Biology subjects

Aldana, A.

Publications and source records attributed to Aldana, A..

5 recordsLinked to original sources

bioRxiv2025

RSPO2-based peptibodies conjugated with pyrrolobenzodiazepine dimer or camptothecin analogs demonstrate potent anti-tumor activity by targeting the three receptors LGR4/5/6

Leucine-rich repeat containing, G protein-coupled receptor 4, 5, and 6 (LGR4/5/6) are three homologous receptors that are co-expressed or alternately expressed at high levels in tumor cells of colorectal cancer (CRC) and high-risk neuroblastoma (NB). Simultaneous targeting of all three receptors may provide increased efficacy or overcome drug resistance due to tumor heterogeneity and cancer cell plasticity. LGR4/5/6 all bind to R-spondins (RSPOs) with high affinity and potentiate Wnt/{beta}-catenin signaling in response. Previously, we showed that a peptibody based on a mutant RSPO4 furin domain that bound to LGR4/5/6 without potentiating Wnt/{beta}-catenin signaling was able to deliver cytotoxins into cancer cells that express any of the three receptors. We have now generated a mutant RSPO2 furin domain that retains high affinity binding to LGR4/5/6 without signaling activity. Peptibodies based on this RSPO2 furin mutant were conjugated with either pyrrolobenzodiazepine dimer (PBD) or camptothecin derivative (CPT2), and the resulting peptibody-drug conjugates (PDCs) showed potent and specific cytotoxic activity in NB and CRC cell lines expressing any of LGR4/5/6 in vitro and robust anti-tumor activity in vivo. The results support the potential of RSPO2-based PDCs for the treatment of CRC, high-risk NB, and other cancers that express any of LGR4/5/6.

pharmacology and toxicology↗

bioRxiv2024

NetMedPy: A Python package for Large-Scale Network Medicine Screening

SummaryNetwork medicine leverages the quantification of information flow within sub-cellular networks to elucidate disease etiology and comorbidity, as well as to predict drug efficacy and identify potential therapeutic targets. However, current Network Medicine toolsets often lack computationally efficient data processing pipelines that support diverse scoring functions, network distance metrics, and null models. These limitations hamper their application in large-scale molecular screening, hypothesis testing, and ensemble modeling. To address these challenges, we introduce NetMedPy, a highly efficient and versatile computational package designed for comprehensive Network Medicine analyses. AvailabilityNetMedPy is an open-source Python package under an MIT license. Source code, documentation, and installation instructions can be downloaded from https://github.com/menicgiulia/NetMedPy and https://pypi.org/project/NetMedPy. The package can run on any standard desktop computer or computing cluster.

bioinformatics↗

bioRxiv2021

Discrete dynamic model of the mammalian sperm acrosome reaction: the influence of acrosomal pH and biochemical heterogeneity

The acrosome reaction (AR) is an exocytotic process essential for mammalian fertilization. It involves diverse biochemical and physiological changes that culminate in the release of the acrosomal content to the extracellular medium as well as a reorganization of the plasma membrane (PM) that allows sperm to interact and fuse with the egg. In spite of many efforts, there are still important pending questions regarding the molecular mechanism regulating the AR. Particularly, the contribution of acrosomal alkalinization to AR triggering in physiological conditions is not well understood. Also, the dependence of the proportion of sperm capable of undergoing AR on the biochemical heterogeneity within a sperm population has not been studied. Here we present a discrete mathematical model for the human sperm AR, based on the biophysical and biochemical interactions among some of the main components of this complex exocytotic process. We show that this model can qualitatively reproduce diverse experimental results, and that it can be used to analyze how acrosomal pH (pHa) and cell heterogeneity regulate AR. Our results confirm that pHa increase can on its own trigger AR in a subpopulation of sperm, and furthermore, it indicates that this is a necessary step to trigger acrosomal exocytosis through progesterone, a known physiological inducer of AR. Most importantly, we show that the proportion of sperm undergoing AR is directly related to the detailed structure of the population biochemical heterogeneity.

systems biology↗

bioRxiv2021

Mathematical model reveals that heterogeneity in the number of ion transporters regulates the fraction of mouse sperm capacitation

Capacitation is a complex maturation process mammalian sperm must undergo in the female genital tract to be able to fertilize an egg. This process involves, amongst others, physiological changes in flagellar beating pattern, membrane potential, intracellular ion concentrations and protein phosphorylation. Typically, in a capacitation medium, only a fraction of sperm achieve this state. The cause for this heterogeneous response is still not well understood and remains an open question. Here, one of our principal results is to develop a discrete regulatory network, with mostly deterministic dynamics in conjunction with some stochastic elements, for the main biochemical and biophysical processes involved in the early events of capacitation. The model criterion for capacitation requires the convergence of specific levels of a select set of nodes. Besides reproducing several experimental results and providing some insight on the network interrelations, the main contribution of the model is the suggestion that the degree of variability in the total amount and individual number of ion transporters among spermatozoa regulates the fraction of capacitated spermatozoa. This conclusion is consistent with recently reported experimental results. Based on this mathematical analysis, experimental clues are proposed for the control of capacitation levels. Furthermore, cooperative and interference traits that become apparent in the modelling among some components also call for future theoretical and experimental studies. Author summaryFertilization is one of the fundamental processes for the preservation of life. In mammals, sperm undergo a complex process during their passage through the female tract known as capacitation, which enables them for fertilization. At the present time, it is accepted from experimental observation, though not understood, that only a fraction of the sperm is capacitated. In this work, by means of a network mathematical model for regulatory sperm intracellular signaling processes involved in mice capacitation, we find that the variability in the distribution of the number of ion transporters intervenes in the regulation of the capacitation fraction. Experimental verification of this suggestion could open a line of research geared to the regulation of the degree of heterogeneity in the number of ion transporters as a fertility control. The model also uncovers, through in silico overactivation and loss of function of network nodes, synergetic traits which again call for experimental verification.

developmental biology↗

bioRxiv2019

CaV3.1 channel pore pseudo-symmetry revealed by selectivity filter mutations in their domains I/II

There is growing evidence indicating that the pore structure of voltage-gated ion channels (VGICs) influences gating besides their conductance. Regarding low voltage-activated (LVA) Ca2+ channels, it has been demonstrated that substitutions of the pore aspartate (D) by a glutamate (D-to-E substitution) in domains III and IV alter channel gating properties such as a positive shift in the channel activation voltage dependence. In the present report, we evaluated the effects of E-to-D substitution in domains I and II on the CaV3.1 channel gating properties. Our results indicate that substitutions in these two domains differentially modify the gating properties of CaV3.1 channels. The channel with a single mutation in domain I (DEDD) presented slower activation and faster inactivation kinetics and a slower recovery from inactivation, as compared with the WT channel. In contrast, the single mutant in domain II (EDDD) presented a small but significant negative shift of activation voltage dependence with faster activation and slower deactivation kinetics. Finally, the double mutant channel (DDDD) presented intermediate properties with respect to the two single mutants but with fastest deactivation kinetics. Overall, our results indicate that single amino acid modification of the selectivity filter of LVA Ca2+ channels in distinct domains differentially influence their gating properties, suggesting a pore pseudo-symmetry.\n\nStatement of significancePrevious reports of low voltage-activated (LVA) Ca2+ channels have demonstrated that pore aspartate (D) in domains III and IV equally modulates the channel gating properties, supporting a hypothesis of pore symmetry in LVA Ca2+ channels. In the present report, we evaluated the effects of glutamate (E)-to-D pore substitution in domains I and II on the CaV3.1 channel gating properties. Our results indicate that substitutions in these two domains differentially modify the gating properties of CaV3.1 channels, therefore suggesting a pore pseudo-symmetry in them. Interestingly, our pore mutations affect inactivation of CaV3.1 Ca2+ channels indicating a selectivity filter contribution to this process similar to the recent proposed paradigm for high voltage-activated Ca2+ channels.

biophysics↗