Deciphering cellular states of innate tumor drug responses

BACKGROUND: The molecular mechanisms underlying innate tumor drug resistance, a major obstacle to successful cancer therapy, remain poorly understood. In colorectal cancer (CRC), molecular studies have focused on drug-selected tumor cell lines or individual candidate genes using samples derived from patients already treated with drugs, so that very little data are available prior to drug treatment. RESULTS: Transcriptional profiles of clinical samples collected from CRC patients prior to their exposure to a combined chemotherapy of folinic acid, 5-fluorouracil and irinotecan were established using microarrays. Vigilant experimental design, power simulations and robust statistics were used to restrain the rates of false negative and false positive hybridizations, allowing successful discrimination between drug resistance and sensitivity states with restricted sampling. A list of 679 genes was established that intrinsically differentiates, for the first time prior to drug exposure, subsequently diagnosed chemo-sensitive and resistant patients. Independent biological validation performed through quantitative PCR confirmed the expression pattern on two additional patients. Careful annotation of interconnected functional networks provided a unique representation of the cellular states underlying drug responses. CONCLUSION: Molecular interaction networks are described that provide a solid foundation on which to anchor working hypotheses about mechanisms underlying in vivo innate tumor drug responses. These broad-spectrum cellular signatures represent a starting point from which by-pass chemotherapy schemes, targeting simultaneously several of the molecular mechanisms involved, may be developed for critical therapeutic intervention in CRC patients. The demonstrated power of this research strategy makes it generally applicable to other physiological and pathological situations

Arabidopsiscell wall composition determines disease resistance specificity and fitness

[EN] Plant cell walls are complex structures subject to dynamic remodeling in response to developmental and environmental cues and play essential functions in disease resistance responses. We tested the specific contribution of plant cell walls to immunity by determining the susceptibility of a set of Arabidopsis cell wall mutants (cwm) to pathogens with different parasitic styles: a vascular bacterium, a necrotrophic fungus, and a biotrophic oomycete. Remarkably, most cwm mutants tested (29/34; 85.3%) showed alterations in their resistance responses to at least one of these pathogens in comparison to wild-type plants, illustrating the relevance of wall composition in determining disease-resistance phenotypes. We found that the enhanced resistance of cwm plants to the necrotrophic and vascular pathogens negatively impacted cwm fitness traits, such as biomass and seed yield. Enhanced resistance of cwm plants is not only mediated by canonical immune pathways, like those modulated by phytohormones or microbeassociated molecular patterns, which are not deregulated in the cwm tested. Pectin-enriched wall fractions isolated from cwm plants triggered immune responses in wild-type plants, suggesting that wall-mediated defensive pathways might contribute to cwm resistance. Cell walls of cwm plants show a high diversity of composition alterations as revealed by glycome profiling that detect specific wall carbohydrate moieties. Mathematical analysis of glycome profiling data identified correlations between the amounts of specific wall carbohydrate moieties and disease resistance phenotypes of cwm plants. These data support the relevant and specific function of plant wall composition in plant immune response modulation and in balancing disease resistance/development trade-offs.SIThis work has been also financially supported by the Severo Ochoa Program for Centers of Excellence in R&D from the Agencia Estatal de Investigación of Spain (Grant SEV-2016-0672 (2017-2021) to the Centro de Biotecnología y Genómica de Plantas). In the frame of this program, H.M. was a postdoctoral fellow. H.M. was also supported by an Individual Fellowship grant (SignWALLINg-624721) from the European Union. E.M. was a Juan de la Cierva Postdoctoral Fellow from MINECO, and L.B. was a Formacion Personal Investigador fellow of MICIU. The generation of the CCRC-series of plant cell glycan-directed monoclonal antibodies used in this work was supported by the US NSF (DBI-0421683 and IOS 0923992) to M.G.H

Transcriptional Responses of Arabidopsis thaliana during Wilt Disease Caused by the Soil-Borne Phytopathogenic Bacterium, Ralstonia solanacearum

Bacterial wilt is a common disease that causes severe yield and quality losses in many plants. In the present study, we used the model Ralstonia solanacearum-Arabidopsis thaliana pathosystem to study transcriptional changes associated with wilt disease development. Susceptible Col-5 plants and RRS1-R-containing resistant Nd-1 plants were root-inoculated with R. solanacearum strains harbouring or lacking the matching PopP2 avirulence gene. Gene expression was marginally affected in leaves during the early stages of infection. Major changes in transcript levels took place between 4 and 5 days after pathogen inoculation, at the onset of appearance of wilt symptoms. Up-regulated genes in diseased plants included ABA-, senescence- and basal resistance-associated genes. The influence of the plant genetic background on disease-associated gene expression is weak although some genes appeared to be specifically up-regulated in Nd-1 plants. Inactivation of some disease-associated genes led to alterations in the plant responses to a virulent strain of the pathogen. In contrast to other pathosystems, very little overlap in gene expression was detected between the early phases of the resistance response and the late stages of disease development. This observation may be explained by the fact that above-ground tissues were sampled for profiling whereas the bacteria were applied to root tissues

Development genes and plant disease susceptibility to pathogens

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Development genes and plant disease susceptibility to pathogens

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CLAVATA genes and plant disease susceptibility

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CLAVATA genes and plant disease susceptibility

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CLAVATA1, a gene involved in plant development and in Arabidopsis susceptibility to the bacterial pathogen Ralstonia solanacearum

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CLAVATA1, a gene involved in plant development and in Arabidopsis susceptibility to the bacterial pathogen Ralstonia solanacearum

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Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway

Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module