Biology subjects

Brodsky, J.

Publications and source records attributed to Brodsky, J..

6 recordsLinked to original sources

bioRxiv2026

Surface Display For Phage Assisted Continuous Evolution: A Platform For Evolving / Screening Nanobodies In Prokaryote Systems

Despite >50 years of methods development, specific antibodies are still generated at low throughput and remain in high demand across biotechnology. Most biologics and immunoprobes are monoclonal antibodies, developed using a combination of inoculating animals with a target antigen, engineered candidate libraries, and multiple rounds of selection using phage or yeast display. Here we introduce a synthetic biology scheme to eliminate the need for nearly all of these steps, by combining Surface display on E. coli and Phage display with the microvirus {Phi}X174, Assisting Continuous Evolution (SurPhACE). Instead of building libraries for screening, SurPhACE runs a closed evolutionary program. A typical experiment can have 1011 mutant candidates under active selection, with complete turnover of the mutant population every 30min, or >5x1012 unique mutants per day, using less than 100mL of bacterial culture media. We demonstrate SurPhACE for optimizing a nanobody to a related epitope, and develop novel nanobodies for an arbitrary target using a minimal starting library to establish a proof of concept and identify best practices for this scalable method for generating protein binders.

synthetic biology↗

bioRxiv2026

An endoplasmic reticulum resident molecular chaperone, GRP170, prevents stress-induced glomerular injury

The glomerulus, a unique capillary network in the nephron, filters an entire blood volume approximately 300 times a day. Specialized epithelial cells known as podocytes form a critical component of the glomerular filtration barrier, and diseases linked to podocyte injury include minimal change disease, focal segmental glomerulosclerosis, and diabetic kidney disease. Because podocytes are terminally differentiated, their ability to respond to external stress is critical. The unfolded protein response (UPR), a cellular stress pathway, is associated with glomerular injury, although the role of the UPR in glomerular injury is undefined. The UPR is initially protective, leading to upregulation of molecular chaperones, a class of proteins that promote protein folding and are required to survive oxidative and ischemic injury. An unresolved UPR, however, leads to apoptosis. We previously found that one molecular chaperone, GRP170, provides protection against acute kidney injury since GRP170 depletion led to UPR induction and widespread kidney injury. Here we generated a new podocyte specific GRP170 knock out mouse (GRP170Pd-/-). Surprisingly, GRP170Pd-/- mice were born healthy, and podocyte development appeared normal. Within a month, however, the knockout mice exhibited profound glomerular injury manifesting as proteinuria, hypoalbuminemia, hyperlipidemia, and kidney injury. Concomitant with glomerular injury, we observed increased expression of the pro-apoptotic UPR target, CHOP, in podocytes. Together, our new model not only defines a protective role for GRP170 against glomerular injury but also provides a new model to test the therapeutic potential of small molecule UPR modulators to treat glomerular injury.

physiology↗

bioRxiv2025

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one system to systematically characterize how the phage-bacteria arms race shapes C. acnes evolution and community composition on individual people. Our analysis reveals a surprising lack of phage-mediated selection despite global prevalence of C. acnes phages. Analysis of anti-phage defense systems across 3,205 bacterial genomes revealed a limited, phylogenetically restricted defense repertoire under weak selective pressure to diversify or be maintained. Functional assays did not reveal alternative phage resistance mechanisms or fitness costs associated with defense gene carriage that could explain this limited immune arsenal. This lack of pressure to maintain phage resistance could not be explained by lack of phage colonization, as examination of 471 global human facial skin metagenomes demonstrated that even in samples with high virus-to-microbe ratio, phage-sensitive clades dominate on-person populations. Together, these findings indicate that phage pressure, while present, does not play a critical role in determining strain fitness and success within C. acnes populations on human skin. We propose that this observed weak phage-mediated selective pressure can be explained by the anatomy of skin: C. acnes growth is thought to occur at the bottom of pores, where exposure to phage may be limited by physical barriers. Together, this portrait of a static arms race provides a strong contrast with other microbial species in different ecosystems and expands understanding of phage-bacteria interactions in the human microbiome.

genomics↗

bioRxiv2025

Aicardi-Goutieres Syndrome Associated ADAR G1007R mutation dominantly induces neuroinflammation in mouse brain

The ADARG1007Rmutation is one of the most frequent mutations found in type six Aicardi-Goutieres Syndrome (AGS), a severe inflammatory encephalopathy in pediatric patients. We report here a mouse model bearing an human equivalent ADARG1007R mutation, and the heterozygous mice recapitulated some pathologic features of ADARG1007R AGS patients, including early-onset brain inflammation in heterozygous individuals and interferon-stimulated gene (ISG) expression within deep brain areas. Furthermore, we demonstrated that brain inflammation could be reversed by deletion of the cellular RNA receptor MDA5, which blocks the cellular RNA sensing signaling pathway. This model provides a unique tool for studying the molecular mechanisms underlying the heterozygous ADARWT/G1007R mutation in AGS brain pathogenesis. It may also be a valuable platform for developing personalized therapies for patients with this specific mutation.

neuroscience↗

bioRxiv2025

Role of the NuRD complex and altered proteostasis in cancer cell quiescence

Cytotoxic chemotherapy remains the primary treatment for ovarian cancer (OvCa). Development of chemoresistance typically results in patient death within two years. As such, understanding chemoresistance is critical. One underexplored mechanism of chemotherapy resistance is quiescence. Quiescent cells, which have reversibly exited the cell cycle, are refractory to most chemotherapies which primarily target rapidly proliferating cells. Here, we report that CHD4 and MBD3, components of the nucleosome remodeling and deacetylase (NuRD) complex, are downregulated in quiescent OvCa cells (qOvCa). Indicating a direct role for NuRD complex downregulation in the induction of quiescence, either CHD4 or MBD3 knockdown or histone deacetylase inhibitors (HDACi), such as vorinostat, induce quiescence in OvCa cells. RNA-Seq analysis of HDACi-treated cells confirmed expression changes consistent with induction of quiescence. We also find that both primary qOvCa and vorinostat-induced qOvCa demonstrate altered proteostasis, including increased proteasome activity and autophagy, and combination therapy of HDACi and proteasome inhibitors or autophagy inhibitors demonstrated profound synergistic death of OvCa cells. Finally, we overlapped RNA-Seq signatures from quiescent ovarian cancer cells with genes essential for quiescence in yeast to identify a "quiescent cell core signature." This core quiescent cell signature appeared to be conserved across multiple cancer types, suggesting new therapeutic targets.

cancer biology↗

bioRxiv2023

Ts-Biotag, a multimodal reporter of Tie2 expression, labels microglia in a model of neuro injury.

The Ts-Biotag transgenic mouse reports the expression of receptor tyrosine kinase Tie2, a known marker of angiogenic states for both vascular endothelial cells and macrophages. We demonstrate Ts-Biotag labeling and Tie2 expression in a neural injury model to find the majority of labeling occurs in the myeloid derived and brain resident cell type, microglia. Additionally the ligand of Tie2, Ang1, is dynamically expressed, first in astrocytes then neural progenitor during wound signaling and healing. These results offer a Tie2 specific, in vivo view of a neuroimmune response to injury, suggesting a microglia/neural progenitor intercellular interaction guides recovery from a brain lesion. Graphical AbstractThe Ts-Biotag mouse reports expression of Tie2 for any imaging modality compatible with avidinated agents. Mice were given a transcranial cryo-injury and Ts-Biotag activity was followed for 7 days with MRI and histology, showing local and systemic Ts-Biotag labeling. Histology of WT and labeled bone marrow chimeras showed the protein Tie2 expressed in microglia, which assembled at the border of the lesion 1-2d post injury before invading by day 7. The main ligand of Tie2, Ang1, was first expressed systemically by astrocytes, then by neural progenitor cells proximal to and within the lesion. These results elucidate an axis of intercellular signaling involved in the resolution of inflammation and partial healing of a CNS injury. O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/527655v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@c11887org.highwire.dtl.DTLVardef@1316a54org.highwire.dtl.DTLVardef@13be2a5org.highwire.dtl.DTLVardef@9cf9bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗