Biology subjects

Sherman, A.

Publications and source records attributed to Sherman, A..

13 recordsLinked to original sources

bioRxiv2026

Nup98 regulates the G1/S transition

Nuclear pore complexes (NPCs) are embedded throughout the nuclear envelope of all eukaryotic cells and are composed of 30 unique proteins called nucleoporins (Nups). While Nups primarily function at NPCs, multiple Nups function in the nucleoplasm independent of the NPC. We previously found that Nup98-96 is necessary for entry into S phase in Drosophila cells, however, the mechanism is unknown. Here, we demonstrate that Nup98-96 is one of only a subset of Nup genes that can promote entry into S phase. We identify that transcripts dependent on Nup98-96 in Drosophila cells are enriched in cell cycle processes and that many of these transcripts are also dependent on the cell cycle regulator, E2f1. Importantly, we find that entry into S phase can be rescued by co-depleting the CycE/CDK2 inhibitor, dacapo, in Nup98-96-depleted cells. Furthermore, Nup96-98 promotes S phase entry across multiple cell and tissue types and cell cycle contexts. Critically, overexpression of Nup98 has a dominant-negative effect on entry into S phase in larval salivary glands, suggesting that Nup98, not Nup96, promotes entry into S phase. Our work identifies Nup98 as a key regulator of the G1/S transition in metazoans.

molecular biology↗

bioRxiv2026

Dual Knockout of StAMY23 and StVINV Improves Postharvest Storage Traits in Potato

Starch is the primary carbohydrate reserve in potato (Solanum tuberosum L.) tubers and a critical determinant of their industrial value. The rate of starch degradation during postharvest storage directly influences key traits such as endodormancy (ED) duration and cold-induced sweetening (CIS), which affect sprouting behavior. In this study, we used CRISPR/Cas9 genome editing to knockout StAMY23, a gene encoding -amylase involved in starch breakdown. stamy23 plants exhibited higher yield and extended tuber ED postharvest, without significantly altering CIS or starch granule content. To further reduce CIS, we knockout StAMY23 in VACUOLAR INVERTASE knockout (stvinv) backgrounds, generating stamy23/stvinv double-knockouts plants. These lines showed significantly reduced CIS, prolonged ED, and elevated starch content, along with altered starch granule content. Collectively, our findings demonstrate that simultaneous downregulation of StAMY23 and StVINV can additively enhance desirable postharvest traits, providing a promising strategy for improving potato storage quality through precision genome editing.

plant biology↗

bioRxiv2026

Enhancing adeno-associated virus cellular entry through receptor engineering

Adeno-associated viruses (AAV) are approved for gene therapy of several genetic disorders; however, key aspects of AAV cellular entry remain poorly understood. We previously identified carboxypeptidase D (AAVR2) as an AAV receptor distinct from the multi-serotype AAV receptor KIAA0319L (AAVR). In this study, we investigate the molecular mechanisms and biological roles of AAVR and AAVR2 in mediating AAV gene transfer. Using proximity-dependent biotin identification (BioID), we defined the interactome of AAVR in the presence or absence of AAV8 and identified various proteins involved in viral entry including AAVR2. We confirmed a direct physical interaction between AAVR and AAVR2, mediated by non-AAV interacting regions in the C-termini. Further, we identified functional motifs within the carboxy-terminal tails of both receptors to facilitate the engineering of chimeric receptors with enhanced activity. Functional assays demonstrated that the overexpression of AAVR or AAVR2 enhances the cellular attachment and entry of AAV in a serotype-specific manner. Finally, we generated a stable cell line expressing a minimal functional AAVR2 with increased sensitivity for in vitro potency testing for AAVR2-engaging serotypes like AAV8. Collectively, these findings reveal significant functional similarities in AAV receptor biology and establish a framework for engineering receptor-guided modalities.

molecular biology↗

bioRxiv2025

Crafting Mathematical Models for Type 2 Diabetes Progression: Leveraging Longitudinal Data

Mathematical modeling is a powerful quantitative tool to investigate the pathogenesis of type 2 diabetes (T2D). Most modeling work on the progression of T2D has been formulated by modifying the pioneering model of Topp et al, which established the paradigm of glucotoxicity as the main driver of pathogenesis. However, certain parameter values in the Topp model deviate from physiological data, leading to predictions that deviate from clinical scenarios. Moreover, the simple structure of the model limits its explanatory capacity for clinical data. Leveraging a four-dimensional longitudinal dataset from Southwest Native Americans who progressed from normal glucose tolerance to T2D, we developed a series of models, starting with a minimally modified version of the Topp model and iteratively incorporating additional model elements to account for new biological mechanisms until optimal data fit was achieved. The notable variability of the individual trajectories was overcome by the non-linear mixed-effect modeling approach. Despite the absence of a discernible common trend among the individual trajectories of each variable, the model effectively captured the diverse glucose-insulin dynamics of individuals progressing to T2D. The reliability of the model was reinforced by its successful cross-validation against a subset of individuals progressing only to prediabetes. The systematic model selection process aided in navigating the trade-off between model complexity and practicability, culminating in a robust framework to address controversial questions in the diabetes field in future research.

systems biology↗

bioRxiv2024

Glioma-derived M-CSF and IL-34 license M-MDSCs to suppress CD8+ T cells in a NOS-dependent manner

Glioblastoma (GBM) is the most common malignant primary brain tumor, resulting in poor survival despite aggressive therapies. GBM is characterized by a highly heterogeneous and immunosuppressive tumor microenvironment (TME) made up predominantly of infiltrating peripheral immune cells. One significant immune cell type that contributes to glioma immune evasion is a population of immunosuppressive cells, termed myeloid-derived suppressor cells (MDSCs). Previous studies suggest that a subset of myeloid cells, expressing monocytic (M)-MDSC markers and dual expression of chemokine receptors CCR2 and CX3CR1, utilize CCR2 to infiltrate the TME. This study evaluated the mechanism of CCR2+/CX3CR1+ M-MDSC differentiation and T cell suppressive function in murine glioma models. We determined that bone marrow-derived CCR2+/CX3CR1+ cells adopt an immune suppressive cell phenotype when cultured with glioma-derived factors. Glioma secreted CSF1R ligands M-CSF and IL-34 were identified as key drivers of M-MDSC differentiation while adenosine and iNOS pathways were implicated in M-MDSC suppression of T cells. Mining a human GBM spatial RNAseq database revealed a variety of different pathways that M-MDSCs utilize to exert their suppressive function that are driven by complex niches within the microenvironment. These data provide a more comprehensive understanding of the mechanism of M-MDSCs in glioblastoma. Simple SummaryCurrently there are no effective therapies for glioblastoma. Infiltrating myeloid cells contribute significantly to the immune suppressive tumor microenvironment that is characteristic of GBM. Monocytic myeloid derived suppressor cells are chief immune suppressive cells found in the glioma microenvironment. Understanding the mechanisms of M-MDSC differentiation and T cell suppression is imperative for generating therapies that target this tumor supportive cell population. In this study we found that glioma secreted CSF1R ligands, M-CSF and IL-34, license M-MDSCs to suppress CD8 T cells. These M-MDSCs partially utilize nitric oxide synthase to illicit their suppressive activity. However, spatial RNAseq points to glioma microenvironment niches driving M-MDSC heterogeneity. Our findings identify key regulators of differentiation and suppressive mechanisms of M-MDSCs and confirm the importance of targeting this cell population in glioma.

cancer biology↗

bioRxiv2024

Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase

Epigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1. Here, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system. Methylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification. Collectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.

plant biology↗

bioRxiv2024

A male-essential microRNA is key for avian sex chromosome dosage compensation

Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyses of a Z-chromosome-linked microRNA (miR-2954) with strongly male-biased expression that was previously proposed to play a key role in sex chromosome dosage compensation1. We knocked out miR-2954 in chicken, which resulted in early embryonic lethality of homozygous knockout males, likely due to the highly specific upregulation of dosage-sensitive Z-linked target genes of miR-2954. Our evolutionary gene expression analyses further revealed that these dosage-sensitive target genes have become upregulated on the single Z in female birds during evolution. Altogether, our work unveils a scenario where evolutionary pressures on females following W gene loss led to the evolution of transcriptional upregulation of dosage-sensitive genes on the Z not only in female but also in male birds. The resulting overabundance of transcripts in males resulting from the combined activity of two dosage-sensitive Z gene copies was in turn offset by the emergence of a highly targeted miR-2954-mediated transcript degradation mechanism during avian evolution. Our findings demonstrate that birds have evolved a unique sex chromosome dosage compensation system in which a microRNA has become essential for male survival.

evolutionary biology↗

bioRxiv2024

Systemically targeting monocytic MDSCs using dendrimers and their cell-level biodistribution kinetics

The focus of nanoparticles in vivo trafficking has been mostly on their tissue-level biodistribution and clearance. Recent progress in the nanomedicine field suggests that the targeting of nanoparticles to immune cells can be used to modulate the immune response and enhance therapeutic delivery to the diseased tissue. In the presence of tumor lesions, monocytic-myeloid-derived suppressor cells (M-MDSCs) expand significantly in the bone marrow, egress into peripheral blood, and traffic to the solid tumor, where they help maintain an immuno-suppressive tumor microenvironment. In this study, we investigated the interaction between PAMAM dendrimers and M-MDSCs in two murine models of glioblastoma, by examining the cell-level biodistribution kinetics of the systemically injected dendrimers. We found that M-MDSCs in the tumor and lymphoid organs can efficiently endocytose hydroxyl dendrimers. Interestingly, the trafficking of M-MDSCs from the bone marrow to the tumor contributed to the deposition of hydroxyl dendrimers in the tumor. M-MDSCs showed different capacities of endocytosing dendrimers of different functionalities in vivo. This differential uptake was mediated by the unique serum proteins associated with each dendrimer surface functionality. The results of this study set up the framework for developing dendrimer-based immunotherapy to target M-MDSCs for cancer treatment.

bioengineering↗

bioRxiv2021

Transcriptomic heterogeneity of Sox2-expressing pituitary cells

The mammalian pituitary gland is a complex organ consisting of hormone-producing cells (HPC), nonhormonal folliculostellate cells (FSC) and pituicytes, vascular pericytes and endothelial cells, and putative Sox2-expressing stem cells. Here, we used scRNAseq analysis of adult female rat pituitary cells to study the heterogeneity of pituitary cells with a focus on evaluating the transcriptomic profile of the Sox2-expressing population. Samples containing whole pituitary and separated anterior and posterior lobe cells allowed the identification of all expected pituitary resident cell types and lobe-specific subpopulations of vascular cells. Sox2 was expressed uniformly in all FSC, pituicytes, and a fraction of HPC. FSC comprised two subclusters; FSC1 contained more cells but expressed less genetic diversity compared to FSC2. The latter contained proliferative cells, expressed genes consistent with stem cell niche formation, including tight junctions, and shared genes with HPC. The FSC2 transcriptome profile was also consistent with the activity of pathways regulating cell proliferation and stem cell pluripotency, including the Hippo and Wnt pathways. The expression of other stem cell marker genes was common for FSC and pituicytes (Sox9, Cd9, Hes1, Vim, S100b) or cell type-specific (FSC: Prop1, Prrx1, Pitx1, Pitx2, Lhx3; pituicytes: Fgf10, Tbx3, Lhx2, Nkx2-1, Rax). FSC and pituicytes also expressed other astroglial marker genes, some common and other distinct, consistent with their identities as astroglial cells of the pituitary. These data suggest functional heterogeneity of FSC, with a larger fraction representing classical FSC, and a smaller fraction containing active stem-like cells and HPC-committed progenitors.

neuroscience↗

bioRxiv2021

Direct cryopreservation of poultry/avian embryonic reproductive cells: A low-tech, cost-effective and efficient method for safeguarding genetic diversity

Chickens are an important resource for smallholder farmers who raise locally adapted, genetically distinct breeds for eggs and meat. The development of efficient reproductive technologies to conserve and regenerate chicken breeds safeguards existing biodiversity and secures poultry genetic resources for climate resilience, biosecurity, and future food production. The majority of the over 1600 breeds of chicken are raised in low and lower to middle income countries (LMICs) under resource limited, small scale production systems, which necessitates a low tech, cost effective means of conserving diversity is needed. Here, we validate a simple biobanking technique using cryopreserved embryonic chicken gonads. The gonads are quickly isolated, visually sexed, pooled by sex, and cryopreserved. Subsequently, the stored material is thawed and dissociated before injection into sterile host chicken embryos. By using pooled GFP and RFP-labelled donor gonadal cells and Sire Dam Surrogate (SDS) mating, we demonstrate that chicks deriving entirely from male and female donor germ cells are hatched. This technology will enable ongoing efforts to conserve chicken genetic diversity for both commercial and small holder farmers, and to preserve existing genetic resources at poultry research facilities.

developmental biology↗

bioRxiv2020

RECAS9: Recombining wild species introgression via mitotic gene editing in barley

Genetic loci underlying variation in traits with agronomic importance or genetic risk factors in human diseases have been identified by linkage analysis and genome-wide association studies. However, narrowing down the mapping to the individual causal genes and variations within these is much more challenging, and so is the ability to break linkage drag between beneficial and unfavourable loci in crop breeding. We developed RECAS9 as a transgene-free approach for precisely targeting recombination events by delivering CRISPR/Cas9 ribonucleotide protein (RNP) complex into heterozygous mitotic cells for the barley (Hordeum vulgare) Heat3.1 locus. A wild species (H. spontaneum) introgression in this region carries the agronomical unfavourable tough rachis phenotype (non-brittle) allele linked with a circadian clock accelerating QTL near GIGANTEA gene. We delivered RNP, which was targeted between two single nucleotide polymorphism (SNPs), to mitotic calli cells by particle bombardment. We estimated recombination events by next generation sequencing (NGS) and droplet digital PCR (ddPCR). While NGS analysis grieved from confounding effects of PCR recombination, ddPCR analysis allowed us to associate RNP treatment on heterozygous individuals with significant increase of homologous directed repair (HDR) between cultivated and wild alleles, with recombination rate ranging between zero to 57%. These results show for the first time in plants a directed and transgene free mitotic recombination driven by Cas9 RNP, and provide a starting point for precise breeding and fine scale mapping of beneficial alleles from crop wild relatives.

genetics↗

bioRxiv2020

DNA damage induced during mitosis undergoes DNA repair synthesis

Understanding the mitotic DNA damage response (DDR) is critical to our comprehension of cancer, premature aging and developmental disorders which are marked by DNA repair deficiencies. In this study we use a micro-focused-laser to induce DNA damage in selected mitotic chromosomes to study the subsequent repair response. Our findings demonstrate that (1) mitotic cells are capable of DNA repair as evidenced by DNA synthesis at damage sites, (2) Repair is attenuated when DNA-PKcs and ATM are simultaneously compromised, (3) Laser damage may permit the observation of previously undetected DDR proteins when damage is elicited by other methods in mitosis, and (4) Twenty five percent of mitotic DNA-damaged cells undergo a subsequent mitosis. Together these findings suggest that mitotic DDR is more complex than previously thought and may involve factors from multiple repair pathways that are better understood in interphase.

cell biology↗

bioRxiv2019

Type 2 Diabetes: One Disease, Many Pathways

Diabetes is a chronic, progressive disease that calls for longitudinal data and analysis. We introduce a longitudinal mathematical model that is capable of representing the metabolic state of an individual at any point in time during their progression from normal glucose tolerance to type 2 diabetes (T2D) over a period of years. As an application of the model, we account for the diversity of pathways typically followed, focusing on two extreme alternatives, one that goes through impaired fasting glucose (IFG) first, and one that goes through impaired glucose tolerance (IGT) first. These two pathways are widely recognized to stem from distinct metabolic abnormalities in hepatic glucose production and peripheral glucose uptake, respectively. We confirm this but go beyond to show that IFG and IGT lie on a continuum ranging from high hepatic insulin resistance and low peripheral insulin resistance to low hepatic resistance and high peripheral resistance. We show that IFG generally incurs IGT, and IGT generally incurs IFG on the way to T2D, highlighting the difference between innate and acquired defects and the need to assess patients early to determine their underlying primary impairment and appropriately target therapy. We also consider other mechanisms, showing that IFG can result from impaired insulin secretion, that non-insulin dependent glucose uptake can also mediate or interact with these pathways, and that impaired incretin signaling can accelerate T2D progression. We consider whether hyperinsulinemia can cause insulin resistance in addition to being a response to it and suggest that this is a minor effect.

physiology↗