Biology subjects

Henty-Ridilla, J. L.

Publications and source records attributed to Henty-Ridilla, J. L..

10 recordsLinked to original sources

bioRxiv2026

Breaking the bottleneck: semi-automated quantification of actin filament dynamics

Actin reconstitution assays visualized by total internal reflection fluorescence (TIRF) microscopy have been crucial for defining mechanisms of filament assembly, disassembly, and higher-order organization. Yet quantitative analysis remains slow, labor-intensive, and subject to investigator bias. We developed SMAUG (Single filament Measurement and Analysis Using a GUI), a semi-automated image analysis interface that extends TSOAX filament segmentation and tracking with user-verified trace analysis of time-lapse TIRF images. SMAUG generates kymographs and quantifies filament nucleation, elongation, pausing, junctions, and filament-associated fluorescence while retaining measurements at the individual filament level. We tested the approach across actin reconstitution assays producing concentration-dependent polymerization, formin-stimulated elongation, capping-induced arrest, Arp2/3 branching, and fascin-mediated bundling. SMAUG reproduced manual measurement while reducing analysis time and revealed where dense networks and bundled filaments require user validation. Together, TSOAX and SMAUG provide a semi-automated approach for quantitative analysis of actin filament dynamics.

cell biology↗

bioRxiv2026

Constitutively active mDia1 enables visualization of actin assembly in filopodia

Visualizing individual actin filaments in living cells is notoriously difficult. Formins, which track filament plus ends, are powerful probes of actin assembly, yet their behavior in cells is incompletely understood. We dissect the formin mDia1 to reveal how regulatory states control filament assembly. Using TIRF microscopy, we directly compare new regulatory mutants with canonical activity constructs (full-length, FH1-C, FH2-C, and {Delta}DAD). A two amino-acid substitution mutant, mDia1(CA), is constitutively active and drives strong actin nucleation and elongation. In cells, SNAP-mDia1(CA) is enriched in filopodia, where it forms bright, persistent signals at the tips and dim puncta in the shafts. SNAP-mDia1(CA) increases filopodia number but not elongation rate or length, regardless of its use as an overexpression or rescue construct. Although mDia1(CA) is not a universal actin plus-end tracker in this system, its selective enrichment at filopodial plus ends establishes it as a mechanistically distinct probe for interrogating filopodial actin dynamics.

cell biology↗

bioRxiv2024

Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation

Chromatin organization controls DNAs accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNAs influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.

biochemistry↗

bioRxiv2023

Coordination of actin plus-end dynamics by IQGAP1, formin, and capping protein

Cell processes require precise regulation of actin polymerization that is mediated by plus-end regulatory proteins. Detailed mechanisms that explain plus-end dynamics involve regulators with opposing roles, including factors that enhance assembly, e.g., the formin mDia1, and others that stop growth (Capping Protein, CPz). We explore IQGAP1s roles regulating actin filament plus-ends and the consequences of perturbing its activity in cells. We confirm that IQGAP1 pauses elongation and interacts with plus ends through two residues (C756 and C781). We directly visualize the dynamic interplay between IQGAP1 and mDia1, revealing that IQGAP1 displaces the formin to influence actin assembly. Using four-color TIRF we show that IQ-GAP1s displacement activity extends to formin-CPz decision complexes, promoting end-binding protein turnover at plusends. Loss of IQGAP1 or its plus-end activities disrupts morphology and migration, emphasizing its essential role. These results reveal a new role for IQGAP1 in promoting protein turnover on filament ends and provide new insights into how plus-end actin assembly is regulated in cells.

cell biology↗

bioRxiv2022

Purification of Human β and γ Actin from Budding Yeast

Biochemical studies of human actin and its binding partners rely heavily on abundant and easily purified -actin from skeletal muscle. Therefore, muscle actin has been used to evaluate and determine the activities of most actin regulatory proteins and there is an underlying concern that these proteins perform differently with actin present in non-muscle cells. To provide easily accessible and relatively abundant sources of human {beta}- or {gamma}-actin (i.e., cytoplasmic actins), we developed Saccharomyces cerevisiae strains that express each as their sole source of actin. Both {beta}- or {gamma}-actin purified in this system polymerize and interact with various binding partners, including profilin, mDia1 (formin), fascin, and thymosin-{beta}4 (T{beta}4). Notably, T{beta}4 and profilin bind to {beta}- or {gamma}-actin with higher affinity than to -actin, emphasizing the value of testing actin ligands with specific actin isoforms. These reagents will make specific isoforms of actin more accessible for future studies of actin regulation.

biochemistry↗

bioRxiv2022

Biochemical characterization of actin assembly mechanisms with ALS-associated profilin variants

Eight separate mutations in the actin-binding protein profilin-1 have been identified as a rare cause of amyotrophic lateral sclerosis (ALS). Profilin is essential for many neuronal cell processes through its regulation of lipids, nuclear signals, and cytoskeletal dynamics, including actin filament assembly. Direct interactions between profilin and actin monomers inhibit actin filament polymerization. In contrast, profilin can also stimulate polymerization by simultaneously binding actin monomers and proline-rich tracts found in other proteins. Whether the ALS-associated mutations in profilin compromise these actin assembly functions is unclear. We performed a quantitative biochemical comparison of the direct and formin-mediated impact for the eight ALS-associated profilin variants on actin assembly using classic protein-binding and single-filament microscopy assays. We determined that the binding constant of each profilin for actin monomers generally correlates with the actin nucleation strength associated with each ALS-related profilin. In the presence of formin, the A20T, R136W, Q139L, and C71G variants failed to activate the elongation phase of actin assembly. This diverse range of formin-activities is not fully explained through profilin-PLP interactions, as all ALS-associated variants bind a formin-derived PLP peptide with similar affinities. However, chemical denaturation experiments suggest that the folding stability of these profilins impact some of these effects on actin assembly. Thus, changes in profilin protein stability and alterations in actin filament polymerization may both contribute to the profilin-mediated actin disruptions in ALS.

biochemistry↗

bioRxiv2021

Functional fluorescently-tagged human profilin

Profilin-1 (PFN1) is a cytoskeletal protein that regulates the dynamics of actin and microtubule assembly. Thus, PFN1 is essential for the normal division, motility, and morphology of cells. Unfortunately, conventional fusion and direct labeling strategies compromise different facets of PFN1 function. As a consequence, the only methods used to determine known PFN1 functions have been indirect and often deduced in cell-free biochemical assays. We engineered and characterized two genetically encoded versions of tagged PFN1 that behave identical to each other and the tag-free protein. In biochemical assays purified proteins bind to PIP lipids, catalyze nucleotide exchange on actin monomers, stimulate formin-mediated actin filament assembly, and impact microtubule dynamics. Halo-PFN1 or mApple-PFN1 restored morphological and cytoskeletal functions in PFN1-deficient mammalian cells. In biochemical assays, mAp-PFN1 bound tubulin dimers (kD = 1.89 M) and the sides of microtubules in vitro. Titrations of self-labeling Haloligands were used to visualize molecules of PFN1. This approach combined with specific function-disrupting point-mutants (Y6D and R88E) revealed PFN1 bound to microtubules in live cells. Cells expressing the ALS-associated G118V disease variant did not associate with actin filaments or microtubules. Thus, these tagged PFN1s are reliable tools for studying the dynamic interactions of PFN1 with actin or microtubules in vitro as well as in important cell processes or disease-states.

cell biology↗

bioRxiv2021

TGFβ2 regulates human trabecular meshwork cell contractility via ERK and ROCK pathways with distinct signaling crosstalk dependent on the culture substrate

Transforming growth factor beta 2 (TGF{beta}2) is a major contributor to the pathologic changes occurring in human trabecular meshwork (HTM) cells in primary open-angle glaucoma. Receptor binding of TGF{beta}2 activates non-canonical extracellular-signal-regulated kinase (ERK) and Rho-associated kinase (ROCK) signaling pathways, both broadly affecting HTM cell behavior. However, exactly how these signaling pathways converge to regulate pathologic HTM cell contractility associated with glaucomatous dysfunction is unclear. Here, we investigated the molecular mechanism underlying TGF{beta}2-induced pathologic HTM cell contractility, and the crosstalk between ERK and ROCK signaling pathways. We compared soft biomimetic hydrogels composed of collagen type I, elastin-like polypeptide, and hyaluronic acid with conventional stiff glass coverslips. Results show that HTM cell morphology and filamentous (F)-actin organization was affected by the underlying culture substrate: TGF{beta}2 increased HTM cell contractility via ERK and ROCK signaling pathways by differentially regulating F-actin, -smooth muscle actin, fibronectin, and phospho-myosin light chain in cells grown on hydrogels compared to glass. Importantly, we showed that ERK inhibition further increased TGF{beta}2-induced phospho-myosin light chain levels in HTM cells on hydrogels, but not on glass, which translated into hypercontractility of three-dimensional (3D) HTM cell-laden hydrogels. ROCK inhibition had precisely the opposite effects and potently relaxed the TGF{beta}2-induced hydrogels. This suggests that ERK signaling negatively regulates ROCK-mediated HTM cell contractility, and that impairment of this crosstalk balance contributes to the pathologic contraction associated with the glaucomatous stressor TGF{beta}2. These findings emphasize the critical importance of using 3D tissue-mimetic extracellular matrix substrates for investigating HTM cell physiology and glaucomatous pathophysiology in vitro.

cell biology↗

bioRxiv2020

Inhibition of ITK differentiates GVT and GVHD in allo-HSCT

Allogeneic hematopoietic stem cell transplantation is a life-saving treatment for many malignant and nonmalignant diseases. Donor T cells contained within the graft prevent tumor recurrence via graft-versus-tumor (GVT) effects, however, also cause graft-versus-host disease (GVHD). Novel treatment strategies are therefore needed to allow maintenance of GVT while suppressing GVHD. Here we show using murine models, that targeting IL-2-inducible T cell kinase (ITK) in donor T cells reduces GVHD while preserving the beneficial GVT effects. Donor T cells from Itk-/- mice exhibit significantly reduced production of inflammatory cytokines and migration to GVHD target organs such as liver and small intestine, while maintaining GVT efficacy against primary B-ALL tumors. Itk-/- T cells exhibited reduced expression of IRF4 and decreased JAK/STAT signaling activity, but preserved cytotoxicity, which was accompanied by upregulation of Eomesodermin (Eomes), which was necessary for GVT function. A novel peptide inhibitor ITK signaling is also able to prevent GVHD. This novel peptide inhibitor also reduced cytokine production in mice and human T cells. Altogether, our data suggest that inhibiting ITK could be a therapeutic strategy to reduce GVHD while preserving the beneficial GVT effects following allo-HSCT treatment. Key PointsO_LIInhibiting ITK by a novel peptide significantly reduces GVHD but retains GVT. C_LIO_LIITK deficient donor T cells exhibit minimal GVHD, but maintain GVT activity. C_LIO_LIITK deficient donor T cells exhibit significantly reduced production of inflammatory cytokines and migration to GVHD target organs. C_LIO_LIEomes is required for GVT effect. C_LI

immunology↗

bioRxiv2019

Profilin 1 Controls the Assembly, Organization, and Dynamics of Leading Edge Actin Structures Through Internetwork Competition and Collaboration

How actin monomers are distributed to different networks remains poorly understood. One emerging concept is that the monomer pool is limited and heterogenous, causing biased assembly and internetwork competition. However, most knowledge regarding monomer distribution comes from studies where competing networks are discrete. In metazoans, many actin-based structures are complex, containing competing networks that overlap and are functionally interdependent. Addressing how monomers control the assembly and organization of these complex structures is critical to understanding how actin functions in cells. Here, we identify the monomer-binding protein profilin 1 (PFN1) as a major determinant of actin assembly, organization, and network homeostasis in mammalian cells. At the leading edge, PFN1 controls the localization and activity of the assembly factors Arp2/3 and Mena/VASP, with discrete stages of internetwork competition and collaboration occurring at different PFN1 concentrations. This causes substantial changes to leading edge actin architecture and the types of structures that form there.

cell biology↗