Biology subjects

Martinez, M. J.

Publications and source records attributed to Martinez, M. J..

7 recordsLinked to original sources

bioRxiv2026

A pathogen α-L-arabinofuranosidase degrades host-derived immunogenic oligosaccharides to suppress plant immunity

Plant cell wall fragments released during pathogen attack can act as signalling molecules that trigger immune responses. Successful pathogens have potentially evolved diverse strategies to evade host recognition, including minimizing the accumulation of cell wall-derived elicitors. However, the mechanisms underlying this process remain largely unknown. Here, we characterized ZtGH54, an -L-arabinofuranosidase from the wheat pathogen Zymoseptoria tritici, that is essential for the acquisition of sugar nutrients from arabinan and arabinoxylan wall polysaccharides. ZtGH54 also hydrolyzes immunogenic oligosaccharides derived from arabinoxylan to prevent host recognition. Remarkably, this strategy is effective only in a subset of wheat cultivars, as the contribution of ZtGH54 to virulence is cultivar-dependent. While a ZtGH54 substrate is broadly recognized in wheat, one of the products generated by ZtGH54, xylotetraose, is recognized only by specific wheat cultivars, revealing natural variation in the perception of xylan-derived oligosaccharides. These findings establish ZtGH54 as a key virulence factor that simultaneously exploits cell wall host resources and suppresses wheat immunity through the precise hydrolysis of plant cell wall-derived signals.

plant biology↗

bioRxiv2025

BUB1B MITOTIC KINASE DRIVES THERAPY RESISTANT PROSTATE CANCER

Castration-resistant prostate cancer (CRPC) that progresses despite treatment with potent AR antagonists such as enzalutamide is a major clinical problem. Through an unbiased systems biology approach, we previously identified a therapeutically relevant seven gene set that drives CRPC. The mitotic checkpoint kinase, BUB1B (BUBR1) is a key member of this gene set, and we report here that BUB1B is a tractable and promising new therapeutic target in aggressive, treatment-resistant PC. We found that high BUB1B expression is correlated with PC progression and aggressiveness. In established CRPC cells, BUB1B depletion blocked cell proliferation through cell cycle arrest and mitosis delay. Ectopic expression of BUB1B, at levels found in CRPC, conferred castration-resistant growth of androgen-dependent PC cells in vitro and in vivo. We showed that BUB1B kinase activity was essential for CRPC progression, as only wild type (wt) BUB1B and neither of two kinase-dead mutants promoted castration-resistant growth of androgen-dependent PC cells. Rescue experiments with wt or kinase-dead mutants showed further that BUB1B kinase activity was also required to maintain proliferation of established CRPC cells. While persistent androgen receptor (AR) signaling is a mechanism of CRPC progression, BUB1B promotion of CRPC was not dependent on AR as assessed through AR knockdown. Consistent with an AR-bypass mechanism, ectopic expression of BUB1B rendered PC cells resistant to enzalutamide in vitro and in vivo. Our data points to BUB1B as a key driver of CRPC progression and enzalutamide resistance and suggests that targeting BUB1B kinase is a promising therapeutic approach for lethal, treatment-resistant disease. Statement of significanceWe document a novel role for BUB1B kinase as a critical driver of castration- and enzalutamide-resistant prostate cancer, highlighting the therapeutic potential of BUB1B kinase inhibition to overcome lethal treatment-resistant disease.

cancer biology↗

bioRxiv2024

Zymoseptoria tritici stealth infection is facilitated by stage-specific down-regulation of a β-glucanase

Plant cell walls constitute a major defence barrier against pathogens, although it is unclear how specific cell wall components impact pathogen colonisation. Pathogens secrete cell wall degrading enzymes (CWDEs) to facilitate plant colonisation, but damaged, infected cells are often a source of cell wall-derived oligosaccharides that trigger host immunity. The mechanisms by which pathogens minimize the release of cell wall-derived oligosaccharides while colonizing the host remain to be elucidated. We combined biochemical, molecular genetics and transcriptomic analyses to functionally characterize a glycoside hydrolase (ZtGH45) from the wheat pathogen Zymoseptoria tritici. ZtGH45 gene is expressed during the necrotrophic phase of the fungus, coinciding with an accumulation of wheat {beta}-1,3/1,4-mixed-linked glucan (MLG)-derived oligosaccharides. We show that overexpression of ZtGH45 enhances {beta}-1,3/1,4-glucan hydrolysis and the derived oligosaccharides trigger an immune response in wheat, which hinders Z. tritici virulence. The results demonstrate that tight regulation of ZtGH45 is critical for the infection process to prevent early accumulation of MLG oligosaccharides that would prematurely induce host immunity counterbalancing fungal virulence. We suggest that the balance between plant cell wall degradation by fungal CWDE and the release of immunogenic wall-derived oligosaccharides governs the outcome of host invasion by pathogens.

plant biology↗

bioRxiv2024

Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning

Cancer is a group of complex diseases, with tumor heterogeneity, durable drug efficacy, emerging resistance, and host toxicity presenting major challenges to the development of effective cancer therapeutics. While traditionally used methods have remained limited in their capacity to overcome these challenges in cancer drug development, efforts have been made in recent years toward applying "big data" to cancer research and precision oncology. By curating, standardizing, and integrating data from various databases, we developed deep learning architectures that use perturbation and baseline transcriptional signatures to predict efficacious small molecule compounds and genetic dependencies in cancer. A series of internal validations followed by prospective validation in prostate cancer cell lines were performed to ensure consistent performance and model applicability. We report SensitivitySeq, a novel bioinformatics tool for prioritizing small molecule compounds and gene dependencies in silico to drive the development of targeted therapies for cancer. To the best of our knowledge, this is the first supervised deep learning approach, validated in vitro, to predict drug sensitivity using baseline cancer cell line gene expression alongside cell line-independent perturbation-response consensus signatures. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/623715v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@9f48bcorg.highwire.dtl.DTLVardef@16056f7org.highwire.dtl.DTLVardef@1ed9095org.highwire.dtl.DTLVardef@1af3fce_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2'-hydroxylases acting upstream of stilbene synthases

Mulberry (Morus alba L.) is considered a millenary medicinal plant and a food source for silkworms. Different M. alba extracts offer a variety of biological and pharmacological properties that are in part attributed to stilbenoids, a small group of phenylpropanoids that include resveratrol and oxyresveratrol. These are naturally present in non-renewable parts of mulberry trees, impeding their efficient extraction. As a way to bypass this spatiotemporal restriction, we generated cell suspensions from mulberry twigs and demonstrated that the combined use of methyl jasmonate and methyl- or hydroxypropyl-{beta}-cyclodextrins elicited a high production of resveratrol and oxyresveratrol, both intra and extracellularly. To identify oxyresveratrol-producing enzymes (unknown to date), we first improved the structural and functional annotation of the mulberry genome by integrating short and long-read sequencing data. We further combined this data with transcriptome, metabolite and proteome time-series evidence to identify a complete set of elicited phenylpropanoid- and stilbenoid-related genes. These included 22 stilbene synthase (STS) genes and a group of six p-coumaroyl-CoA 2-hydroxylases (C2Hs) that were highly co-expressed with resveratrol and oxyresveratrol accumulation. We transiently transformed Nicotiana benthamiana plants and grapevine (Vitis vinifera L.) cell suspensions to functionally validate the role of C2Hs as the first committed step of oxyresveratrol synthesis, providing an alternative substrate for STSs by hydroxylating p-coumaroyl-coA into 24-dihydroxycinnamoyl-CoA. We offer tools for genomic and transcriptomic exploration in the context of jasmonate elicitation aiding in the characterization of novel stilbenoid-modifying and regulatory genes in the Morus genus.

molecular biology↗

bioRxiv2023

Inhibition of the serine/threonine kinase BUB1 reverses taxane resistance in prostate cancer

Background: Men with incurable castration resistant prostate cancer (CRPC) are typically treated with taxanes; however, drug resistance rapidly develops. Thus, overcoming taxane resistant PC is a major clinical need. We previously identified a seven gene network in aggressive CRPC, which includes the mitotic serine threonine kinase BUB1, a major regulator of the spindle assembly checkpoint (SAC). Alterations in mitotic kinases (and SAC malfunction) are associated with advanced PC and taxane resistance development and thereby represent potential vulnerabilities. Methods: We evaluated BUB1 expression in publicly available data sets and in existing and newly generated taxane resistant PC cells. The effects of BUB1 depletion on the growth of a panel of PC and non-tumorigenic prostate epithelial cells was determined. We examined the capacity of pharmacologic inhibition of BUB1 kinase to reverse taxane-resistant PC growth. We evaluated the role of the prevalent androgen receptor variant AR-V7, in regulating BUB1 expression and taxane resistance. Results: BUB1 mRNA was over-expressed in PC, metastatic castration resistant prostate cancer (mCRPC) and in tumors of patients treated with taxane-based chemotherapeutics compared to benign prostate tissue. Furthermore, BUB1 levels were elevated in taxane resistant PC cell lines compared to their sensitive counterparts. BUB1 depletion decreased growth of CRPC cells through delayed mitosis but did not affect proliferation of androgen dependent (ADPC) or non-tumorigenic prostate epithelial cells. Furthermore, BUB1 inhibition with the specific kinase inhibitor, BAY1816032, re-sensitized taxane resistant CRPC cells to the clinically used drugs, docetaxel and cabazitaxel. Consistent with AR-V7 regulation of BUB1, we also found that AR-V7 was elevated in taxane resistant CRPC cells. Moreover, ectopic expression of AR-V7 in CRPC cells that lack this protein resulted in increased BUB1 and conferred docetaxel resistance. BUB1 pharmacologic inhibition in combination with taxanes sensitized AR-V7 expressing CRPC cells to docetaxel treatment. Conclusion: These data support BUB1 as an exploitable and therapeutically tractable vulnerability in taxane resistant CRPC including in AR variant driven CRPC.

cancer biology↗

bioRxiv2020

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19.

The objective of this study was to assess the performance of direct real time RT-PCR detection of SARS-CoV-2 in heated saliva samples, avoiding the RNA isolation step. Oropharyngeal and nasopharyngeal swabs together with saliva samples were obtained from 51 patients clinically diagnosed as potentially having COVID-19. Two different methods were compared: 1. RNA was extracted from 500 l of sample using a MagNA Pure Compact Instrument with an elution volume of 50l and 2. 700{micro}L of saliva were heat-inactivated at 96{degrees}C for 15 minutes, and directly subjected to RT-PCR. One step real time RT-PCR was performed using 5 l of extracted RNA or directly from 5 l of heated sample. RT-PCR was performed targeting the SARS-CoV-2 envelope (E) gene region. Diagnostic performance was assessed using the results of the RT-PCR from nasopharyngeal and oropharyngeal swabs as the gold standard. The overall sensitivity, specificity, positive and negative predictive values were 81.08%, 92.86%, 96.77% and 65.00%, respectively when RNA extraction was included in the protocol with saliva, whereas sensitivity, specificity, positive and negative predictive values were 83.78%, 92.86%, 68.42% and 96.88%, respectively, for the heat-inactivation protocol. However, when the analysis was performed exclusively on saliva samples with a limited time from the onset of symptoms (<9 days, N=28), these values were 90%, 87.5%, 44% and 98.75% for the heat-inactivation protocol. The study showed that RT-PCR can be performed using saliva in an RNA extraction free protocol, showing good sensitivity and specificity.

microbiology↗