Biology subjects

Terrazas, M.

Publications and source records attributed to Terrazas, M..

3 recordsLinked to original sources

bioRxiv2025

Dually-decorated palmitate-containing lipid nanoparticles for the targeted delivery of siRNAs against HER2 and Hsp27 in HER2+ breast cancer

Ionizable lipid nanoparticles (LNPs) have enabled significant advances in oligonucleotide therapeutics, culminating in the clinical approval of an siRNA-based formulation. Unfortunately, practical use of siRNA containing LNPs is still hampered by difficulties, one of them directing LNPs toward specific cells. To improve cell-specific delivery, we have developed a new generation of palmitate-containing ionizable LNPs functionalized with two distinct ligands: i) a targeting peptide (octreotide, Oct), for selective recognition of somatostatin receptor 2 (SSTR2)-expressing tumor cells, and ii) a cell penetrating peptide (penetratin, RK16) to enhance intracellular delivery. This dually-decorated LNP was used to co-deliver two siRNAs targeting key mediators of drug resistance in HER2+ breast cancer -Hsp27 and HER2- demonstrating strong potential for combinatorial RNAi-based therapies. The Oct moiety conferred high selectivity toward malignant SSTR2-overexpresing (SSTR2OE) HER2+ BC cells, even in heterogeneous environments containing non-tumor epithelial cells. Simultaneously, the RK16 peptide facilitated enhanced intracellular delivery, resulting in improved antiproliferative activity and a notable reduction in the SSTR2-overexpressing cell population compared to non-functionalized LNPs. Taken together, the structural design and biological performance of this novel class of LNP formulation establish it as a versatile and innovative delivery platform for ON-based targeted therapies. By simply altering the targeting peptide moiety and siRNA combination, this dually-functionalized LNP system could be readily adapted for a broad range of tumors and combination treatment strategies. Finally, the inclusion of palmitic acid in the LNP composition selectively contributes to cytotoxicity in palmitate sensitive cell lines, such as SK-BR-3, offering an additional therapeutic advantage when targeting these tumor subtypes.

biochemistry↗

bioRxiv2024

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism

By combining in-silico, biophysical and in-cellulo experiments, we decipher the topology, physical and potential biological properties of hybrid-parallel nucleic acids triplexes; an elusive structure at the basis of life. We found that hybrid triplex topology follows a stability order: r(Py)-d(Pu){middle dot}r(Py)> r(Py)-d(Pu){middle dot}d(Py)> d(Py)-d(Pu){middle dot}d(Py)> d(Py)-d(Pu){middle dot}r(Py). The r(Py)-d(Pu){middle dot}d(Py) triplex is expected to be the preferred in the cell as it avoids the need to open the duplex reducing the torsional stress required for triplex formation in the r(Py)-d(Pu){middle dot}r(Py) topology. Upon a massive collection of melting data, we have created the first predictor for hybrid triplex stability. Leveraging this predictor, we conducted a comprehensive scan to assess the likelihood of the human genome and transcriptome to engage in triplex formation. Our findings unveil a remarkable inclination - of both the human genome and transcriptome - to generate hybrid triplex formation, particularly within untranslated (UTRs) and regulatory regions, thereby corroborating the existence of a triplex-mediated regulatory mechanism. Furthermore, we found a correlation between nucleosome linkers and TFS which agree with a putative role of triplexes in arranging chromatin structure and local/global level.

molecular biology↗

bioRxiv2020

THE IMPACT OF THE HYDROXYMETHYLCYTOSINE EPIGENETIC SIGNATURE ON DNA STRUCTURE AND FUNCTION

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties not too different to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methyl-cytosine (mC) and 5-hydroxymethyl-cytosine (hmC) generally lead to more rigid duplexes with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). On the contrary, our simulations suggest that methylated-DNA binding domains (MBD), associated with repression activities, are very sensitive to the substitution d(mCpG)[->] d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) [->] d(hmCpG) change. Overall, while changes in gene activity due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

biochemistry↗