Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features.

BACKGROUND: Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the emergence and evolution of cancer clones at this early stage of expansion and spread are poorly understood. We aimed to delineate the routes of evolution and cancer spread within the prostate and to seminal vesicles and lymph nodes, linking these to histological features that are used in diagnostic risk stratification. METHODS: We performed whole-genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and lymph nodes of five treatment-naive patients with locally advanced disease. We spatially mapped the clonal composition of cancer across the prostate and the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes in each individual by analysing a total of > 19,000 copy number corrected single nucleotide variants. RESULTS: In each patient, we identified sample locations corresponding to the earliest part of the malignancy. In patient 10, we mapped the spread of cancer from the apex of the prostate to the seminal vesicles and identified specific genomic changes associated with the transformation of adenocarcinoma to amphicrine morphology during this spread. Furthermore, we show that the lymph node metastases in this patient arose from specific cancer clones found at the base of the prostate and the seminal vesicles. In patient 15, we observed increased mutational burden, altered mutational signatures and histological changes associated with whole genome duplication. In all patients in whom histological heterogeneity was observed (4/5), we found that the distinct morphologies were located on separate branches of their respective evolutionary trees. CONCLUSIONS: Our results link histological transformation with specific genomic alterations and phylogenetic branching. These findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes causally linked to morphological transformation. Our study demonstrates the value of integrating multi-region sequencing with histopathological data to understand tumour evolution and identify mechanisms of prostate cancer spread.

Local groundwater decline exacerbates response of dryland riparian woodlands to climatic drought.

Dryland riparian woodlands are considered to be locally buffered from droughts by shallow and stable groundwater levels. However, climate change is causing more frequent and severe drought events, accompanied by warmer temperatures, collectively threatening the persistence of these groundwater dependent ecosystems through a combination of increasing evaporative demand and decreasing groundwater supply. We conducted a dendro-isotopic analysis of radial growth and seasonal (semi-annual) carbon isotope discrimination (Δ13 C) to investigate the response of riparian cottonwood stands to the unprecedented California-wide drought from 2012 to 2019, along the largest remaining free-flowing river in Southern California. Our goals were to identify principal drivers and indicators of drought stress for dryland riparian woodlands, determine their thresholds of tolerance to hydroclimatic stressors, and ultimately assess their vulnerability to climate change. Riparian trees were highly responsive to drought conditions along the river, exhibiting suppressed growth and strong stomatal closure (inferred from reduced Δ13 C) during peak drought years. However, patterns of radial growth and Δ13 C were quite variable among sites that differed in climatic conditions and rate of groundwater decline. We show that the rate of groundwater decline, as opposed to climate factors, was the primary driver of site differences in drought stress, and trees showed greater sensitivity to temperature at sites subjected to faster groundwater decline. Across sites, higher correlation between radial growth and Δ13 C for individual trees, and higher inter-correlation of Δ13 C among trees were indicative of greater drought stress. Trees showed a threshold of tolerance to groundwater decline at 0.5 m year-1 beyond which drought stress became increasingly evident and severe. For sites that exceeded this threshold, peak physiological stress occurred when total groundwater recession exceeded ~3 m. These findings indicate that drought-induced groundwater decline associated with more extreme droughts is a primary threat to dryland riparian woodlands and increases their susceptibility to projected warmer temperatures.

Performance of a Native Butterfly and Introduced Moth on Native and Introduced Lineages of Phragmites australis.

This study examined the performance of Poanes viator (Edwards) (Hesperiidae), a native North American skipper, and Rhizedra lutosa (Hübner) (Noctuidae), an introduced moth, reared on native and non-native, invasive lineages of Phragmites australis. Poanes viator is a generalist on monocots and larvae were also fed leaves of Zizania aquatica, a native macrophyte that the skipper commonly uses as a host plant. Larval survival and duration, pupal weight, and pupation time were compared for P. viator feeding on leaf tissue and R. lutosa feeding on rhizomes of either native or introduced plants. We also tested an artificial diet supplemented with P. australis rhizome powder as a potential food for rearing other stalk and rhizome boring Lepidoptera. In experiments using excised plant tissues, some individuals of both species fed and developed to the pupal stage on native and introduced plants, but overall, larval survival rates were low. Plant species/haplotype identity did not cause strong differences in larval survival for either species. However, P. viator larvae only pupated when feeding on native plants (Zizania aquatica and native P. australis haplotypes), whereas R. lutosa successfully pupated on both native and introduced P. australis. Although larval survival was low, 100% of P. viator and 95% of R. lutosa that reached the pupal stage emerged as adults. Rhizedra lutosa larvae fed an artificial diet supplemented with P. australis rhizome powder had significantly greater survival and pupal weights, and shorter pupation times than larvae fed rhizomes only. Several specialist Lepidopteran species are being considered for approval as biological control agents for the non-native P. australis haplotype, and the convenience and increased larval performance make this artificial diet a good alternative for rearing organisms.

Biology of an Adventive Population of the Armored Scale Rhizaspidiotus donacis, a Biological Control Agent of Arundo donax in California.

Arundo donax (giant reed) is invasive in Mediterranean, sub-, and tropical riparian systems worldwide. The armored scale Rhizaspidiotus donacis is approved for biocontrol in North America, but an adventive population was recently discovered in southern California. We documented this population's distribution, phylogeny, phenology, potential host spillover to Phragmites spp., and potential for parasitism by a common biocontrol parasitoid of citrus scale. The adventive scale was found within a single watershed and is genetically closest to Iberian scale genotypes. Rhizaspidiotus donacis developed on Phragmites haplotypes but at much lower densities than Arundo. The adventive population is univoltine, producing crawlers from March-June. Aphytis melinus parasitoids exhibited sustained interest in R. donacis during choice and no-choice trials and oviposition resulted in a small second generation. Rhizaspidiotus donacis appears limited in distribution by its univoltinism and sessile adult females. This presents challenges for broad biocontrol implementation but allows for targeted application. The genetic differentiation between imported biocontrol samples and adventive populations presents an opportunity for exploring benefits of hybrids and/or alternative genotypes where establishment has been difficult. While unlikely to occur in situ, spillover to vulnerable endemic Phragmites or deleterious parasitoid effects on scale biocontrol agents warrants consideration when planning use of R. donacis.

Does hybrid Phragmites australis differ from native and introduced lineages in reproductive, genetic, and morphological traits?

PREMISE OF THE STUDY: Hybridization between previously isolated species or lineages can stimulate invasiveness because of increased genetic diversity and inherited traits facilitating competitive and reproductive potential. We evaluated differences in stand characteristics and sexual and vegetative reproduction among native, introduced, and hybrid Phragmites australis lineages in the southwestern United States. We also assessed the degree of hybridization among lineages and backcrossing of hybrids with parental lineages. METHODS: Growth and morphological characteristics were measured in native, introduced, and hybrid Phragmites stands to evaluate relative cover and dominance in associated plant communities. Panicles were collected from stands to evaluate germination, dormancy, and differences in seed traits. Seedlings from germination trials were genotyped to determine frequency of crossing and backcrossing among lineages. KEY RESULTS: Introduced and hybrid Phragmites stands had significantly greater stem and panicle densities than native stands and were more likely to be dominant members of their respective plant communities. Hybrid seed outputs were significantly greater, but hybrid seeds had lower germination rates than those from native and introduced lineages. We detected a novel hybridization event between native and introduced lineages, but found no strong evidence of hybrids backcrossing with parental lineages. CONCLUSIONS: Hybrid Phragmites in the Southwest exhibits reproductive, genetic, and morphological characteristics from both parental lineages that facilitate dispersal, establishment, and aggressive growth, including high reproductive output, rhizome viability, and aboveground biomass, with smaller seeds and greater genetic diversity than its progenitors. Our results show hybrids can inherit traits that confer invasiveness and provide insight for managing this species complex and other cryptic species with native and introduced variants with potential for intraspecific hybridization.

An Oncolytic Virus Expressing a T-cell Engager Simultaneously Targets Cancer and Immunosuppressive Stromal Cells.

: Effective immunotherapy of stromal-rich tumors requires simultaneous targeting of cancer cells and immunosuppressive elements of the microenvironment. Here, we modified the oncolytic group B adenovirus enadenotucirev to express a stroma-targeted bispecific T-cell engager (BiTE). This BiTE bound fibroblast activation protein on cancer-associated fibroblasts (CAF) and CD3ε on T cells, leading to potent T-cell activation and fibroblast death. Treatment of fresh clinical biopsies, including malignant ascites and solid prostate cancer tissue, with FAP-BiTE-encoding virus induced activation of tumor-infiltrating PD1+ T cells to kill CAFs. In ascites, this led to depletion of CAF-associated immunosuppressive factors, upregulation of proinflammatory cytokines, and increased gene expression of markers of antigen presentation, T-cell function, and trafficking. M2-like ascites macrophages exhibited a proinflammatory repolarization, indicating spectrum-wide alteration of the tumor microenvironment. With this approach, we have actively killed both cancer cells and tumor fibroblasts, reversing CAF-mediated immunosuppression and yielding a potent single-agent therapeutic that is ready for clinical assessment. SIGNIFICANCE: An engineered oncolytic adenovirus that encodes a bispecific antibody combines direct virolysis with endogenous T-cell activation to attack stromal fibroblasts, providing a multimodal treatment strategy within a single therapeutic agent.

Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage.

Internalization of ligand-activated type I IGF receptor (IGF1R) is followed by recycling to the plasma membrane, degradation or nuclear translocation. Nuclear IGF1R reportedly associates with clinical response to IGF1R inhibitory drugs, yet its role in the nucleus is poorly characterized. Here, we investigated the significance of nuclear IGF1R in clinical cancers and cell line models. In prostate cancers, IGF1R was predominantly membrane localized in benign glands, while malignant epithelium contained prominent internalized (nuclear/cytoplasmic) IGF1R, and nuclear IGF1R associated significantly with advanced tumor stage. Using ChIP-seq to assess global chromatin occupancy, we identified IGF1R-binding sites at or near transcription start sites of genes including JUN and FAM21, most sites coinciding with occupancy by RNA polymerase II (RNAPol2) and histone marks of active enhancers/promoters. IGF1R was inducibly recruited to chromatin, directly binding DNA and interacting with RNAPol2 to upregulate expression of JUN and FAM21, shown to mediate tumor cell survival and IGF-induced migration. IGF1 also enriched RNAPol2 on promoters containing IGF1R-binding sites. These functions were inhibited by IGF1/II-neutralizing antibody xentuzumab (BI 836845), or by blocking receptor internalization. We detected IGF1R on JUN and FAM21 promoters in fresh prostate cancers that contained abundant nuclear IGF1R, with evidence of correlation between nuclear IGF1R content and JUN expression in malignant prostatic epithelium. Taken together, these data reveal previously unrecognized molecular mechanisms through which IGFs promote tumorigenesis, with implications for therapeutic evaluation of anti-IGF drugs.Significance: These findings reveal a noncanonical nuclear role for IGF1R in tumorigenesis, with implications for therapeutic evaluation of IGF inhibitory drugs. Cancer Res; 78(13); 3497-509. ©2018 AACR.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora).

Experimental studies to determine the nature of ecological interactions between invasive and native species are necessary for conserving and restoring native species in impacted habitats. Theory predicts that species boundaries along environmental gradients are determined by physical factors in stressful environments and by competitive ability in benign environments, but little is known about the mechanisms by which hydrophytes exclude halophytes and the life history stage at which these mechanisms are able to operate. The ongoing invasion of the South American Spartina densiflora in European marshes is causing concern about potential impacts to native plants along the marsh salinity gradient, offering an opportunity to evaluate the mechanisms by which native hydrophytes may limit, or even prevent, the expansion of invasive halophytes. Our study compared S. densiflora seedling establishment with and without competition with Phragmites australis and Typha domingensis, two hydrophytes differing in clonal architecture. We hypothesized that seedlings of the stress tolerant S. densiflora would be out-competed by stands of P. australis and T. domingensis. Growth, survivorship, biomass patterns and foliar nutrient content were recorded in a common garden experiment to determine the effect of mature P. australis and T. domingensis on the growth and colonization of S. densiflora under fresh water conditions where invasion events are likely to occur. Mature P. australis stands prevented establishment of S. densiflora seedlings and T. domingensis reduced S. densiflora establishment by 38%. Seedlings grown with P. australis produced fewer than five short shoots and all plants died after ca. 2 yrs. Our results showed that direct competition, most likely for subterranean resources, was responsible for decreased growth rate and survivorship of S. densiflora. The presence of healthy stands of P. australis, and to some extent T. domingensis, along river channels and in brackish marshes may prevent the invasion of S. densiflora by stopping the establishment of its seedlings.

Discovery and SAR of 2-arylbenzotriazoles and 2-arylindazoles as potential treatments for Duchenne muscular dystrophy.

Families of 2-arylbenzotriazoles and 2-arylindazoles that show positive effects in screens predictive of endogenous utrophin upregulation have been identified. Synthesis and structure-activity relationships are described leading to compounds with attractive in vitro profiles.

Daily treatment with SMTC1100, a novel small molecule utrophin upregulator, dramatically reduces the dystrophic symptoms in the mdx mouse.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a lethal, progressive muscle wasting disease caused by a loss of sarcolemmal bound dystrophin, which results in the death of the muscle fibers leading to the gradual depletion of skeletal muscle. There is significant evidence demonstrating that increasing levels of the dystrophin-related protein, utrophin, in mouse models results in sarcolemmal bound utrophin and prevents the muscular dystrophy pathology. The aim of this work was to develop a small molecule which increases the levels of utrophin in muscle and thus has therapeutic potential. METHODOLOGY AND PRINCIPAL FINDINGS: We describe the in vivo activity of SMT C1100; the first orally bioavailable small molecule utrophin upregulator. Once-a-day daily-dosing with SMT C1100 reduces a number of the pathological effects of dystrophin deficiency. Treatment results in reduced pathology, better muscle physiology leading to an increase in overall strength, and an ability to resist fatigue after forced exercise; a surrogate for the six minute walk test currently recommended as the pivotal outcome measure in human trials for DMD. CONCLUSIONS AND SIGNIFICANCE: This study demonstrates proof-of-principle for the use of in vitro screening methods in allowing identification of pharmacological agents for utrophin transcriptional upregulation. The best compound identified, SMT C1100, demonstrated significant disease modifying effects in DMD models. Our data warrant the full evaluation of this compound in clinical trials in DMD patients.

Discovery of 2-arylbenzoxazoles as upregulators of utrophin production for the treatment of Duchenne muscular dystrophy.

A series of novel 2-arylbenzoxazoles that upregulate the production of utrophin in murine H2K cells, as assessed using a luciferase reporter linked assay, have been identified. This compound class appears to hold considerable promise as a potential treatment for Duchenne muscular dystrophy. Following the delineation of structure-activity relationships in the series, a number of potent upregulators were identified, and preliminary ADME evaluation is described. These studies have resulted in the identification of 1, a compound that has been progressed to clinical trials.

Susceptibility of native and non-native common reed to the non-native mealy plum aphid (Homoptera: Aphididae) in North America.

An aggressive, non-native haplotype (distinct genetic lineage within a species) of Phragmites australis is invading brackish and freshwater systems in the eastern United States, potentially displacing native haplotypes. We studied the differential susceptibility of native and non-native populations collected from sites throughout North America to the non-native aphid, Hyalopterus pruni. In a greenhouse study, we found significantly higher aphid populations on native haplotypes than on the non-native haplotype 2 mo after infestation. Aphid feeding caused chlorosis and death of native stems, and in some cases, killed whole native genets. The non-native plants remained relatively undamaged. In a field study, non-native plants had significantly lower aphid densities than native plants or remained aphid free. There was an interactive effect in which aphid populations increased on the native plants over the 1-mo study period but remained low on non-native plants over the same period. The susceptibility of native North American populations of P. australis to non-native aphid infestation may indirectly affect the ability of these native plants to compete with non-native plant populations, ultimately contributing to the decline of native haplotypes.

Induction of protective immunity against lethal anthrax challenge with a patch.

BACKGROUND: Transcutaneous immunization (TCI) is a needle-free technique that delivers antigens and adjuvants to potent epidermal immune cells. To address critical unmet needs in biodefense against anthrax, we have designed a novel vaccine delivery system using a dry adhesive patch that simplifies administration and improves tolerability of a subunit anthrax vaccine. METHODS: Mice and rabbits were vaccinated with recombinant protective antigen of Bacillus anthracis and the heat-labile toxin of Escherichia coli. Serologic changes, levels of toxin-neutralizing antibodies (TNAs), and pulmonary and nodal responses were monitored in the mice. A lethal aerosolized B. anthracis challenge model was used in A/J mice, to demonstrate efficacy. RESULTS: The level of systemic immunity and protection induced by TCI was comparable to that induced by intramuscular vaccination, and peak immunity could be achieved with only 2 doses. The addition of adjuvant in the patch induced superior TNA levels, compared with injected vaccination. CONCLUSIONS: Anthrax vaccine patches stimulated robust and functional immune responses that protected against lethal challenge. Demonstration of responses in the lung suggests that a mechanism exists for protection against challenge with aerosolized anthrax spores. A formulated, pressure-sensitive, dry adhesive patch, which is stable and can be manufactured in large scale, elicited comparable immunoglobulin G and TNA responses, suggesting that an anthrax vaccine patch is feasible and should advance into clinical evaluation.