Biology subjects

Karimi, E.

Publications and source records attributed to Karimi, E..

6 recordsLinked to original sources

bioRxiv2025

KLHL41 orchestrates sarcomere assembly and size to drive skeletal muscle hypertrophy in vivo

Sarcomere assembly and growth are fundamental processes essential for the development, function, and repair of skeletal muscle. However, the mechanisms underlying sarcomere formation and assembly in vivo, which are critical for the formation of functional myofibers in vertebrates, remain poorly understood. Defects in sarcomeres contribute to muscle dysfunction in numerous genetic and acquired myopathies, yet the lack of a clear understanding of specific sarcomeric defects has hindered the development of effective therapies. Nemaline myopathy (NM) is caused by mutations in genes that primarily affect sarcomere structure and function. The disease is clinically heterogeneous, with the congenital form being the most severe. Using zebrafish models of congenital forms of NM, we investigated sarcomere assembly in vivo during skeletal muscle development to identify key steps contributing to myofibril formation and muscle growth under both normal and disease conditions. Our findings demonstrate that the gene encoding the sarcomeric protein KLHL41 plays a critical role in the formation and directional organization of new sarcomeres within developing myofibrils, facilitating both radial and longitudinal muscle growth. Dysregulation of sarcomeric proteins and impaired protein turnover in the KLHL41-NM zebrafish model resulted in the development of sarcomeric defects. Moreover, we show that the interaction between the KLHL41-troponin complex is essential for muscle growth and cross-bridge regulation in developing muscle. These studies address a significant gap in the understanding of sarcomeric defects in myopathies and will help guide the development of targeted therapies aimed at rescuing these processes.

genetics↗

bioRxiv2023

Characterization of NEB mutations in patients reveals novel nemaline myopathy disease mechanisms and omecamtiv mecarbil force effects

Nebulin, a critical protein of the skeletal muscle thin filament, plays important roles in physiological processes such as regulating thin filament length (TFL), cross-bridge cycling, and myofibril alignment. Mutations in the nebulin gene (NEB) cause NEB-based nemaline myopathy (NEM2), a genetically heterogeneous disorder characterized by hypotonia and muscle weakness, currently lacking therapies targeting the underlying pathological mechanisms. In this study, we examined a cohort of ten NEM2 patients, each with unique mutations, aiming to understand their impact on mRNA, protein, and functional levels. Results show that truncation mutations affect NEB mRNA stability and lead to nonsense-mediated decay of the mutated transcript. Moreover, a high incidence of cryptic splice site activation was found in patients with splicing mutations which is expected to disrupt the actin-binding sites of nebulin. Determination of protein levels revealed patients with relatively normal nebulin levels and others with markedly reduced nebulin. We observed a positive relation between the reduction in nebulin and a reduction in TFL, and a positive relation between the reduction in nebulin level and the reduction in tension (both maximal and submaximal tension). Interestingly, our study revealed a duplication mutation in nebulin that resulted in a larger nebulin protein and longer TFL. Additionally, we investigated the effect of Omecamtiv mecarbil (OM), a small-molecule activator of cardiac myosin, on force production of type I muscle fibers of NEM2 patients. OM treatment substantially increased submaximal tension across all NEM2 patients ranging from 87-318%, with the largest effects in patients with the lowest level of nebulin. In summary, this study indicates that post-transcriptional or post-translational mechanisms regulate nebulin expression. Moreover, we propose that the pathomechanism of NEM2 involves not only shortened but also elongated thin filaments, along with the disruption of actin-binding sites resulting from splicing mutations. Significantly, our findings highlight the potential of OM treatment to improve skeletal muscle function in NEM2 patients, especially those with large reductions in nebulin levels.

genetics↗

bioRxiv2022

Machine learning meets classical computer vision for accurate cell identification

High-parameter multiplex immunostaining techniques have revolutionized our ability to image healthy and diseased tissues with unprecedented depth; however, accurate cell identification and segmentation remain significant downstream challenges. Identifying individual cells with high precision is a requisite to reliably and reproducibly interpret acquired data. Here we introduce CIRCLE, a cell identification pipeline that combines classical and modern machine learning-based computer vision algorithms to address the shortcomings of current cell segmentation tools for 2D images. CIRCLE is a fully automated hybrid cell detection model, eliminating subjective investigator bias and enabling high-throughput image analysis. CIRCLE accurately distinguishes cells across diverse tissues microenvironments, resolves low-resolution structures, and can be applied to any 2D image that contains nuclei. Importantly, we quantitatively demonstrate that CIRCLE outperforms current state-of-the-art image segmentation tools using multiple accuracy measures. As high-throughput multiplex imaging grows closer toward standard practice for histology, integration of CIRCLE into analysis protocols will deliver unparalleled segmentation quality.

cell biology↗

bioRxiv2021

A critical role for E2-p53 interaction during the human papillomavirus 16 life cycle

Human papillomaviruses (HPV) are causative agents in ano-genital and oral cancers; HPV16 is the most prevalent type detected in human cancers. The HPV16 E6 protein targets p53 for proteasomal degradation to facilitate proliferation of the HPV16 infected cell. However, in HPV16 immortalized cells E6 is predominantly spliced (E6*) and unable to degrade p53. Here we demonstrate that human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), and HPV16 positive oropharyngeal cancers, retain significant expression of p53. In addition, p53 levels can be increased in HPV16+ head and neck cancer cell lines following treatment with cisplatin. Introduction of full-length E6 into HFK+HPV16 resulted in attenuation of cellular growth (in hTERT immortalized HFK, E6 expression promoted enhanced proliferation). An understudied interaction is that between E2 and p53 and we investigated whether this was important for the viral life cycle. We generated mutant genomes with E2 unable to interact with p53 resulting in profound phenotypes in primary HFK. The mutant induced hyper-proliferation, but an ultimate arrest of cell growth; {beta}-galactosidase staining demonstrated increased senescence, and COMET assays showed increased DNA damage compared with HFK+HPV16 wild type cells. There was failure of the viral life cycle in organotypic rafts with the mutant HFK resulting in premature differentiation and reduced proliferation. The results indicate that the E2-p53 interaction is critical during the HPV16 life cycle, and that disruption of this interaction has anti-viral potential. We discuss potential mechanisms to explain these phenotypes. ImportanceHuman papillomaviruses are causative agents in around 5% of all cancers. There are currently no antivirals available to combat these infections and cancers, therefore it remains a priority to enhance our understanding of the HPV life cycle. Here we demonstrate that an interaction between the viral replication/transcription/segregation factor E2 and the tumor suppressor p53 is critical for the HPV16 life cycle. HPV16 immortalized cells retain significant expression of p53, and the critical role for the E2-p53 interaction demonstrates why this is the case. If the E2-p53 interaction is disrupted then HPV16 immortalized cells fail to proliferate, have enhanced DNA damage and senescence, and there is premature differentiation during the viral life cycle. Results suggest that targeting the E2-p53 interaction would have therapeutic benefits, potentially attenuating the spread of HPV16.

molecular biology↗

bioRxiv2021

Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus

Ectocarpus subulatus is one of the few brown algae found in river habitats. Its ability to tolerate freshwater is due, in part, to its uncultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. The acclimation to low salinity of fresh water-tolerant and intolerant holobionts was then compared. Salinity had a significant impact on bacterial gene expression as well as the expression of algae- and bacteria-associated viruses in all holobionts, albeit in different ways for each holobiont. On the other hand, gene expression of the algal host and metabolite profiles were affected almost exclusively in the fresh water intolerant holobiont. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, we identified vitamin K synthesis as one possible bacterial service missing specifically in the fresh water-intolerant holobiont in low salinity. We also noticed an increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a compound that regulates quorum sensing. This could have caused a shift in bacterial behavior in the intolerant holobiont, resulting in virulence or dysbiosis. Originality-Significance StatementThe importance of symbiotic microbes for the health and stress resistance of multicellular eukaryotes is widely acknowledged, but understanding the mechanisms underlying these interactions is challenging. They are especially difficult to separate in systems with one or more uncultivable components. We bridge the gap between fully controlled, cultivable model systems and purely environmental studies through the use of a multi-omics approach and metabolic models on experimentally modified "holobiont" systems. This allows us to generate two promising working hypotheses on the mechanisms by which uncultivated bacteria influence their brown algal hosts fresh water tolerance.

ecology↗

bioRxiv2020

Isolation and genome sequencing of 14 Spongia sp. bacterial associates expands the taxonomic and functional breadth of the cultivatable marine sponge microbiome

Marine sponges live with complex microbial consortia, which have been considered as potential sources of novel natural products. However, the usual recalcitrance of host-associated microorganisms to cultivation makes studying sponge symbionts challenging. To tackle this complexity, exploration of cultivated sponge-associated bacteria and their coding potential is unavoidable. In this study, we isolate and report the draft genome sequences of 14 bacterial strains from the marine sponge Spongia sp. using R2A and VXA media. The strains belong to the classes Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, and Cytophagia spanning 11 formally described genera plus two potentially novel genera in the Rhodobacteraceae family and one potentially novel family in the Cytophagales order. Functional genomics revealed presumed symbiosis factors typical of specific taxonomic groups (i.e. taurine metabolism genes among the Alphaproteobacteria, chitinase encoding genes and eukaryotic-like proteins in the Cytophagia genome) while multidrug efflux pumps, also important in host-microbe interactions, were common across all genomes. Moreover, we detected 76 secondary-metabolite biosynthetic gene clusters putatively involved in the production of drug-like compounds or signalling molecules across all genomes, warranting future biotechnologically driven research into their coding potential.

microbiology↗