Biology subjects

Lorenzo-Martin, L. F.

Publications and source records attributed to Lorenzo-Martin, L. F..

5 recordsLinked to original sources

bioRxiv2025

PAN-CANCER ANALYSES IDENTIFY ONCOGENIC DRIVERS, EXPRESSION SIGNATURES, AND THERAPEUTIC VULNERABILITIES IN RHO GTPase PATHWAY GENES

RHO family GTPases are key regulators of cancer-related processes such as cytoskeletal dynamics, cell migration, proliferation, and survival. Despite this, a comprehensive understanding of RHO signaling alterations across tumors is still lacking. Here, we present a pan-cancer analysis of 484 genes encoding RHO GTPases, regulators, proximal effectors, distal downstream signaling elements, and components of their proximal interactomes using data from over 10,000 tumor samples and 33 tumor types present in The Cancer Genome Atlas (TCGA). In addition, we have utilized available data from genome-wide functional dependency screens performed in more than 1,000 gene-edited cancer cell lines. This study has uncovered positively selected mutations in both well-known and previously uncharacterized RHO pathway genes. Transcriptomic profiling reveals widespread and tumor-specific differential expression patterns, some of them correlating with copy number changes. Interestingly, certain regulators exhibit consistent expression profiles across tumors opposite to those predicted from their canonical roles. Coexpression and gene set enrichment analyses highlight coordinated transcriptional programs involving some RHO GTPase pathway genes and their linkage to key cancer hallmarks, including extracellular matrix reorganization, cell motility, cell cycle progression, cell survival, and immune modulation. Functional screens further identify context-specific dependencies on several deregulated RHO GTPase pathway genes. Altogether, this study provides a comprehensive map of RHO GTPase pathway alterations in cancer and identifies new oncogenic drivers, expression-based signatures, and therapeutic vulnerabilities that could guide future mechanistic and translational research.

cancer biology↗

bioRxiv2023

VAV2-DEPENDENT REGULATION OF RIBOSOME BIOGENESIS IN KERATINOCYTES AND ORAL SQUAMOUS CELL CARCINOMA

VAV2 is an activator of RHO GTPases that promotes and maintains regenerative proliferation-like states in normal keratinocytes and oral squamous cell carcinoma (oSCC) cells, respectively. Here, we demonstrate that VAV2 also plays critical roles in the regulation of ribosome biogenesis in those cells, a program associated with poor prognosis of human papilloma virus negative oSCC patients. Mechanistic analyses indicate that VAV2 regulates this process in a catalysis-dependent manner using a conserved pathway composed of the GTPases RAC1 and RHOA, members of the PAK and ROCK family kinases, and the transcriptional factors c-MYC and YAP/TAZ. This pathway directly promotes RNA polymerase I activity and the ensuing synthesis of 47S pre-rRNA precursors. This process is further consolidated by the upregulation of ribosome biogenesis factors and the acquisition of the YAP/TAZ-dependent cell undifferentiation state. Finally, we show that RNA polymerase I is a therapeutic Achilles heel for both keratinocytes and hnSCC patient derived cells endowed with high VAV2 catalytic activity. Collectively, these findings highlight the therapeutic potential of the VAV2 and ribosome biogenesis pathways in both preneoplastic and late progression stages of oSCC.

cancer biology↗

bioRxiv2023

Dissection and reconstruction of the colorectal cancer tumor microenvironment

Patient-derived organoids (PDOs) are the reference in vitro human disease models. However, the utility of colorectal cancer (CRC) PDOs is hindered by the lack of a tumor microenvironment (TME). To address this limitation, we built a living biobank of CRC PDOs with autologous stromal and immune TME. We characterized the original tumors and traditional monocultures using single-cell RNA-seq (scRNA-seq) and whole exome sequencing (WES) to obtain insights into cell type selection and phenotypic drift in culture. Subsequently, we developed culture conditions supporting all cell types to recapitulate the CRC-TME around PDOs. From the transcriptomes of >180k cells obtained from 260 such co-cultures, we illuminated the mutual influence of cells within CRC tumors. Based on original tumor data, atlases of predicted interactions and transcriptional networks elucidated why monocultures were altered and suggested that TME reconstruction more accurately reflected original tumor behavior. We found that inflammatory signals were absent in vitro and recovered upon co-culture with tumor-infiltrating lymphocytes (TILs). We also functionally confirmed that stromal, not cancer cells, mediated immune evasion. Additionally, stroma induced an invasive phenotype in cancer cells. From this deep dive into CRC-TME interactions, we built the human CRC-TME atlas (https://crc-tme.com/), an online portal for interactive exploration of gene expression data, prediction of cell-cell interactions at the pathway and receptor/ligand levels, transcriptional networks, and more. We anticipate PDO cultures with reconstructed TMEs will be valuable for discovery efforts, preclinical studies, and personalized medicine, with the atlas as a framework and inspiration for future CRC-TME studies.

cancer biology↗

bioRxiv2022

The Rho GTPase exchange factor Vav2 promotes extensive age-dependent rewiring of the skin stem cell transcriptome

Both the number and regenerative activity of skin stem cells (SSCs) are regulated by Vav2, a GDP/GTP exchange factor involved in the catalytic stimulation of the GTPases Rac1 and RhoA. However, whether Vav2 signaling changes in SSCs over the mouse lifespan is not yet known. Using a mouse knock-in mouse model, we now show that the expression of a catalytically-active version of Vav2 (Vav2Onc) promotes an extensive rewiring of the overall transcriptome of SSCs, the generation of new transcription factor hubs, and the synchronization of many transcriptional programs associated with specific SSC states and well-defined signaling pathways. Interestingly, this transcriptome rewiring is not fixed in time, as it involves the induction of 15 gene expression waves with diverse distribution patterns during the life of the animals. These expression waves are consistent with the promotion by Vav2Onc of several functional SSC states that differ from those normally observed in wild-type SSCs. These results further underscore the role of Vav2 in the regulation of the functional state of SSCs. They also indicate that, unlike other Vav2-dependent biological processes, the signaling output of this exchange factor is highly contingent on age-dependent intrinsic and/or extrinsic SSC factors that shape the final biological readouts triggered in this cell type. AUTHOR SUMMARYSkin stem cells (SSCs) are essential for the homeostatic balance of the skin, yet little is known to date about the biological and molecular mechanisms that modulate their abundance, long-term stability, or functional states during ageing. To address this issue, in this work we have used a genetically-engineered gain-of-function mouse model for Vav2, a Rho guanine nucleotide exchange factor (GEF) that has been recently shown to be involved in skin stem cell homeostasis. By performing time-course genome-wide expression analyses combined with a number of computational methods, here we show that: (i) Vav2 plays a critical role in regulating the functional state of SSCs, and (ii) the signaling output of constitutively active Vav2 is highly contingent on age-dependent intrinsic and/or extrinsic SSC factors that shape the final biological readouts triggered in this cell type. We believe that these data represent, to our knowledge, one of the first examples of the time-dependent output of an oncogenic version of a Rho GEF along a wide time interval in mice.

cell biology↗

bioRxiv2020

Lysine Acetylation Reshapes The Downstream Signaling Landscape Of Vav1 In Lymphocytes

Vav1 works both as a catalytic Rho GTPase activator and an adaptor molecule. These functions, which are critical for T cell development and antigenic responses, are tyrosine phosphorylation-dependent. However, it is not known whether other posttranslational modifications can modulate the signaling output of this protein. Here, we show that Vav1 becomes acetylated in a stimulation- and SH2 domain-dependent manner. We also demonstrate that the acetylation of four residues located in the catalytic, lysine rich and SH2 domains preferentially buffers the Vav1 adaptor function that favors the stimulation of the nuclear factor of activated T cells. As a result, it modifies the signaling diversification properties normally exhibited by Vav1 in lymphocytes. This new regulatory layer is not shared by Vav family paralogs.

biochemistry↗