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Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis
Full text linkBACKGROUND: Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or "riboSNitches." RESULTS: We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. CONCLUSION: We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term "conditional riboSNitch." We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation
Building an embryo: An auxin gene toolkit for zygotic and somatic embryogenesis in Brazilian pine
No full textMany studies in the model species Arabidopsis thaliana characterized genes involved in embryo formation. However, much remains to be learned about the portfolio of genes that are involved in signal transduction and transcriptional regulation during plant embryo development in other species, particularly in an evolutionary context, especially considering that some genes involved in embryo patterning are not exclusive of land plants. This study, used a combination of domain architecture phylostratigraphy and phylogenetic reconstruction to investigate the evolutionary history of embryo patterning and auxin metabolism (EPAM) genes in Viridiplantae. This approach shed light on the co-optation of auxin metabolism and other molecular mechanisms that contributed to the radiation of land plants, and specifically to embryo formation. These results have potential to assist conservation programs, by directing the development of tools for obtaining somatic embryos. In this context, we employed this methodology with critically endangered and non-model species Araucaria angustifolia, the Brazilian pine, which is current focus of conservation efforts using somatic embryogenesis. So far, this approach had little success since somatic embryos fail to completely develop. By profiling the expression of genes that we identified as necessary for the emergence of land-plant embryos, we found striking differences between zygotic and somatic embryos that might explain the developmental arrest and be used to improve A. angustifolia somatic culture
Host Plant Adaptation Drives Changes in Diaphorina citri Proteome Regulation, Proteoform Expression, and Transmission of ‘Candidatus Liberibacter asiaticus’, the Citrus Greening Pathogen
Full text linkThe Asian citrus psyllid (Diaphorina citri) is a pest of citrus and the primary insect vector of the bacterial pathogen, ‘Candidatus Liberibacter asiaticus’ (CLas), which is associated with citrus greening disease. The citrus relative Murraya paniculata (orange jasmine) is a host plant of D. citri but is more resistant to CLas compared with all tested Citrus genotypes. The effect of host switching of D. citri between Citrus medica (citron) and M. paniculata plants on the acquisition and transmission of CLas was investigated. The psyllid CLas titer and the proportion of CLas-infected psyllids decreased in the generations after transfer from CLas-infected citron to healthy M. paniculata plants. Furthermore, after several generations of feeding on M. paniculata, pathogen acquisition (20 to 40% reduction) and transmission rates (15 to 20% reduction) in psyllids transferred to CLas-infected citron were reduced compared with psyllids continually maintained on infected citron. Top-down (difference gel electrophoresis) and bottom-up (shotgun MS/MS) proteomics methods were used to identify changes in D. citri protein expression resulting from host plant switching between Citrus macrophylla and M. paniculata. Changes in expression of insect metabolism, immunity, and cytoskeleton proteins were associated with host plant switching. Both transient and sustained feeding on M. paniculata induced distinct patterns of protein expression in D. citri compared with psyllids reared on C. macrophylla. The results point to complex interactions that affect vector competence and may lead to strategies to control the spread of citrus greening disease
Neutrophil phenotypes and functions in cancer: A consensus statement.
Full text linkNeutrophils are the first responders to infection and inflammation and are thus a critical component of innate immune defense. Understanding the behavior of neutrophils as they act within various inflammatory contexts has provided insights into their role in sterile and infectious diseases; however, the field of neutrophils in cancer is comparatively young. Here, we summarize key concepts and current knowledge gaps related to the diverse roles of neutrophils throughout cancer progression. We discuss sources of neutrophil heterogeneity in cancer and provide recommendations on nomenclature for neutrophil states that are distinct in maturation and activation. We address discrepancies in the literature that highlight a need for technical standards that ought to be considered between laboratories. Finally, we review emerging questions in neutrophil biology and innate immunity in cancer. Overall, we emphasize that neutrophils are a more diverse population than previously appreciated and that their role in cancer may present novel unexplored opportunities to treat cancer
Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release
Full text linkArgonaute (Ago) proteins play a central role in post-transcriptional gene regulation through RNA interference (RNAi). Agos bind small RNAs (sRNAs) including small interfering RNAs (siRNAs) and microRNAs (miRNAs) to form the functional core of the RNA-induced silencing complex (RISC). The sRNA is used as a guide to target mRNAs containing either partially or fully complementary sequences, ultimately leading to downregulation of the corresponding proteins. It was previously shown that the kinase CK1α phosphorylates a cluster of residues in the eukaryotic insertion (EI) of Ago, leading to the alleviation of miRNA-mediated repression through an undetermined mechanism. We show that binding of miRNA-loaded human Ago2 to target RNA with complementarity to the seed and 3' supplementary regions of the miRNA primes the EI for hierarchical phosphorylation by CK1α. The added negative charges electrostatically promote target release, freeing Ago to seek out additional targets once it is dephosphorylated. The high conservation of potential phosphosites in the EI suggests that such a regulatory strategy may be a shared mechanism for regulating miRNA-mediated repression
Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy
Full text linkLow CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation
Myodifferentiation of Rhabdomyosarcoma
Full text linkRhabdomyosarcoma is an aggressive pediatric soft tissue malignancy thought to originate from muscle progenitor cells that failed to reach terminal differentiation. A common genetic alteration in rhabdomyosarcoma pathogenesis is a chromosomal translocation that fuses the DNA binding domain of PAX3 to the transcriptional activation domain of FOXO1, resulting in a chimeric transcription factor PAX3-FOXO1. This fusion oncoprotein leads to a myogenic differentiation block, promotes cellular proliferation, and oncogenic transformation. While rhabdomyosarcoma cells express several early myogenic markers such as MYOD1 and desmin, late markers of differentiation are absent and rhabdomyosarcoma cells do not fuse or form functional muscles. We set out to identify factors that cooperate with PAX3-FOXO1 to sustain the myodifferentiation block, the rationale being that perturbations of these gene products could lead to the identification of novel, mechanism-based targets for this disease. To this end, we developed a CRISPR/Cas9 phenotypic screen to identify genetic knockouts that phenocopy loss of PAX3-FOXO1 and lead to rhabdomyosarcoma myodifferentiation
using intracellular staining for an endogenous reporter and fluorescence activated cell sorting. Using this approach, we identified NFYA, NFYB, and NFYC, all members of the heterotrimeric transcription factor complex NF-Y, at the leading edge of knockouts that re-engage forward myodifferentiation and restore lineage fates in this disease. We validated the results of the pooled screen with individual gene knockouts and demonstrated that cells depleted of NF-Y closely resemble cells depleted of PAX3-FOXO1 transcriptome-wide and at a single cell level. The myodifferentiation response following loss of NF-Y is conserved among fusion positive rhabdomyosarcoma models. We characterized genome-wide chromatin occupancy of NF-Y in rhabdomyosarcoma cells using CUT&RUN and showed that it binds a number of cancerpromoting and differentiation-inhibiting genes, including the PAX3 promoter that drives expression of PAX3-FOXO1. Mutagenesis of the NF-Y recognition motif or targeted displacement of NF-Y from the PAX3 promoter partially recapitulates the effects of NF-Y knockout. Since NF-Y binds primarily gene promoters and PAX3-FOXO1 binds enhancers, yet they control an overlapping set of genes, we examined genomic interactions in 3D space
and uncovered a subset of genes where NF-Y and PAX3-FOXO1 participate in coordinated long-range interactions, including SIX1, a recently described master regulator of
rhabdomyosarcoma differentiation state. Taken together, we conclude that NF-Y is a key transcription factor complex, whose function is coordinated with PAX3-FOXO1 to drive
rhabdomyosarcoma pathogenesis
Sleep Disruption and Cancer: Chicken or the Egg?
Full text linkSleep is a nearly ubiquitous phenomenon across the phylogenetic tree, highlighting its essential role in ensuring fitness across evolutionary time. Consequently, chronic disruption of the duration, timing, or structure of sleep can cause widespread problems in multiple physiological systems, including those that regulate energy balance, immune function, and cognitive capacity, among others. Many, if not all these systems, become altered throughout the course of cancer initiation, growth, metastatic spread, treatment, and recurrence. Recent work has demonstrated how changes in sleep influence the development of chronic diseases, including cancer, in both humans and animal models. A common finding is that for some cancers (e.g., breast), chronic disruption of sleep/wake states prior to disease onset is associated with an increased risk for cancer development. Additionally, sleep disruption after cancer initiation is often associated with worse outcomes. Recently, evidence suggesting that cancer itself can affect neuronal circuits controlling sleep and wakefulness has accumulated. Patients with cancer often report difficulty falling asleep, difficulty staying asleep, and severe fatigue, during and even years after treatment. In addition to the psychological stress associated with cancer, cancer itself may alter sleep homeostasis through changes to host physiology and via currently undefined mechanisms. Moreover, cancer treatments (e.g., chemotherapy, radiation, hormonal, and surgical) may further worsen sleep problems through complex biological processes yet to be fully understood. This results in a "chicken or the egg" phenomenon, where it is unclear whether sleep disruption promotes cancer or cancer reciprocally disrupts sleep. This review will discuss existing evidence for both hypotheses and present a framework through which the interactions between sleep and cancer can be dissociated and causally investigated
The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest
Full text linkWildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities' response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi-bacteria (F:B) proportions between different trails (p = 2 × 10-16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism
Centering the needs of transgender, non-binary, and gender-diverse populations in neuroendocrine models of gender-affirming hormone therapy
No full textThe majority of studies attempting to address the healthcare needs of the millions of transgender, non-binary, and/or gender diverse (TNG) individuals rely on human subjects, overlooking the benefits of translational research in animal models. Researchers have identified many ways in which gonadal steroid hormones regulate neuronal gene expression, connectivity, activity, and function across the brain to control behavior. However, these discoveries primarily benefit cisgender populations. Research into the effects of exogenous hormones such as estradiol, testosterone, and progesterone has direct translational benefit for TNG individuals on gender affirming hormone therapies (GAHT). Despite this potential, endocrinological healthcare for TNG individuals remains largely unimproved. Here, we outline important areas of translational research that could address the unique healthcare needs of TNG individuals on GAHT. We highlight key biomedical questions regarding GAHT that can be investigated using animal models. We discuss how contemporary research fails to address the needs of GAHT-users and identify equitable practices for cisgender scientists engaging with this work. We conclude that if necessary and important steps are taken to address these issues, translational research on GAHT will greatly benefit the healthcare outcomes of TNG people