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Biology subjects

Islam, M. R.

Publications and source records attributed to Islam, M. R..

At least 19 recordsLinked to original sources

CRISPR-mediated Correction of Oncogenic AS-NMD in Splicing Factor Mutant Cancer

Alternative splicing coupled to nonsense-mediated mRNA decay (AS-NMD) evolved as a master regulator of gene expression. Dysregulated AS-NMD has been identified as the root of many human maladies, from developmental defects to deadly cancer. Poison exons (PEs) are highly conserved alternative exons that contain a premature termination codon and elicit AS-NMD when included in a transcript. Cancer cells often exploit the inclusion of PEs to downregulate tumor suppressors or the exclusion of PEs to upregulate oncoproteins. Therefore, PEs have drawn significant attention as a novel therapeutic avenue for cancer and other diseases. Here, we examine a therapeutic proof-of-concept for manipulating PE-mediated oncogenic AS-NMD using a CRISPR-based approach. Using paired guide RNA, we successfully deleted a PE of a tumor suppressor (EZH2) from the genome of SRSF2-mutated leukemia. This editing resulted in EZH2 mRNAs without a PE, escaped AS-NMD, and restored the protein expression. This subsequently reinstated H3K27 histone methylation and rescued defective chromatin regulation associated with impaired hematopoietic stem cell differentiation. Finally, we showed the preferential advantages of CRISPR over the antisense technology we recently developed targeting the PE of EZH2. Therefore, the CRISPR strategy shows compelling evidence as a therapeutic approach targeting PE in cancer and other human diseases.

cancer biology↗

Targeting EZH2 Oncogenic Splicing: Decoding the Regulatory Network and Antisense Correction

Recurrent mutations in splicing factors (SFs) have been established as crucial drivers of tumorigenesis in several types of blood cancer, and also common in a variety of solid tumors. Mutations change the RNA-binding preferences of SFs, promote global splicing alterations, and often generate erroneous mRNAs that are then degraded by nonsense-mediated mRNA decay (NMD). Consequently, several critical genes linked to hematopoiesis are dysregulated, leading to blood cancer. Although the field has progressed considerably in identifying aberrant genes and affected pathways, effective therapies have not yet emerged in SF-mutated cancers. To address this key gap, we instigated a gene-specific targeted strategy by unlocking the regulatory network. As a proof-of-concept, we scrutinized a tumor suppressor gene EZH2, which is a bona fide target in SRSF2-mutated cancer. We precisely defined splicing cis-elements in EZH2 transcripts and illustrated the dynamic choreography of regulatory proteins in the entire splicing and NMD catalytic pathways. We uncovered a highly coordinated cross-regulation between splicing and NMD promoted by mutant SRSF2 by enhancing the deposition of critical spliceosome- and NMD-associated factors, augmenting mRNA decay to ablate tumor suppression. We then designed antisense oligonucleotides (ASOs) targeting important regulatory sites. Our lead ASO successfully corrects aberrant splicing and NMD, restores the expression and function of EZH2, and partially rescues hematopoietic defects and cellular properties. Our study demonstrates that ASO pharmacology is an actionable strategy for clinical development, challenging the existing paradigms in SF-mutated cancers.

cancer biology↗

Stage-specific screening reveals complex resilience pathways to cold stress in rice

Rice cultivation in Bangladeshs northern and northeastern regions face a critical challenge - cold stress during the seedling and reproductive stages, which can drastically reduce yield. As a precursor to generate improved elite lines, a diverse panel of rice germplasm was screened to identify genotypes with resilience to low temperature at both key developmental phases. Seedling-stage tolerance was assessed using an artificial cold-water tank, while reproductive-stage tolerance was evaluated under both natural field conditions and controlled cold screening facilities. Performance was measured through a combination of quantitative traits (plant height, days to heading, panicle length) and qualitative indicators (panicle degeneration, panicle exsertion, spikelet fertility). Two breeding lines - BR8907-B-1-2-CS1-4-CS2-P3-4 and BR8909-B-12-2-CS1-4-CS2-P2-3-2, demonstrated seedling-stage cold tolerance with minimum leaf discoloration and the highest survival rate across three experimental batches. Five genotypes (Bhutan, IR83222-F11-173, Rata Boro, BRRI dhan74, BR11712-4R-227) showed tolerance during the reproductive stage. Three lines (Bhutan, BR11712-4R-227, and BR12266-44-11-32-5-1-1-HR10-B) showed moderately tolerant to tolerant across both stages. Six genotypes, including BR10317-5R-25, IR18A1859, and BRRI dhan28 were consistently vulnerable to cold stress at both stages. Principal Component Analysis (PCA) revealed that under field conditions, both seedling and reproductive traits contributed to shared components - suggesting overlapping physiological mechanisms. However, under controlled environments, the traits separated distinctly, pointing to stage-specific genetic control. These results are consistent with reports of distinct QTLs contributing to cold tolerance at different stages, highlighting the complex nature of cold tolerance and informing breeding strategies for enhanced cold resilience in rice.

plant biology↗

Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

BackgroundThe gram-negative bacterium Burkholderia gladioli can cause diseases in a wide range of hosts, including humans and plants. In rice, it produces Bacterial Panicle Blight (BPB), an emerging disease that is threatening the production of this staple food worldwide. Recently, BPB has affected several rice fields in Bangladesh, and B. gladioli has been reported as the causative agent in one of these fields, raising questions about how the pathogen was introduced into the country. Understanding the introduction routes into Bangladesh and the pathogenicity mechanisms of B. gladioli is essential to develop sustainable management strategies to control BPB. ResultsTo investigate the origin of pathogenic B. gladioli strains and their introduction routes into Bangladesh, we sequenced the complete genomes of 19 strains isolated from symptomatic rice panicles from four major rice-growing districts of the country (Rangpur, Faridpur, Natore, and Mymensingh). A phylogenetic analysis encompassing all 320 publicly available B. gladioli genomes along with the 19 newly sequenced genomes revealed five independent introduction events into Bangladesh--four of which showed close phylogenetic links to clinical isolates from the USA--and no evidence of inter-district dissemination within the country. Many host transitions (35 human-to-plant and 1 plant-to-human) were inferred across the phylogeny, highlighting the pathogens versatile and cross-kingdom transmission dynamics. Analysis of the presence/absence patterns of 37 virulence-related genes across all 339 B. gladioli strains indicated that human-to-plant host transitions often coincided with loss of the tsr and motB genes--which are associated with bacterial motility--, suggesting convergent adaptive shifts in response to host switches. ConclusionOur findings shed light on the introduction pathways of pathogenic B. gladioli strains into Bangladesh and highlight specific virulence-related genes as potentially responsible for cross-kingdom host shifts.

genomics↗

Inflammatory reprogramming of human brain endothelial cells compromises blood-brain barrier integrity in Alzheimer's disease

Blood-brain barrier (BBB) dysfunction is an early feature of Alzheimers disease (AD), yet the endothelial gene-regulatory programs involved remain incompletely understood. We integrate postmortem human single-nucleus transcriptomics with iPSC-based BBB models to define a conserved, inflammation-driven pathway that compromises barrier integrity. We identify an NF-{kappa}B-associated endothelial gene module endoM2 that is elevated in AD, inversely correlated with cognition, and enriched for inflammation and endothelial-to-mesenchymal transition signatures. Cytokine stimulation of iPSC-derived brain endothelial cells induces morphological remodeling, lipid accumulation, junctional disruption, and transcriptomic shifts that mirror endoM2. A targeted drug screen identifies the NF-{kappa}B inhibitor BAY11-7082 as protective against cytokine-induced changes. In our perfusable iPSC-derived BBB-Chip that recapitulates human BBB signatures, single-cell profiling reveals inflammatory endothelial state-specific programs reflecting those in AD brains and demonstrates that BAY11-7082 suppresses cytokine-triggered dysfunction and reverses inflammation-associated gene activation. Together, these findings position cerebrovascular inflammation as a therapeutic target to preserve BBB integrity in AD.

neuroscience↗

Knowledge Graph-Based Framework for Detecting Horizontal Gene Transfer Events Driving Antimicrobial Resistance

Horizontal gene transfer (HGT) is a key mechanism driving the rapid dissemination of antimicrobial resistance (AMR) among bacterial populations, posing a severe threat to global public health. Traditional detection methods for HGT, such as phylogenetic incongruence and compositional analysis, are often limited in their scope and accuracy. To address these challenges, we propose a comprehensive knowledge graph (KG)-based framework that integrates genomic, environmental, biochemical, and ontological datasets to detect and analyze HGT events contributing to AMR. Our KG captures relationships among genes, plasmids, species, mobile genetic elements, antibiotics, and ecological factors using curated sources like NCBI, CARD, ICEberg, MGnify, and KEGG. We enrich nodes and edges with biological (e.g., GC content, codon bias) and chemical (e.g., binding affinities, environmental exposure) signatures and apply ontology-based semantic enrichment using ARO and GO. A Graph Neural Network (GNN) trained on the KG achieves high accuracy (92%) and F1-score (0.90) in predicting HGT events, outperforming conventional methods. Community detection identifies AMR dissemination hubs, while environmental analyses reveal strong correlations between antibiotic concentrations and resistance gene prevalence. Our framework demonstrates strong biological and chemical validation and provides a scalable, interpretable, and data-rich tool for AMR surveillance, with implications for clinical, agricultural, and environmental microbiology.

bioinformatics↗

Combined CSF1R Inhibition and Sensory Gamma Stimulation Provide Protective Effects in a Mouse Model of Alzheimers Disease

The CSF1R inhibitor PLX3397, an FDA-approved treatment for a rare cancer, has been shown to reduce microglia count, lower inflammation, and increase synaptic markers in mouse models of Alzheimers disease (AD). However, the effects of PLX3397 on neural function in AD remain largely unknown. Here, we characterized the effects of PLX3397 treatment in 5xFAD mice. While PLX3397 increased synaptic density, it reduced the percentage of neurons phase-locked to gamma oscillations. This neural decoupling was closely associated with gene expression changes related to synapse organization. We investigated whether Gamma ENtrainment Using Sensory (GENUS) stimulation could counterbalance the neural circuit alterations induced by PLX3397. GENUS + PLX3397 restored gamma phase-locking, reshaped gene expression signatures, and improved learning and memory better than either treatment alone in 5xFAD mice. These findings suggest that CSF1R inhibitors like PLX3397 may benefit from a multimodal approach combining microglial targeting with non-invasive sensory stimulation to support neural physiology and improve cognitive function in AD.

neuroscience↗

Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in a mouse model of Down syndrome

Down syndrome (DS) has been linked with deficits in hippocampal dependent cognitive tasks and adult neurogenesis, yet treatment options are still very limited. We and others previously showed that a non-invasive multisensory gamma stimulation using light and sound at 40 Hz ameliorated Alzheimers disease pathology and symptoms in mouse models. In this study, we tested the effects of 40 Hz multisensory stimulation in the Ts65Dn mice, a mouse model of DS. For three weeks, mice were exposed daily to one hour of stimulation or one hour of ambient light and sound. Mice receiving the stimulation showed improved object recognition and spatial working memory. Using single nuclei RNA-seq and experimental validations in mouse hippocampal samples, we identified underlying expression changes in gene regulatory networks and demonstrated increased adult neurogenesis and reorganization of synapses as potential mechanisms for these improved cognitive phenotypes. Together, our data reveal a novel effect of multisensory gamma stimulation on adult neurogenesis and beneficial effects of 40 Hz treatment on cognitive function in DS model mice. Significance StatementWe present strong evidence, using a well-characterized mouse model, that the cognitive and neurogenesis deficits in Down syndrome can be improved through non-invasive multi-sensory gamma stimulation. Employing a systems biology approach, we provide extensive hippocampal single-cell resolution gene expression signatures and changes in gene regulatory networks in response to sensory gamma stimulation.

neuroscience↗

Capturing sclera anisotropy using direct collagen fiber models. Linking microstructure to macroscopic mechanical properties.

Because of the crucial role of collagen fibers on soft tissue mechanics, there is great interest in techniques to incorporate them in computational models. Recently we introduced a direct fiber modeling approach for sclera based on representing the long-interwoven fibers. Our method differs from the conventional continuum approach to modeling sclera that homogenizes the fibers and describes them as statistical distributions for each element. At large scale our method captured gross collagen fiber bundle architecture from histology and experimental intraocular pressure-induced deformations. At small scale, a direct fiber model of a sclera sample reproduced equi-biaxial experimental behavior from the literature. In this study our goal was a much more challenging task for the direct fiber modeling: to capture specimen-specific 3D fiber architecture and anisotropic mechanics of four sclera samples tested under equibiaxial and four non-equibiaxial loadings. Samples of sclera from three eyes were isolated and tested in five biaxial loadings following an approach previously reported. Using microstructural architecture from polarized light microscopy we then created specimen-specific direct fiber models. Model fiber orientations agreed well with the histological information (adjusted R2s>0.89). Through an inverse-fitting process we determined model characteristics, including specimen-specific fiber mechanical properties to match equibiaxial loading. Interestingly, the equibiaxial properties also reproduced all the non-equibiaxial behaviors. These results indicate that the direct fiber modeling method naturally accounted for tissue anisotropy within its fiber structure. Direct fiber modeling is therefore a promising approach to understand how macroscopic behavior arises from microstructure.

bioengineering↗

Comparing continuum and direct fiber models of soft tissues.An ocular biomechanics example reveals that continuum models may artificially disrupt the strains at both the tissue and fiber levels

Collagen fibers are the main load-bearing component of soft tissues but difficult to incorporate into models. Whilst simplified homogenization models suffice for some applications, a thorough mechanistic understanding requires accurate prediction of fiber behavior, including both detailed fiber-level strains and long-distance transmission. Our goal was to compare the performance of a continuum model of the optic nerve head (ONH) built using conventional techniques with a fiber model we recently introduced which explicitly incorporates the complex 3D organization and interaction of collagen fiber bundles [1]. To ensure a fair comparison, we constructed the continuum model with identical geometrical, structural, and boundary specifications as for the fiber model. We found that: 1) although both models accurately matched the intraocular pressure (IOP)-induced globally averaged displacement responses observed in experiments, they diverged significantly in their ability to replicate specific 3D tissue-level strain patterns. Notably, the fiber model faithfully replicated the experimentally observed depth-dependent variability of radial strain, the ring-like pattern of meridional strain, and the radial pattern of circumferential strain, whereas the continuum model failed to do so; 2) the continuum model disrupted the strain transmission along each fiber, a feature captured well by the fiber model. These results demonstrate limitations of the conventional continuum models that rely on homogenization and affine deformation assumptions, which render them incapable of capturing some complex tissue-level and fiber-level deformations. Our results show that the strengths of explicit fiber modeling help capture intricate ONH biomechanics. They potentially also help modeling other fibrous tissues. Statement of SignificanceUnderstanding the mechanics of fibrous tissues is crucial for advancing knowledge of various diseases. This study uses the ONH as a test case to compare conventional continuum models with fiber models that explicitly account for the complex fiber structure. We found that the fiber model captured better the biomechanical behaviors at both the tissue level and the fiber level. The insights gained from this study demonstrate the significant potential of fiber models to advance our understanding of not only glaucoma pathophysiology but also other conditions involving fibrous soft tissues. This can contribute to the development of therapeutic strategies across a wide range of application

bioengineering↗

METTL3 shapes m6A epitranscriptomic landscape for successful human placentation

Methyltransferase-like 3 (METTL3), the catalytic enzyme of methyltransferase complex for m6A methylation of RNA, is essential for mammalian development. However, the importance of METTL3 in human placentation remains largely unexplored. Here, we show that a fine balance of METTL3 function in trophoblast cells is essential for successful human placentation. Both loss-of and gain-in METTL3 functions are associated with adverse human pregnancies. A subset of recurrent pregnancy losses and preterm pregnancies are often associated with loss of METTL3 expression in trophoblast progenitors. In contrast, METTL3 is induced in pregnancies associated with fetal growth restriction (FGR). Our loss of function analyses showed that METTL3 is essential for the maintenance of human TSC self-renewal and their differentiation to extravillous trophoblast cells (EVTs). In contrast, loss of METTL3 in human TSCs promotes syncytiotrophoblast (STB) development. Global analyses of RNA m6A modification and METTL3-RNA interaction in human TSCs showed that METTL3 regulates m6A modifications on the mRNA molecules of critical trophoblast regulators, including GATA2, GATA3, TEAD1, TEAD4, WWTR1, YAP1, TFAP2C and ASCL2, and loss of METTL3 leads to depletion of mRNA molecules of these critical regulators. Importantly, conditional deletion of Mettl3 in trophoblast progenitors of an early post-implantation mouse embryo also leads to arrested self-renewal. Hence, our findings indicate that METLL3 is a conserved epitranscriptomic governor in trophoblast progenitors and ensures successful placentation by regulating their self-renewal and dictating their differentiation fate.

developmental biology↗

Characterization of the novel SmsHSP24.1 Promoter: Unveiling its abiotic stress-inducible expression in transgenic Eggplant (Solanum melongena L.)

Promoters play a pivotal role in regulating gene expression, orchestrating vital processes in plants, including their responses to various environmental stresses. In this study, we focus on the comprehensive characterization of the SmsHSP24.1 promoter, a novel cis-acting element, within the context of transgenic Eggplant (Solanum melongena L.). This detailed analysis shed light on the intricate mechanisms governing SmsHSP24.1 promoter-driven gene regulation, particularly in response to adverse environmental challenges such as heat, salt and drought stressors offering valuable insights into its role in plant stress adaptation. The advances in our understanding of promoter-driven gene regulation also contribute to the broader goal of enhancing crop resilience to abiotic stresses, positioning the SmsHSP24.1 promoter as a promising tool in agricultural biotechnology applications. HighlightsO_LIDemonstrated that the full-length 2.0 kb SmsHSP24.1 promoter significantly enhances gene expression under heat stress, with an observable decline in expression with promoter truncation. C_LIO_LIIdentified specific regulatory elements within the SmsHSP24.1 promoter that are decisive for inducible expression in response to abiotic stresses such as heat, salt, and drought. C_LIO_LIHighlighted the utility of the SmsHSP24.1 promoter in crop improvement programs, offering a tool for developing transgenic plant tolerance to combined stresses. C_LI

plant biology↗

Beyond the Sin3/HDAC Complex: FAM60A emerges as a regulator of RNA Splicing

FAM60A, traditionally linked to chromatin remodeling within the Sin3/HDAC complex, has emerged as a critical regulator in RNA splicing. Employing an integrative approach that combines immunological assays, CRISPR/Cas9 technology, comprehensive genomics, proteomics, and advanced cross-linking mass spectrometry, complemented by sophisticated 3D molecular modeling, our study challenges and extends the existing understanding of FAM60As functional dynamics. Contravening previous perceptions, our findings elucidate that FAM60A does not interact directly with SIN3A, rather establishes direct interactions with SAP30 and HDAC1, redefining its relationship with the Sin3/HDAC complex. These interactions, deciphered through detailed 3D structural analysis supported by cross-linking constraints, signify a complex architectural role of FAM60A within chromatin remodeling processes. Moreover, our research unveils FAM60As pivotal role in RNA processing, particularly in splicing regulation. Through extensive molecular interactions with a diverse array of mRNA-binding proteins and principal spliceosome components, FAM60A emerges as a key regulator of RNA splicing. This expanded role delineates its influence on gene expression regulation, spotlighting its capacity to modulate critical cellular processes. In sum, this study unveils FAM60As key role in gene regulation and RNA splicing, and suggests new paths for cellular and therapeutic research.

molecular biology↗

A single-cell transcriptomic analysis of the mouse hippocampus after voluntary exercise

Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-{kappa}B, Wnt/{beta}-catenin, Notch, retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important resource dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline.

neuroscience↗

Genetic Gains in IRRIs Rice Salinity Breeding and Elite Panel Development as a Future Breeding Resource

Genetic gain is a crucial parameter to check the breeding programs success and help optimize future breeding strategies for enhanced genetic gains. In this work, IRRIs historical data from the Philippines and Bangladesh of the salinity breeding program was used to estimate the genetic gains and identify the best lines based on higher breeding values for yield as a future genetic resource. Two-stage mixed-model approach accounting for experimental design factors and pedigrees was adopted to obtain the breeding values for yield and estimate genetic trends under the salinity conditions. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha for the Philippines and 0.31% per annum with a yield advantage of 14.02 kg/ha for Bangladesh datasets was observed. For the released varieties, genetic gain was 0.12% per annum with a yield advantage of 2.2 kg/ha/year and 0.14% per annum with a yield advantage of 5.9 kg/ha/year, respectively. Further, based on higher breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of >2400 kg/ha in the Philippines and >3500 kg/ha in Bangladesh with a selection accuracy >0.4 were selected for formulating the elite breeding panel as a future breeding resource. Conclusively, higher genetic gains are pivotal in IRRIs rice salinity breeding program, which requires a holistic breeding approach with a major paradigm shift in breeding strategies to enhance genetic gains. Key MessageEstimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains.

genetics↗

Fibrous Finite Element Modeling of the Optic Nerve Head Region

The optic nerve head (ONH) region at the posterior pole of the eye is supported by a fibrous structure of collagen fiber bundles. Discerning how the fibrous structure determines the region biomechanics is crucial to understand normal physiology, and the roles of biomechanics on vision loss. The fiber bundles within the ONH structure exhibit complex three-dimensional (3D) organization and continuity across the various tissue components. Computational models of the ONH, however, usually represent collagen fibers in a homogenized fashion without accounting for their continuity across tissues, fibers interacting with each other and other synergistic effects in a fibrous structure. We present a novel fibrous finite element (FFE) model of the ONH that incorporates discrete collagen fiber bundles and their histology-based 3D organization to study ONH biomechanics as a fibrous structure. The FFE model was constructed using polarized light microscopy data of porcine ONH cryosections, representing individual fiber bundles in the sclera, dura and pia maters with beam elements and canal tissues as continuum structures. The FFE model mimics the histological in-plane orientation and width distributions of collagen bundles as well as their continuity across different tissues. Modeling the fiber bundles as linear materials, the FFE model predicts the nonlinear ONH response observed in an inflation experiment from the literature. The model also captures important microstructural mechanisms including fiber interactions and long-range strain transmission among bundles that have not been considered before. The FFE model presented here advances our understanding of the role of fibrous collagen structure in the ONH biomechanics. Statement of SignificanceThe microstructure and mechanics of the optic nerve head (ONH) are central to ocular physiology. Histologically, the ONH region exhibits a complex continuous fibrous structure of collagen bundles. Understanding the role of the fibrous collagen structure on ONH biomechanics requires high-fidelity computational models previously unavailable. We present a novel computational model of the ONH that incorporates histology-based fibrous collagen structure derived from polarized light microscopy images. The model predictions agree with experiments in the literature, and provide insight into important microstructural mechanisms of fibrous tissue biomechanics, such as long-range strain transmission along fiber bundles. Our model can be used to study the microstructural basis of biomechanical damage and the effects of collagen remodeling in glaucoma.

bioengineering↗

A novel miR-99b-5p-Zbp1 pathway in microglia contributes to the pathogenesis of schizophrenia

Schizophrenia is a psychiatric disorder that is still not readily treatable. Pharmaceutical advances in the treatment of schizophrenia have mainly focused on the protein coding part of the human genome. However, the vast majority of the human transcriptome consists of non-coding RNAs. MicroRNAs are small non-coding RNAs that control the transcriptome at the systems level. In the present study we analyzed the microRNAome in blood and postmortem brains of controls and schizophrenia patients and found that miR-99b-5p was downregulated in both the prefrontal cortex and blood of patients. At the mechanistic level we show that inhibition of miR-99b-5p leads to schizophrenia-like phenotypes in mice and induced inflammatory processes in microglia linked to synaptic pruning. The miR-99b-5p-mediated inflammatory response in microglia depended on Z-DNA binding protein 1 (Zbp1) which we identified as a novel miR-99b-5p target. Antisense oligos (ASOs) against Zbp1 ameliorated the pathological phenotypes caused by miR-99b-5p inhibition. In conclusion, we report a novel miR-99b-5p-Zbp1 pathway in microglia that contributes to the pathogenesis of schizophrenia. Our data suggest that strategies to increase the levels of miR-99b-5p or inhibit Zbp1 could become a novel therapeutic strategy.

neuroscience↗

A direct fiber approach to model sclera collagen architecture and biomechanics

Sclera collagen fiber microstructure and mechanical behavior are central to eye physiology and pathology. They are also complex, and are therefore often studied using modeling. Most models of sclera, however, have been built within a conventional continuum framework. In this framework, collagen fibers are incorporated as statistical distributions of fiber characteristics such as the orientation of a family of fibers. The conventional continuum approach, while proven successful for describing the macroscale behavior of the sclera, does not account for the sclera fibers are long, interwoven and interact with one another. Hence, by not considering these potentially crucial characteristics, the conventional approach has only a limited ability to capture and describe sclera structure and mechanics at smaller, fiber-level, scales. Recent advances in the tools for characterizing sclera microarchitecture and mechanics bring to the forefront the need to develop more advanced modeling techniques that can incorporate and take advantage of the newly available highly detailed information. Our goal was to create a new computational modeling approach that can represent the sclera fibrous microstructure more accurately than with the conventional continuum approach, while still capturing its macroscale behavior. In this manuscript we introduce the new modeling approach, that we call direct fiber modeling, in which the collagen architecture is built explicitly by long, continuous, interwoven fibers. The fibers are embedded in a continuum matrix representing the non-fibrous tissue components. We demonstrate the approach by doing direct fiber modeling of a rectangular patch of posterior sclera. The model integrated fiber orientations obtained by polarized light microscopy from coronal and sagittal cryosections of pig and sheep. The fibers were modeled using a Mooney- Rivlin model, and the matrix using a Neo-Hookean model. The fiber parameters were determined by inversely matching experimental equi-biaxial tensile data from the literature. After reconstruction, the direct fiber model orientations agreed well with the microscopy data both in the coronal plane (adjusted R2=0.8234) and in the sagittal plane (adjusted R2=0.8495) of the sclera. With the estimated fiber properties (C10=5746.9 MPa; C01=-5002.6MPa, matrix shear modulus 200kPa), the models stress-strain curves simultaneously fit the experimental data in radial and circumferential directions (adjusted R2s 0.9971 and 0.9508, respectively). The estimated fiber elastic modulus at 2.16% strain was 5.45GPa, in reasonable agreement with the literature. During stretch, the model exhibited stresses and strains at sub-fiber level, with interactions among individual fibers which are not accounted for by the conventional continuum methods. Our results demonstrate that direct fiber models can simultaneously describe the macroscale mechanics and microarchitecture of the sclera, and therefore that the approach can provide unique insight into tissue behavior questions inaccessible with continuum approaches. HighlightsCollagen fibers are the main load-bearing component of eye tissues. Conventional sclera modeling ignores that fibers are long, interwoven and interact. We demonstrate a direct fiber model with long, interwoven and interacting fibers. Collagen fiber mechanical properties were estimated using inverse fitting. The model captures simultaneously sclera fiber structure and macroscale mechanics.

bioengineering↗