Biology subjects

Dos Reis Marques, R.

Publications and source records attributed to Dos Reis Marques, R..

5 recordsLinked to original sources

bioRxiv2026

Matrix stiffness and stress relaxation regulate matrix-bound nanovesicle release from alginate hydrogels

Matrix-bound nanovesicles (MBVs) are a recently discovered subclass of small extracellular vesicles (EVs) that reside within the extracellular matrix of non-mineralized tissues throughout the body. Functionally, MBVs exhibit unique immunomodulatory properties that have been leveraged therapeutically to treat various tissue pathologies, including periprosthetic osteolysis, rheumatoid arthritis, and skeletal muscle injury. However, like other EVs, the therapeutic efficacy of MBV applications is limited by delivery methods, namely bolus injections, that offer poor control of EV persistence and bioavailability at the site of administration. We hypothesized that a superior MBV delivery platform could be developed by entrapping MBVs in a tunable, engineered alginate matrix to control retention and release of MBVs on therapeutically relevant timescales. To this end, we encapsulated dermal fibroblast MBVs in bioinert alginate hydrogels of varying stiffness and stress relaxation rates to determine the impact of matrix mechanical properties on MBV release and retention over a 14-day period. We found that stiffer matrices increased MBV release compared to their softer counterparts. Additionally, fast-relaxing matrices exhibited release of MBVs in the first four days of release experiments, in contrast with slow-relaxing matrices, which promoted long-term sequestration of nearly all encapsulated MBVs regardless of differences in matrix stiffness. Our results offer promise that alginate hydrogels can be utilized for more precise control of MBV delivery in the body and may overcome limitations associated with current EV administration methods.

bioengineering↗

bioRxiv2026

Defining characteristics of mesenchymal stem cell-derived matrix-bound nanovesicles compared to conditioned culture medium extracellular vesicles

Matrix-bound nanovesicles (MBVs) are a type of small extracellular vesicle (EV) embedded in the extracellular matrix (ECM) throughout the body. MBVs have been previously isolated from various tissues and in vitro-cultured cell sheets, demonstrating remarkable attributes in regenerative medicine. However, differences between MBVs and conditioned culture medium-derived EVs (liquid-EVs) have yet to be characterized, and the field currently lacks specific protein markers that can identify MBVs from other EV subtypes. Here, we isolate MBVs and liquid-EVs from bone marrow mesenchymal stem cell (MSC) sheets and define differences in size, protein, and zeta potential between these EVs. We show that there is a correlation between cell-driven ECM deposition and MBV and liquid-EV production. We also find that MBVs are smaller, contain less protein per particle, and possess lower zeta potential than liquid-EVs. Interestingly, MBVs also comprise a distinct tetraspanin profile compared to liquid-EVs, with MBVs containing more CD63 and little to no CD81. Finally, we define that CD63, LAMP1, Alix, ITG{beta}1, and GRP94 and their abundance, may be markers specifically used to identify MBVs from liquid-EVs. Our study paves the way for the characteristic differentiation between MBVs from liquid-EVs, elucidates their differences in biogenesis, and reveals a potential connection between EV and ECM production.

bioengineering↗

bioRxiv2026

Reversibility of Nuclear and 3D Genomic Changes in Non-Cancerous Fibroblasts After Constricted Migration

Metastatic cancer cells and healthy fibroblasts must traverse constrictive spaces to reach secondary sites. After passing through multiple constrictions, cancer cells often experience stable changes to their nucleus morphology, 3D genome structure, and migratory phenotype. Here, we investigate whether fibroblasts (BJ-5ta), which are non-cancerous and have an inherent ability to migrate to fulfill roles in wound repair, likewise experience nuclear and 3D genomic changes with constricted migration. We find that BJ-5ta cells do not get progressively better at migrating with sequential attempts but do experience nuclear deformations and 3D genome alterations at the compartment level after constricted migration. Transient compartment shifts spatially rearranged genes associated with preparation for and response to migration. Unlike the stable changes associated with long term phenotype changes in cancer cells, however, the nucleus deformations recovered back to unmigrated levels following proliferation and cell movement. Some compartment changes persist and might influence responses to future stimuli, but most 3D genome changes revert to the unmigrated state after cell proliferation. Our study shows that non-cancerous migratory cells are not more robust against alterations caused by constricted migration but can recover from the ones that do arise more readily than cancer cells. Significance StatementO_LICancer cells experience stable phenotype shifts and 3D genome changes after constricted migration, but it is unknown whether these changes would occur in innately migratory non-cancerous fibroblasts. C_LIO_LIFibroblasts (BJ-5ta) show reversible nuclear morphology and 3D genome alterations after constricted migration. C_LIO_LIOur results reveal the connection between basic nucleus mechanobiology and genome structure in fibroblasts, showing how these cells adapt and respond to the forces of constriction during processes such as wound healing. C_LI

cell biology↗

bioRxiv2023

Amorphous calcium phosphate-coated surfaces as a model for bone microenvironment in prostate cancer

Bone metastasis remains one of the biggest challenges in the treatment of prostate cancer, and other solid tumors such as breast, lung, and colon. Modeling a complex microenvironment in-vitro, such as the bone niche, requires interrogation of cell-cell interactions, specific extracellular matrix proteins and a high calcium environment. Here, we present a fast and cost-effective system in which commercially available, non-adhesive, cell culture vessels are coated with amorphous calcium phosphate (ACP) as a surrogate for bone matrix. We further present modified protocols for subculturing cells, as well as nucleic acid and protein collection in high calcium samples. We find that prostate epithelial cell lines show increased adhesion and proliferation when cultured in these surfaces, as well as independence from androgen starvation. We observe gene expression changes on ACP surfaces in early adenocarcinoma cell lines which may reflect alterations relevant to prostate cancer progression. Summary statementTo model the role of calcium in the microenvironment of the metastatic bone niche, we developed a cost-effective way to coat cell culture vessels in bioavailable calcium, and show that it has an effect on prostate cancer cell survival

cancer biology↗

bioRxiv2021

Alterations in chromosome spatial compartmentalization classify prostate cancer progression

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression, genomic aberrations, and cellular morphology. These processes are in turn dependent in part on the 3D structure of chromosomes, packaged inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, ranging from normal epithelium to bone metastasis. Here, we describe how chromatin compartmentalization identity (A-open vs. B-closed) changes with progression: specifically, we find that 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches could prelude transcription activation and are accompanied by changes in the structure, size, and boundaries of the topologically associating domains (TADs). Further, compartmentalization changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation: one of the main drivers of prostate cancer. These results suggest that discrete, 3D genome structure changes play a deleterious role in prostate cancer progression. SummaryThrough a systematic analysis of chromosome conformation capture in a cohort of cells that model cancer progression, San Martin et.al. find that rearrangement of the 3D genome structure in prostate cancer is a potential mechanism for disease exacerbation and that genome-wide compartment identity can classify cancer according to progression.

cancer biology↗