Pole position: How plant cells polarize along the axes.

Having a sense of direction is a fundamental cellular trait that can determine cell shape, division orientation, or function, and ultimately the formation of a functional, multicellular body. Cells acquire and integrate directional information by establishing discrete subcellular domains along an axis with distinct molecular profiles, a process known as cell polarization. Insight into the principles and mechanisms underlying cell polarity has been propelled by decades of extensive research mostly in yeast and animal models. Our understanding of cell polarity establishment in plants, which lack most of the regulatory molecules identified in other eukaryotes, is more limited, but significant progress has been made in recent years. In this review, we explore how plant cells coordinately establish stable polarity axes aligned with the organ axes, highlighting similarities in the molecular logic used to polarize both plant and animal cells. We propose a classification system for plant cell polarity events and nomenclature guidelines. Finally, we provide a deep phylogenetic analysis of polar proteins and discuss the evolution of polarity machineries in plants.

Microtubule associated protein WAVE DAMPENED2-LIKE (WDL) controls microtubule bundling and the stability of the site of tip-growth in Marchantia polymorpha rhizoids.

Tip-growth is a mode of polarized cell expansion where incorporation of new membrane and wall is stably restricted to a single, small domain of the cell surface resulting in the formation of a tubular projection that extends away from the body of the cell. The organization of the microtubule cytoskeleton is conserved among tip-growing cells of land plants: bundles of microtubules run longitudinally along the non-growing shank and a network of fine microtubules grow into the apical dome where growth occurs. Together, these microtubule networks control the stable positioning of the growth site at the cell surface. This conserved dynamic organization is required for the spatial stability of tip-growth, as demonstrated by the formation of sinuous tip-growing cells upon treatment with microtubule-stabilizing or microtubule-destabilizing drugs. Microtubule associated proteins (MAPs) that either stabilize or destabilize microtubule networks are required for the maintenance of stable tip-growth in root hairs of flowering plants. NIMA RELATED KINASE (NEK) is a MAP that destabilizes microtubule growing ends in the apical dome of tip-growing rhizoid cells in the liverwort Marchantia polymorpha. We hypothesized that both microtubule stabilizing and destabilizing MAPs are required for the maintenance of the stable tip-growth in liverworts. To identify genes encoding microtubule-stabilizing and microtubule-destabilizing activities we generated 120,000 UV-B mutagenized and 336,000 T-DNA transformed Marchantia polymorpha plants and screened for defective rhizoid phenotypes. We identified 119 mutants and retained 30 mutants in which the sinuous rhizoid phenotype was inherited. The 30 mutants were classified into at least 4 linkage groups. Characterisation of two of the linkage groups showed that MAP genes-WAVE DAMPENED2-LIKE (WDL) and NIMA-RELATED KINASE (NEK)-are required to stabilize the site of tip growth in elongating rhizoids. Furthermore, we show that MpWDL is required for the formation of a bundled array of parallel and longitudinally orientated microtubules in the non-growing shank of rhizoids where MpWDL-YFP localizes to microtubule bundles. We propose a model where the opposite functions of MpWDL and MpNEK on microtubule bundling are spatially separated and promote tip-growth spatial stability.

A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs.

Land plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, with lateral organs arising independently in different lineages. Vascular plants and bryophytes (basally diverging land plants) develop lateral organs from meristems of sporophytes and gametophytes, respectively. Understanding the mechanisms of lateral organ development among divergent plant lineages is crucial for understanding the evolutionary process of morphological diversification of land plants. However, our current knowledge of lateral organ differentiation mechanisms comes almost entirely from studies of seed plants, and thus, it remains unclear how these lateral structures evolved and whether common regulatory mechanisms control the development of analogous lateral organs. Here, we performed a mutant screen in the liverwort Marchantia polymorpha, a bryophyte, which produces gametophyte axes with nonphotosynthetic scalelike lateral organs. We found that an Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1 (ALOG) family protein, named M. polymorpha LATERAL ORGAN SUPRESSOR 1 (MpLOS1), regulates meristem maintenance and lateral organ development in Marchantia. A mutation in MpLOS1, preferentially expressed in lateral organs, induces lateral organs with misspecified identity and increased cell number and, furthermore, causes defects in apical meristem maintenance. Remarkably, MpLOS1 expression rescued the elongated spikelet phenotype of a MpLOS1 homolog in rice. This suggests that ALOG genes regulate the development of lateral organs in both gametophyte and sporophyte shoots by repressing cell divisions. We propose that the recruitment of ALOG-mediated growth repression was in part responsible for the convergent evolution of independently evolved lateral organs among highly divergent plant lineages, contributing to the morphological diversification of land plants.

Enhancing communication between foundation doctors and radiologists: a quality improvement project.

Facilitating radiological imaging for patients is an essential task for foundation year (FY) doctors. Achieving competence in this task can significantly enhance patient management. We evaluated the confidence and skills of FY doctors in facilitating radiological imaging before and after introduction of formal training. Twenty surgical FYs working at a large teaching hospital were surveyed to evaluate their baseline level of competence in booking and discussing imaging with radiology colleagues. Parameters were measured on a Likert scale, including confidence in discussing requests and satisfaction of their own performance following discussions with radiologists. Eight radiology consultants were surveyed to evaluate their opinions on FYs' communication and established areas for improvement. A teaching session was then delivered to improve communication skills. Furthermore, Previous investigation results, Answer you need from the scan, Clinical status and story, Crucial: how urgent is the scan, Safety (PACCSS) poster was introduced to remind the FYs of the salient information required when discussing imaging. One month after the intervention, the initial participants were resurveyed. Based on a 10-point Likert scale, the FYs demonstrated a mean improvement in self-reported confidence (2.1±1.1, p<0.01), and in satisfaction of own performance after a discussion (1.7±1.1, p<0.01). We identified deficiencies in surgical FY doctors' confidence and skills in facilitating radiological imaging. There was a demonstrable benefit with focused training in improving these skills. This could potentially provide significant benefits in patient care and management. Interspecialty communication should be introduced into undergraduate and postgraduate educational curriculum.

MpWIP regulates air pore complex development in the liverwort Marchantia polymorpha.

The colonisation of the land by plants was accompanied by the evolution of complex tissues and multicellular structures comprising different cell types as morphological adaptations to the terrestrial environment. Here, we show that the single WIP protein in the early-diverging land plant Marchantia polymorpha L. is required for the development of the multicellular gas exchange structure: the air pore complex. This 16-cell barrel-shaped structure surrounds an opening between epidermal cells that facilitates the exchange of gases between the chamber containing the photosynthetic cells inside the plant and the air outside. MpWIP is expressed in cells of the developing air pore complex and the morphogenesis of the complex is defective in plants with reduced MpWIP function. The role of WIP proteins in the control of different multicellular structures in M. polymorpha and the flowering plant Arabidopsis thaliana suggests that these proteins controlled the development of multicellular structures in the common ancestor of land plants. We hypothesise that WIP genes were subsequently co-opted in the control of morphogenesis of novel multicellular structures that evolved during the diversification of land plants.

Who is willing to participate in research? A screening model for an anxiety and depression trial in the epilepsy clinic.

OBJECTIVE: Anxiety and depression in epilepsy are prevalent, associated with poor outcomes, underrecognized, undertreated, and thus a key area of need for treatment research. The objective of this study was to assess factors associated with research participation among epilepsy clinic patients who screened positive for anxiety or depression. This was accomplished by characterizing clinical and psychiatric factors among patients seen in an epilepsy clinic and evaluating which factors were associated with consent for potential research participation, via a combined clinical and research screening model. METHODS: In a pragmatic trial of anxiety and depression treatment in epilepsy, individuals with a positive screen for anxiety and/or depression at a routine epilepsy clinic visit were invited to opt-in (via brief electronic consent) to further eligibility assessment for a randomized treatment study. Information on psychiatric symptoms and treatment characteristics were collected for dual clinical care and research screening purposes. Cross-sectional association of demographic, clinical, and psychiatric factors with opting-in to research was analyzed by multiple logistic regression. RESULTS: Among N = 199 unique adults with a first positive screen for anxiety and/or depression among 786 total screening events, 154 (77.4%) opted-in to further potential research assessment. Higher depression scores and current treatment with an antidepressant were independently associated with opting-in to research (depression odds ratio (OR) = 1.13 per 1-point increase in Neurological Disorders Depression Inventory-Epilepsy (NDDI-E) score, p = 0.028, 95% confidence interval (CI): 1.01-1.26; antidepressant OR = 2.37, p = 0.041, CI: 1.04-5.41). Nearly half of the 199 individuals (43.7%) with anxiety and/or depression symptoms were already being treated with an antidepressant, and 46.7% were receiving neither antidepressant therapy nor mental health specialty care. One-quarter (24.1%) reported a past psychiatric hospitalization, yet only half of these individuals were receiving mental health specialty care. SIGNIFICANCE: Our results demonstrate a high willingness to participate in research using a brief electronic consent approach at a routine clinic visit. Adults with persistent anxiety or depression symptoms despite antidepressant therapy and those with higher depression scores were more willing to consider a randomized treatment study. This has implications for future study design, as individuals already on treatment or those with more severe symptoms are often excluded from traditional research designs. We also found a high burden of psychiatric disease and high prevalence of persistent symptoms despite ongoing antidepressant treatment.

Correlating chemical sensitivity and basal gene expression reveals mechanism of action.

Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ∼19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools are available to the research community through the Cancer Therapeutics Response Portal.

A systematic review of the association between depression and health care utilization in children and adults with sickle cell disease.

Patients with sickle cell disease (SCD) experience a disproportionately high use of health care resources. Several studies have examined depression and other negative mood states as risk factors for increased health care utilization; however, there have been no systematic reviews examining and summarizing this evidence in SCD. The aim of this systematic review, therefore, was to determine whether depression or depressive symptoms are associated with health care utilization among children and adults with SCD. We followed a quantitative systematic review protocol based on the Preferred Reporting Items for Systematic Reviews and Meta- Analyses guidelines and performed a literature search of records from January 1980 to April 2014 using six databases. Empirical studies were eligible if the sample was primarily composed of patients with SCD and included data on depression, mood disorder diagnosis or depressive symptoms and health care utilization. We included 12 studies involving 54 036 unique participants. The prevalence estimates for depression ranged from 2-57%. Seven studies found a significant, or marginally significant, association between depression and utilization while five did not. Patients reporting depression had an estimated 2·8 times greater relative risk of being a high utilizer, and 2·9 versus 1·8 hospitalizations per year on average compared to patients without depression. Overall, depressive symptoms are common in SCD and may increase risk for poor outcomes including health care utilization. The available studies on depression in SCD, however, are limited by small sample sizes, retrospective designs or short follow-up. This systematic review found a modest association between depression and health care utilization in SCD.

The evolution of root hairs and rhizoids.

BACKGROUND: Almost all land plants develop tip-growing filamentous cells at the interface between the plant and substrate (the soil). Root hairs form on the surface of roots of sporophytes (the multicellular diploid phase of the life cycle) in vascular plants. Rhizoids develop on the free-living gametophytes of vascular and non-vascular plants and on both gametophytes and sporophytes of the extinct rhyniophytes. Extant lycophytes (clubmosses and quillworts) and monilophytes (ferns and horsetails) develop both free-living gametophytes and free-living sporophytes. These gametophytes and sporophytes grow in close contact with the soil and develop rhizoids and root hairs, respectively. SCOPE: Here we review the development and function of rhizoids and root hairs in extant groups of land plants. Root hairs are important for the uptake of nutrients with limited mobility in the soil such as phosphate. Rhizoids have a variety of functions including water transport and adhesion to surfaces in some mosses and liverworts. CONCLUSIONS: A similar gene regulatory network controls the development of rhizoids in moss gametophytes and root hairs on the roots of vascular plant sporophytes. It is likely that this gene regulatory network first operated in the gametophyte of the earliest land plants. We propose that later it functioned in sporophytes as the diploid phase evolved a free-living habit and developed an interface with the soil. This transference of gene function from gametophyte to sporophyte could provide a mechanism that, at least in part, explains the increase in morphological diversity of sporophytes that occurred during the radiation of land plants in the Devonian Period.

Sterol transfer by atypical cholesterol-binding NPC2 proteins in coral-algal symbiosis.

Reef-building corals depend on intracellular dinoflagellate symbionts that provide nutrients. Besides sugars, the transfer of sterols is essential for corals and other sterol-auxotrophic cnidarians. Sterols are important cell components, and variants of the conserved Niemann-Pick Type C2 (NPC2) sterol transporter are vastly up-regulated in symbiotic cnidarians. Types and proportions of transferred sterols and the mechanism of their transfer, however, remain unknown. Using different pairings of symbiont strains with lines of Aiptasia anemones or Acropora corals, we observe both symbiont- and host-driven patterns of sterol transfer, revealing plasticity of sterol use and functional substitution. We propose that sterol transfer is mediated by the symbiosis-specific, non-canonical NPC2 proteins, which gradually accumulate in the symbiosome. Our data suggest that non-canonical NPCs are adapted to the symbiosome environment, including low pH, and play an important role in allowing corals to dominate nutrient-poor shallow tropical seas worldwide.

Influence of Spirituality on Depression-Induced Inflammation and Executive Functioning in a Community Sample of African Americans.

African Americans (AAs) are disproportionately affected by cerebrovascular pathology and more likely to suffer from premature cognitive decline. Depression is a risk factor for poorer cognitive functioning, and research is needed to identify factors that serve to mitigate its negative effects. Studies have demonstrated positive influences of spirituality within the AA community. Determining whether spirituality attenuates the effects of depressive symptoms on cognitive functioning and the pathophysiological mechanisms that explain these relationships in AAs is paramount. This study examines the influence of daily spiritual experiences on the relationship between depressive symptoms and cognitive functioning, and how inflammatory markers may partially explain these associations. A sample of 212 (mean age= 45.6) participants completed the Daily Spiritual Experience Scale (DSES), Beck Depression Inventory-II (BDI-II), Trail Making Test A and B (TMT) and Stroop Color and Word Test (Stroop). Blood samples were collected to measure inflammatory mediators (IL-6, IL-1a, TNF-a). Linear regression analyses were used to evaluate associations. Higher BDI-II scores were associated with poorer psychomotor speed and visual scanning, measured by TMT A (B=1.49, P=.01). IL-6 explained a significant amount of variance in this relationship (B=.24, CI 95% [.00, .64]). IL-6 also significantly mediated the relationship between depressive symptoms and psychomotor speed and mental flexibility, measured by TMT B performance (B=.03, CI 95% [.003, .095]). Frequent spiritual experiences among AAs may ameliorate the negative influence of depressive symptoms on cognitive functioning.

Ferumoxytol-enhanced MRI in patients with prior cardiac transplantation.

Objectives: Ultra-small superparamagnetic particles of iron oxide (USPIO)-enhanced MRI can detect cellular inflammation within tissues and may help non-invasively identify cardiac transplant rejection. Here, we aimed to determine the normal reference values for USPIO-enhanced MRI in patients with a prior cardiac transplant and examine whether USPIO-enhanced MRI could detect myocardial inflammation in patients with transplant rejection. Methods: Ten volunteers and 11 patients with cardiac transplant underwent T2, T2* and late gadolinium enhancement 1.5T MRI, with further T2* imaging at 24 hours after USPIO (ferumoxytol, 4 mg/kg) infusion, at baseline and 3 months. Results: Ten patients with clinically stable cardiac transplantation were retained for analysis. Myocardial T2 values were higher in patients with cardiac transplant versus healthy volunteers (53.8±5.2 vs 48.6±1.9 ms, respectively; p=0.003). There were no differences in the magnitude of USPIO-induced change in R2* in patients with transplantation (change in R2*, 26.6±7.3 vs 22.0±10.4 s-1 in healthy volunteers; p=0.28). After 3 months, patients with transplantation (n=5) had unaltered T2 values (52.7±2.8 vs 52.12±3.4 ms; p=0.80) and changes in R2* following USPIO (29.42±8.14 vs 25.8±7.8 s-1; p=0.43). Conclusion: Stable patients with cardiac transplantation have increased myocardial T2 values, consistent with resting myocardial oedema or fibrosis. In contrast, USPIO-enhanced MRI is normal and stable over time suggesting the absence of chronic macrophage-driven cellular inflammation. It remains to be determined whether USPIO-enhanced MRI may be able to identify acute cardiac transplant rejection. Trial registration number: NCT02319278349 (https://clinicaltrials.gov/ct2/show/NCT02319278) Registered 03.12.2014 EUDraCT 2013-002336-24.

Microinjection to deliver protein, mRNA, and DNA into zygotes of the cnidarian endosymbiosis model Aiptasia sp.

Reef-building corals depend on an intracellular symbiosis with photosynthetic dinoflagellates for their survival in nutrient-poor oceans. Symbionts are phagocytosed by coral larvae from the environment and transfer essential nutrients to their hosts. Aiptasia, a small tropical marine sea anemone, is emerging as a tractable model system for coral symbiosis; however, to date functional tools and genetic transformation are lacking. Here we have established an efficient workflow to collect Aiptasia eggs for in vitro fertilization and microinjection as the basis for experimental manipulations in the developing embryo and larvae. We demonstrate that protein, mRNA, and DNA can successfully be injected into live Aiptasia zygotes to label actin with recombinant Lifeact-eGFP protein; to label nuclei and cell membranes with NLS-eGFP and farnesylated mCherry translated from injected mRNA; and to transiently drive transgene expression from an Aiptasia-specific promoter, respectively, in embryos and larvae. These proof-of-concept approaches pave the way for future functional studies of development and symbiosis establishment in Aiptasia, a powerful model to unravel the molecular mechanisms underlying intracellular coral-algal symbiosis.

Efficacy of Pterocarpus angolensis crude extracts against Candida krusei, Staphylococcus aureus, Streptococcus agalactiae and Escherichia coli.

BACKGROUND: The medicinal plants used to treat different ailments in Malawi contain important phytochemicals which have bactericidal and anti-fungal properties. Pterocarpus angolensis, locally known as mlombwa tree, which is found in many parts of Malawi, is one such a plant and was studied. AIMS: In vitro analysis of the antimicrobial properties of Pterocarpus angolensis crude extracts on Staphylococcus aureus, Escherichia coli, Streptococcus agalactiae, Candida krusei and determination of the phytochemicals there in. METHODS: In this study, different organs of P. angolensis, a medicinal plant which is locally used to treat skin diseases, were qualitatively screened for the presence of phytochemical constituents and quantitatively assayed for the antimicrobial activity to ascertain their pharmaceutical potential. The aqueous, dichloromethane and methanolic extracts of the leaves, stem-bark, fruits and roots of the plant were tested against Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae and Candida krusei by the macro tube dilution method. These pathogens were selected due to their significant contribution to infectious disease burden of most hospitals and also the fact that of late, they have shown signs of resistance to conventional antibiotics. RESULTS: The study revealed that P. angolensis contained tannins, flavonoids, saponins and terpenoids. All the extracts exhibited some antimicrobial activity against the test organisms. However, the activity of the extracts depended on concentration and microbial species. The minimum inhibition concentration (MIC) values of the extracts ranged from 0.166 g/ml to 0.01046 g/ml with the dichloromethane and methanolic extracts exhibiting more activity than the aqueous extracts. The minimum bactericidal concentration and minimum fungicidal concentration (MBC and MFC respectively) values of the extracts ranged from 0.166 g/ml to 0.0417 g/ml. CONCLUSION: The results obtained indicate that Pterocarpus angolensis has both antibacterial and antifungal properties and could be used for the treatment of Taenia capitis (ring worm) and other ailments. Use of the isolated and purified compounds from P. angolensis could increase the susceptibility of the tested pathogenic microorganisms in this study.

1-Tetradecanol complex reduces progression of Porphyromonas gingivalis-induced experimental periodontitis in rabbits.

BACKGROUND: It has been recently shown that monounsaturated fatty acids inhibit endothelial activation and reduce tissue responsiveness to cytokines. The present study has been planned to investigate topical application of a novel monounsaturated fatty acid complex (1-tetradecanol complex) for prevention of Porphyromonas gingivalis-induced periodontitis in rabbits. METHODS: Experimental periodontitis was induced in New Zealand white rabbits with silk sutures tied around the mandibular second premolars bilaterally, followed by the topical application of 10(9) colony forming units (CFU) of P. gingivalis. 1-Tetradecanol complex (1-TDC) was topically applied at 1- and 10-mg/ml concentrations in five animals in each group, whereas control animals received olive oil vehicle (five animals) three times per week for 6 weeks. Negative controls included ligature alone (14 animals) or ligature + P. gingivalis (non-treatment; 15 animals). Rabbits were sacrificed after 6 weeks, and mandibular block sections were obtained; tissues were decalcified and embedded in paraffin. Thin sections (5 microm) were stained with hematoxylin and eosin or tartrate-resistant acid phosphatase. Macroscopic and histologic evaluation of samples was followed by the characterization of cellular inflammatory infiltrate and quantitative histomorphometric measurements. RESULTS: Treatment with both concentrations of 1-TDC and vehicle resulted in significant prevention of macroscopic periodontal inflammation and bone loss (75%; P <0.05) compared to the non-treatment (ligature + P. gingivalis) group, where significant periodontal tissue destruction characterized by attachment and bone loss was detected. However, there was no statistically significant difference between the vehicle and both 1-TDC groups. Histologically, 1-TDC inhibited inflammatory cell infiltration and prevented osteoclastogenesis, whereas treatment with vehicle did not show the same effect as in the 1-TDC groups; the difference between vehicle and the higher concentration of 1-TDC (10 mg/ml) was statistically significant. CONCLUSION: Topical application of an esterified monounsaturated fatty acid complex (1-TDC) was found promising in preventing bone loss, inflammatory cell infiltration, and connective tissue destruction in the rabbit periodontitis model.

The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants.

To discover mechanisms that controlled the growth of the rooting system in the earliest land plants, we identified genes that control the development of rhizoids in the liverwort Marchantia polymorpha. 336,000 T-DNA transformed lines were screened for mutants with defects in rhizoid growth, and a de novo genome assembly was generated to identify the mutant genes. We report the identification of 33 genes required for rhizoid growth, of which 6 had not previously been functionally characterized in green plants. We demonstrate that members of the same orthogroup are active in cell wall synthesis, cell wall integrity sensing, and vesicle trafficking during M. polymorpha rhizoid and Arabidopsis thaliana root hair growth. This indicates that the mechanism for constructing the cell surface of tip-growing rooting cells is conserved among land plants and was active in the earliest land plants that existed sometime more than 470 million years ago [1, 2].

RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants.

The colonization of the land by plants, sometime before 470 million years ago, was accompanied by the evolution tissue systems [1-3]. Specialized structures with diverse functions-from nutrient acquisition to reproduction-derived from single cells in the outermost layer (epidermis) were important sources of morphological innovation at this time [2, 4, 5]. In extant plants, these structures may be unicellular extensions, such as root hairs or rhizoids [6-9], or multicellular structures, such as asexual propagules or secretory hairs (papillae) [10-12]. Here, we show that a ROOTHAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix-loop-helix transcription factor positively regulates the development of the unicellular and multicellular structures that develop from individual cells that expand out of the epidermal plane of the liverwort Marchantia polymorpha; mutants that lack MpRSL1 function do not develop rhizoids, slime papillae, mucilage papillae, or gemmae. Furthermore, we discovered that RSL class I genes are also required for the development of multicellular axillary hairs on the gametophyte of the moss Physcomitrella patens. Because class I RSL proteins also control the development of rhizoids in mosses and root hairs in angiosperms [13, 14], these data demonstrate that the function of RSL class I genes was to control the development of structures derived from single epidermal cells in the common ancestor of the land plants. Class I RSL genes therefore controlled the generation of adaptive morphological diversity as plants colonized the land from the water.

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.

UNLABELLED: Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer medicines. Cancer cell-line (CCL) profiling of small-molecule sensitivity has emerged as an unbiased method to assess the relationships between genetic or cellular features of CCLs and small-molecule response. Here, we developed annotated cluster multidimensional enrichment analysis to explore the associations between groups of small molecules and groups of CCLs in a new, quantitative sensitivity dataset. This analysis reveals insights into small-molecule mechanisms of action, and genomic features that associate with CCL response to small-molecule treatment. We are able to recapitulate known relationships between FDA-approved therapies and cancer dependencies and to uncover new relationships, including for KRAS-mutant cancers and neuroblastoma. To enable the cancer community to explore these data, and to generate novel hypotheses, we created an updated version of the Cancer Therapeutic Response Portal (CTRP v2). SIGNIFICANCE: We present the largest CCL sensitivity dataset yet available, and an analysis method integrating information from multiple CCLs and multiple small molecules to identify CCL response predictors robustly. We updated the CTRP to enable the cancer research community to leverage these data and analyses.