Biology subjects

Wardak, A.

Publications and source records attributed to Wardak, A..

5 recordsLinked to original sources

bioRxiv2025

EGFR-targeted affibody-polyIC polyplex kills EGFR-overexpressing cancer cells without activating the EGFR

The epidermal growth factor receptor (EGFR) is aberrantly activated in many human epithelial cancers. This report presents the preparation, purification, and the anti-cancer potency of an anti-EGFR affibody (ZEGFR 1907)-polyethylenimine (PEI)-polyIC complex (PPEA-polyplex). Surface plasmon resonance analysis showed that the ZEGFR 1907 affibody binds tightly to full-length sEGFR with an average equilibrium dissociation constant, KD, value of 6.74 nM. The PPEA-polyplex does not activate the EGFR kinase, but kills tumor cells expressing medium to high levels of EGFR. The PPEA-polyplex stimulates the release of chemotactic cytokines (e.g., GRO-, IFN-{gamma}-inducible protein-10) and promoted PBMC-mediated bystander killing of non-transfected tumor cells. The PPEA-polyplex inhibited the growth of human epidermoid vulval carcinoma (A431) xenografts growing in immunocompromised nude mice. PPEA-polyplexes have the potential to inhibit the growth of tumors in Triple-negative breast cancer (TNBC) patients and other cancers which over-express the EGFR.

cancer biology↗

bioRxiv2023

Implications of variable synaptic weights for rate and temporal coding of cerebellar outputs

Purkinje cell (PC) synapses onto cerebellar nuclei (CbN) neurons convey signals from the cerebellar cortex to the rest of the brain. PCs are inhibitory neurons that spontaneously fire at high rates, and many uniform sized PC inputs are thought to converge onto each CbN neuron to suppress or eliminate firing. Leading theories maintain that PCs encode information using either a rate code, or by synchrony and precise timing. Individual PCs are thought to have limited influence on CbN neuron firing. Here, we find that single PC to CbN synapses are highly variable in size, and using dynamic clamp and modelling we reveal that this has important implications for PC-CbN transmission. Individual PC inputs regulate both the rate and timing of CbN firing. Large PC inputs strongly influence CbN firing rates and transiently eliminate CbN firing for several milliseconds. Remarkably, the refractory period of PCs leads to a brief elevation of CbN firing prior to suppression. Thus, PC-CbN synapses are suited to concurrently convey rate codes, and generate precisely-timed responses in CbN neurons. Variable input sizes also elevate the baseline firing rates of CbN neurons by increasing the variability of the inhibitory conductance. Although this reduces the relative influence of PC synchrony on the firing rate of CbN neurons, synchrony can still have important consequences, because synchronizing even two large inputs can significantly increase CbN neuron firing. These findings may be generalized to other brain regions with highly variable sized synapses.

neuroscience↗

bioRxiv2021

Ion currents through Kir potassium channels are gated by anionic lipids.

Ion currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook gate of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present the first evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this gate is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.

biochemistry↗

bioRxiv2021

Membrane permeabilization is mediated by distinct epitopes in mouse and human orthologs of the necroptosis effector, MLKL

Necroptosis is a lytic programmed cell death pathway with origins in innate immunity that is frequently dysregulated in inflammatory diseases. The terminal effector of the pathway, MLKL, is licensed to kill following phosphorylation of its pseudokinase domain by the upstream regulator, RIPK3 kinase. Phosphorylation provokes the unleashing of MLKLs N-terminal four-helix bundle (4HB or HeLo) domain, which binds and permeabilizes the plasma membrane to cause cell death. The precise mechanism by which the 4HB domain permeabilizes membranes, and how the mechanism differs between species, remains unclear. Here, we identify the membrane binding epitope of mouse MLKL using NMR spectroscopy. Using liposome permeabilization and cell death assays, we validate K69 in the 3 helix, W108 in the 4 helix, and R137/Q138 in the first brace helix as crucial residues for necroptotic signaling. This epitope differs from the phospholipid binding site reported for human MLKL, which comprises basic residues primarily located in the 1 and 2 helices. In further contrast to human and plant MLKL orthologs, in which the 3-4 loop forms a helix, this loop is unstructured in mouse MLKL in solution. Together, these findings illustrate the versatility of the 4HB domain fold, whose lytic function can be mediated by distinct epitopes in different orthologs.

cell biology↗

bioRxiv2020

Fractional diffusion theory of balanced heterogeneous neural networks

Interactions of large numbers of spiking neurons give rise to complex neural dynamics with fluctuations occurring at multiple scales. Understanding the dynamical mechanisms underlying such complex neural dynamics is a long-standing topic of interest in neuroscience, statistical physics and nonlinear dynamics. Conventionally, fluctuating neural dynamics are formulated as balanced, uncorrelated excitatory and inhibitory inputs with Gaussian properties. However, heterogeneous, non-Gaussian properties have been widely observed in both neural connections and neural dynamics. Here, based on balanced neural networks with heterogeneous, non-Gaussian features, our analysis reveals that in the limit of large network size, synaptic inputs possess power-law fluctuations, leading to a remarkable relation of complex neural dynamics to the fractional diffusion formalisms of non-equilibrium physical systems. By uniquely accounting for the leapovers caused by the fluctuations of spiking activity, we further develop a fractional Fokker-Planck equation with absorbing boundary conditions. This body of formalisms represents a novel fractional diffusion theory of heterogeneous neural networks and results in an exact description of the network activity states. This theory is further implemented in a biologically plausible, balanced neural network and identifies a novel type of network state with rich, nonlinear response properties, providing a unified account of a variety of experimental findings on neural dynamics at the individual neuron and the network levels, including fluctuations of membrane potentials and population firing rates. We illustrate that this novel state endows neural networks with a fundamental computational advantage; that is, the neural response is maximised as a function of structural connectivity. Our theory and its network implementations provide a framework for investigating complex neural dynamics emerging from large networks of spiking neurons and their functional roles in neural processing.

neuroscience↗