69438 and 37463) and one single cell dataset were analyzed. Sample gene set enrichment analysis (ssGSEA) method was used to derive immune phenotype with gene expression data. The hierarchical clustering with ssGSEA scores of selected gene sets was used to classify LN tissues. Functional characterization and protein-protein interactions of the differential expression genes (DEGs) of three groups were compared with healthy donors using Metascape (absolute log FC > 1 and adjusted P-value < .05). Kruskal-Walli test and chi-square test were performed to compare the clinical parameters of the different groups. Results We analyzed 96 immune-related gene sets in the glomerular and tubulointerstitial regions of LN kidney biopsy samples. The immune-related genes were categorized into three clusters (Immune-Mild, Immune-Moderate and Immune-Severe) based on the degree of immune pathway activation. Interferon-stimulated genes are a hallmark of LN, with high signals in all three clusters. When compared to other groups, the Immune-Mild cluster from the glomerular region showed no T-cell activation or T cell receptor pathway. Also, the Immune-Mild (tubulointerstitial) group also showed minimal lymphocyte activation or migration. Protein-protein interactions networks with MOCDE components further suggested that STAT1 and ISG15 the hub genes in different clusters. The gene expressions of hub genes were then compared among epithelial cells and 21 immune cells from LN and heath controls. Immune clusters are correlated with clinical phenotypes, in which Immune-Mild Group (Glomerular) showed high prevalence of Class II and V LN, and Immune-Mild (Tubulointerstitial) showed more Class V LN. Immune-Severe group also showed higher degree of proteinuria and blood pressure but lower eGFR compared to Immune-Moderate and Immune-Mild groups. Conclusion A new molecular classification of LN based on the degree of immune pathway activation shows correlation with clinical manifestations and may potentially guide personalized therapy in LN patients.

ALTERED MERISTEM PROGRAM1 sustains cellular differentiation by limiting HD-ZIP III transcription factor gene expression.

Plants show remarkable developmental and regenerative plasticity through the sustained activity of stem cells in meristems. Under certain conditions, pluripotency can even be re-established in cells that have already entered differentiation. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis (Arabidopsis thaliana) causes a set of hypertrophic phenotypes, indicating a defect in the suppression of pluripotency. A role of AMP1 in the miRNA-mediated inhibition of translation has previously been reported, however, how this activity is related to its developmental functions is unclear. Here we examined the functional interaction between AMP1 and the Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors, which are miRNA-controlled determinants of shoot meristem specification. We found that the HD-ZIP III transcriptional output is enhanced in the amp1 mutant and that plant lines with increased HD-ZIP III activity not only developed amp1 mutant-like phenotypes but also showed a synergistic genetic interaction with the mutant. Conversely, the reduction of HD-ZIP III function suppressed the shoot hypertrophy defects of the amp1 mutant. We further provide evidence that the expression domains of HD-ZIP III family members are expanded in the amp1 mutant and that this misexpression occurs at the transcriptional level and does not involve the function of miRNA165/166. Finally, amp1 mutant-specific phenotypes cannot be mimicked by a general inhibition of miRNA function in the AMP1 expression domain. These findings lead us to a model in which AMP1 restricts cellular pluripotency upstream of HD-ZIP III proteins and this control appears to be not directly mediated by the canonical miRNA pathway.

The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell

Abstract Common approaches for deciphering biological networks involve network embedding algorithms. These approaches strictly focus on clustering the genes’ embedding vectors and interpreting such clusters to reveal the hidden information of the networks. However, the difficulty in interpreting the genes’ clusters and the limitations of the functional annotations’ resources hinder the identification of the currently unknown cell’s functioning mechanisms. We propose a new approach that shifts this functional exploration from the embedding vectors of genes in space to the axes of the space itself. Our methodology better disentangles biological information from the embedding space than the classic gene-centric approach. Moreover, it uncovers new data-driven functional interactions that are unregistered in the functional ontologies, but biologically coherent. Furthermore, we exploit these interactions to define new higher-level annotations that we term Axes-Specific Functional Annotations and validate them through literature curation. Finally, we leverage our methodology to discover evolutionary connections between cellular functions and the evolution of species. Availability Data and source code can be accessed at https://gitlab.bsc.es/sdoria/axes-of-biology.git Supplementary information Supplementary data are available online.

Regulatory effects of microRNAs on monocytic HLA-DR surface expression.

Decreased monocytic HLA-DR expression is the most studied biomarker of immune competency in critically ill and autoimmune disease patients. However, the underlying regulatory mechanisms remain largely unknown. One probable HLA-DR dysregulation is through microRNAs. The aim of this study was to investigate the effects of specific microRNAs on HLA-DR expression in human monocytic cells. Four up- and four down-HLA-DR-regulating microRNAs were identified, with hsa-miR-let-7f-2-3p showing the most significant upregulation and hsa-miR-567 and hsa-miR-3972 downregulation. Anti-inflammatory glucocorticoid medication Dexamethasone-decreased HLA-DR was significantly restored by hsa-miR-let-7f-2-3p and hsa-miR-5693. Contrarily, proinflammatory cytokines IFN-γ and TNF-α-increased HLA-DR were significantly reversed by hsa-miR-567. Clinically, paired plasma samples from patients before and one day after cardiac surgery revealed up-regulated expression of hsa-miR-5693, hsa-miR-567, and hsa-miR-3972, following the major surgical trauma. In silico approaches were applied for functional microRNA-mRNA interaction prediction and candidate target genes were confirmed by qPCR analysis. In conclusion, novel monocytic HLA-DR microRNA modulators were identified and validated in vitro. Moreover, both the interaction between the microRNAs and anti- and proinflammatory molecules and the up-regulated microRNAs identified in cardiac surgery highlight the potential clinical relevance of our findings.

Subcellular distribution and Nrf2/Keap1-interacting properties of Glutathione S-transferase P in hepatocellular carcinoma

The oncogene and drug metabolism enzyme glutathione S-transferase P (GSTP) is also a GSH-dependent chaperone of signal transduction and transcriptional proteins with key role in liver carcinogenesis. In this study, we explored this role of GSTP in hepatocellular carcinoma (HCC) investigating the possible interaction of this protein with one of its transcription factor and metronome of the cancer cell redox, namely the nuclear factor erythroid 2–related factor 2 (Nrf2).Expression, cellular distribution, and function as glutathionylation factor of GSTP1-1 isoform were investigated in the mouse model of N-nitrosodiethylamine (DEN)-induced HCC and in vitro in human HCC cell lines. The physical and functional interaction of GSTP protein with Nrf2 and Keap1 were investigated by immunoprecipitation and gene manipulation experiments.GSTP protein increased its liver expression, enzymatic activity and nuclear levels during DEN-induced tumor development in mice; protein glutathionylation (PSSG) was increased in the tumor masses. Higher levels and a preferential nuclear localization of GSTP protein were also observed in HepG2 and Huh-7 hepatocarcinoma cells compared to HepaRG non-cancerous cells, along with increased basal and Ebselen-stimulated levels of free GSH and PSSG. GSTP activity inhibition with the GSH analogue EZT induced apoptotic cell death in HCC cells. Hepatic Nrf2 and c-Jun, two transcription factors involved in GSTP expression and GSH biosynthesis, were induced in DEN-HCC compared to control animals; the Nrf2 inhibitory proteins Keap1 and β−TrCP also increased and oligomeric forms of GSTP co-immunoprecipitated with both Nrf2 and Keap1. Nrf2 nuclear translocation and β−TrCP expression also increased in HCC cells, and GSTP transfection in HepaRG cells induced Nrf2 activation.In conclusion, GSTP expression and subcellular distribution are modified in HCC cells and apparently contribute to the GSH-dependent reprogramming of the cellular redox in this type of cancer directly influencing the transcriptional system Nrf2/Keap1.

Systematic-Narrative Hybrid Literature Review: Crosstalk between Gastrointestinal Renin-Angiotensin and Dopaminergic Systems in the Regulation of Intestinal Permeability by Tight Junctions.

In the first part of this article, the role of intestinal epithelial tight junctions (TJs), together with gastrointestinal dopaminergic and renin-angiotensin systems, are narratively reviewed to provide sufficient background. In the second part, the current experimental data on the interplay between gastrointestinal (GI) dopaminergic and renin-angiotensin systems in the regulation of intestinal epithelial permeability are reviewed in a systematic manner using the PRISMA methodology. Experimental data confirmed the copresence of DOPA decarboxylase (DDC) and angiotensin converting enzyme 2 (ACE2) in human and rodent enterocytes. The intestinal barrier structure and integrity can be altered by angiotensin (1-7) and dopamine (DA). Both renin-angiotensin and dopaminergic systems influence intestinal Na+/K+-ATPase activity, thus maintaining electrolyte and nutritional homeostasis. The colocalization of B0AT1 and ACE2 indicates the direct role of the renin-angiotensin system in amino acid absorption. Yet, more studies are needed to thoroughly define the structural and functional interaction between TJ-associated proteins and GI renin-angiotensin and dopaminergic systems.

A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships.

The activities of most enzymes and drugs depend on interactions between proteins and small molecules. Accurate prediction of these interactions could greatly accelerate pharmaceutical and biotechnological research. Current machine learning models designed for this task have a limited ability to generalize beyond the proteins used for training. This limitation is likely due to a lack of information exchange between the protein and the small molecule during the generation of the required numerical representations. Here, we introduce ProSmith, a machine learning framework that employs a multimodal Transformer Network to simultaneously process protein amino acid sequences and small molecule strings in the same input. This approach facilitates the exchange of all relevant information between the two molecule types during the computation of their numerical representations, allowing the model to account for their structural and functional interactions. Our final model combines gradient boosting predictions based on the resulting multimodal Transformer Network with independent predictions based on separate deep learning representations of the proteins and small molecules. The resulting predictions outperform recently published state-of-the-art models for predicting protein-small molecule interactions across three diverse tasks: predicting kinase inhibitions; inferring potential substrates for enzymes; and predicting Michaelis constants KM. The Python code provided can be used to easily implement and improve machine learning predictions involving arbitrary protein-small molecule interactions.

The interaction effect of high social support and resilience on functional connectivity using seed-based resting-state assessed by 7-Tesla ultra-high field MRI

Recent resilience research has increasingly emphasized the importance of focusing on investigating the protective factors in mentally healthy populations, complementing the traditional focus on psychopathology. Social support has emerged as a crucial element within the complex interplay of individual and socio-environmental factors that shape resilience. However, the neural underpinnings of the relationship between social support and resilience, particularly in healthy subjects, remain largely unexplored. With advances in neuroimaging techniques, such as ultra-high field MRI at 7T and beyond, researchers can more effectively investigate the neural mechanisms underlying these factors. Thus, our study employed ultra-high field rs-fMRI to explore how social support moderates the relationship between psychological resilience and functional connectivity in a healthy cohort. We hypothesized that enhanced social support would amplify resilience-associated connectivity within neural circuits essential for emotional regulation, cognitive processing, and adaptive problem-solving, signifying a synergistic interaction where strong social networks bolster the neural underpinnings of resilience. (n = 30). Through seed-based functional connectivity analyses and interaction analysis, we aimed to uncover the neural correlates at the interplay of social support and resilience. Our findings indicate that perceived social support significantly (p<0.001) alters functional connectivity in the right and left FP, PCC, and left hippocampus, affirming the pivotal roles of these regions in the brain’s resilience network. Moreover, we identified significant moderation effects of social support across various brain regions, each showing unique connectivity patterns. Specifically, the right FP demonstrated a significant interaction effect where high social support levels were linked to increased connectivity with regions involved in socio-cognitive processing, while low social support showed opposite effects. Similar patterns by social support levels were observed in the left FP, with connectivity changes in clusters associated with emotional regulation and cognitive functions. The PCC’s connectivity was distinctly influenced by support levels, elucidating its role in emotional and social cognition. Interestingly, the connectivity of the left hippocampus was not significantly impacted by social support levels, indicating a unique pattern within this region. These insights highlight the importance of high social support levels in enhancing the neural foundations of resilience and fostering adaptive neurological responses to environmental challenges.

Astrocyte Calcium Signaling.

Astrocytes are predominant glial cells that tile the central nervous system and participate in well-established functional and morphological interactions with neurons, blood vessels, and other glia. These ubiquitous cells display rich intracellular Ca2+ signaling, which has now been studied for over 30 years. In this review, we provide a summary and perspective of recent progress concerning the study of astrocyte intracellular Ca2+ signaling as well as discussion of its potential functions. Progress has occurred in the areas of imaging, silencing, activating, and analyzing astrocyte Ca2+ signals. These insights have collectively permitted exploration of the relationships of astrocyte Ca2+ signals to neural circuit function and behavior in a variety of species. We summarize these aspects along with a framework for mechanistically interpreting behavioral studies to identify directly causal effects. We finish by providing a perspective on new avenues of research concerning astrocyte Ca2+ signaling.

Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.

Impact of Interactions between Su(Hw)-Dependent Insulators on the Transvection Effect in Drosophila melanogaster.

Transvection is a phenomenon of interallelic communication in which enhancers can activate a specific promoter located on a homologous chromosome. Insulators play a significant role in ensuring functional interactions between enhancers and promoters. In the presented work, we created a model where two or three copies of the insulator are located next to enhancers and promoters localized on homologous chromosomes. Using the Su(Hw) insulator as a model, we showed that the functional interaction between a pair of insulators promotes enhancer-promoter trans-interactions. The interaction between the three insulators, on the contrary, can lead to the formation of chromatin loops that sterically hinder the full enhancer-promoter interaction. The results of the work suggest the participation of insulators in the regulation of homologous chromosome pairing and in communication between distant genomic loci.

Fibroblasts from HPV-negative oropharynx squamous cell carcinomas stimulate the release of osteopontin from cancer cells via the release of IL-6.

HPV-associated oropharyngeal squamous cell carcinoma (OPSCC) shows distinct biological and clinical behaviour when compared to HPV-negative OPSCC. The overall role of the tumour microenvironment (TME) in head and neck cancer progression and metastasis has been studied intensively, but differences in HPV-negative and HPV-positive OPSCCs are less understood. To investigate the role of cancer-associated fibroblasts (CAFs) and the functional interactions of normal tonsil fibroblasts (NTFs) and OP CAFs with HPV+ and HPV- OPSCC cells and explore novel candidates in tumour-fibroblast crosstalk. A retrospective cohort of 143 primary OPSCCs was characterised using HPV16/18 RNAScope assay, p16 IHC and ɑ-SMA. Four OPSCC, three NTF and 2 new OPSCC CAF cultures were used to assess the cytokine-based interactions using cytokine arrays on conditioned media (CM), followed by co-culture approaches to identify the role of individual cell types and the role of OPN (SPP1) and IL-6 in SCC/fibroblast communication. HPV status was associated with better overall survival. Although ɑ-SMA expression was observed in both OPSCC subtypes, it provided survival stratification only in the HPV-positive group (Log-Rank p = 0.02). Three normal tonsillar fibroblast cultures (NTFs) were characterised by induction of myofibroblastic and senescent phenotypes with similar reactivity to our published NOF phenotype. The OPSCC-derived CAF cultures were characterised and their baseline myofibroblastic and senescence phenotypes varied. Cytokine array analysis of CM to identify novel candidates in the crosstalk between OPSCC tumour cells and NTFs/CAFs identified differences in the cytokine profiles on comparison of HPV+ and HPV- OPSCC cells. Osteopontin (OPN/SPP1) was identified, particularly in HPV-negative OPSCC cell analyses. We have demonstrated that OPN was produced by the OPSCC cells and revealed an associated upregulation of IL-6 in fibroblasts. Treatment of NTFs with rOPN showed alteration in phenotype, including increased contraction and IL-6 production. Antibody-mediated inhibition of CD44v6 attenuated the production of IL-6 by OPN in NTFs. This investigation with OPSCC fibroblasts provides novel insights into the role of CAFs in OPSCC mediated by IL-6 stimulated release of OPN from HPV negative OPSCC cells. The details of HPV-positive SCC cell/fibroblast cytokine crosstalk remain elusive.

Deep Trans-Omic Network Fusion for Molecular Mechanism of Alzheimer's Disease.

There are various molecular hypotheses regarding Alzheimer's disease (AD) like amyloid deposition, tau propagation, neuroinflammation, and synaptic dysfunction. However, detailed molecular mechanism underlying AD remains elusive. In addition, genetic contribution of these molecular hypothesis is not yet established despite the high heritability of AD. The study aims to enable the discovery of functionally connected multi-omic features through novel integration of multi-omic data and prior functional interactions. We propose a new deep learning model MoFNet with improved interpretability to investigate the AD molecular mechanism and its upstream genetic contributors. MoFNet integrates multi-omic data with prior functional interactions between SNPs, genes, and proteins, and for the first time models the dynamic information flow from DNA to RNA and proteins. When evaluated using the ROS/MAP cohort, MoFNet outperformed other competing methods in prediction performance. It identified SNPs, genes, and proteins with significantly more prior functional interactions, resulting in three multi-omic subnetworks. SNP-gene pairs identified by MoFNet were mostly eQTLs specific to frontal cortex tissue where gene/protein data was collected. These molecular subnetworks are enriched in innate immune system, clearance of misfolded proteins, and neurotransmitter release respectively. We validated most findings in an independent dataset. One multi-omic subnetwork consists exclusively of core members of SNARE complex, a key mediator of synaptic vesicle fusion and neurotransmitter transportation. Our results suggest that MoFNet is effective in improving classification accuracy and in identifying multi-omic markers for AD with improved interpretability. Multi-omic subnetworks identified by MoFNet provided insights of AD molecular mechanism with improved details.

Peripheral 5-HT mediates GnIH-induced feeding behavior and energy metabolism disorder in chickens via the 5-HT2C receptor.

Gonadotropin-inhibitory hormone (GnIH) plays a critical role of reproduction in vertebrate since its discovery. Recently, a regulatory role of GnIH in appetite and the energy metabolism has emerged, despite its precise physiological mechanisms remain unknown. Thus, the present study evaluated the effects of a single or long-term GnIH treatments (administered via intraperitoneal injection) on the food intake, weight and glucolipid metabolism of chickens, while investigated the possible neuroendocrinology factors and its mechanism that involved in GnIH-induced obesity and glucolipid metabolism disorder. Our results showed that the intraperitoneal administration of GnIH to chickens resulted in marked body mass increased, hyperlipidemia, hyperglycemia and glucose intolerance. Subsequently, the results of metabolomics and pharmacological inhibition of 5-HT2C receptor studies revealed that blocked 5-HT2C receptor reinforced the effects of GnIH on food intake, body weight and the levels of blood glucose and lipid, resulted in GnIH-induced hyperglycaemia, hyperlipidemia and hepatic lipid deposition even worse, suggesting that peripheral 5-HT via 5-HT2C receptor may act as a negative feedback regulator to interplay with GnIH and jointly homeostatic control of energy balance in chickens. Our present study provide evidence of the cross-talk between GnIH and 5-HT in food intake and energy metabolism at the in vivo pharmacological level and to propose a molecular basis for these interactions, suggesting that functional interaction between GnIH and 5-HT may open new avenues to understand the mechanism of neuroendocrine network involved in appetite and energy metabolism as well as provide a new therapeutic strategy to prevent obesity, diabetes and metabolic disorders.

Equivalent mating system parameters in post‐mining and undisturbed native plant populations confirms restitution of bird‐pollinator function

Abstract The restoration of diverse self‐sustaining ecosystems requires re‐establishment of functional interactions among species. For plant communities, pollinators are usually essential for pollination, seed set and seed quality. A common assumption in ecological restoration for plants pollinated by animals is one of ‘build it and they will come’, which is rarely tested. Beyond seed set, there may be negative genetic consequences for seed quality if pollinators and their behaviour do not reflect those in reference populations. Here, we conduct an ecological genetic assessment of seed quality via mating system parameters in Lambertia multiflora (Proteaceae), a species dependent on nectar‐feeding birds for pollination. Four populations of L. multiflora in disturbed sites that were rehabilitated following mineral sands mining were compared with four native reference populations, near Eneabba, Western Australia. In each population, approximately 10 offspring from each of 10 maternal plants were genotyped with 11 highly polymorphic microsatellite markers. From these data, genetic diversity and mating system parameters were assessed, and found to be equivalent across all populations. Mean allelic diversity and heterozygosity across loci were very high. All populations were completely outcrossing with no bi‐parental inbreeding. Mean correlated paternity, sibship and effective population size estimates for restored and natural populations were not significantly different and reflected uniformly high paternal diversity and wide outcrossing. Equivalent genetic results for restored and natural reference populations indicate successful restitution of bird‐pollinator services for L. multiflora in these post‐mining rehabilitation sites. Synthesis and applications. Reviewing our results with other published studies to date suggests a resilience of bird‐pollinator services in restored plant communities. These findings provide some reassurance to restoration practitioners working in these global south systems where bird pollination is a feature, at least for similar landscape scenarios. Our study also highlights the global contribution of ecological genetics to the objective assessment of functional species interactions in ecological restoration, an increasingly important goal of land managers and regulators seeking to improve restoration standards.