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Earth, 2144. Jack is an anti-patent scientist turned drug pirate, traversing the world in a submarine as a pharmaceutical Robin Hood, fabricating cheap scrips for poor people who can't otherwise afford them. But her latest drug hack has left a trail of lethal overdoses as people become addicted to their work, doing repetitive tasks until they become unsafe or insane. Hot on her trail, an unlikely pair: Eliasz, a brooding military agent, and his robotic partner, Paladin. As they race to stop information about the sinister origins of Jack's drug from getting out, they begin to form an uncommonly close bond that neither of them fully understand. And underlying it all is one fundamental question: Is freedom possible in a culture where everything, even people, can be owned?

Fidanacogene elaparvovec, an adeno-associated virus (AAV) gene-therapy vector for hemophilia B containing a high-activity human factor IX variant (FIX-R338L/FIX-Padua), was associated with sustained factor IX activity in a phase 1-2a study. We conducted a phase 3 open-label study of fidanacogene elaparvovec at a dose of 5×10 vector genome copies per kilogram of body weight. Men 18 to 65 years of age with hemophilia B and a factor IX level of 2% or less were eligible for screening if they had received at least 6 months of therapy with prophylactic factor IX concentrate. The primary end point, tested for noninferiority, was the annualized bleeding rate (treated and untreated bleeding episodes) from week 12 to month 15 after treatment with fidanacogene elaparvovec as compared with the prophylaxis lead-in period. Superiority, additional efficacy end points, and safety were also assessed. Of 316 men who underwent screening for the lead-in study, 204 (64.6%) were not eligible; 188 (59.5%) of those were ineligible owing to the presence of anti-AAV neutralizing antibodies. Of the 45 participants who received fidanacogene elaparvovec, 44 completed at least 15 months of follow-up. The annualized rate of bleeding for all bleeding episodes decreased by 71%, from 4.42 (95% confidence interval [CI], 1.80 to 7.05) at baseline to 1.28 (95% CI, 0.57 to 1.98) after gene therapy, a treatment difference of -3.15 episodes (95% CI, -5.46 to -0.83; P = 0.008). This result shows the noninferiority and superiority of fidanacogene elaparvovec to prophylaxis. At 15 months, the mean factor IX activity was 26.9% (median, 22.9%; range, 1.9 to 119.0) by one-stage SynthASil assay. A total of 28 participants (62%) received glucocorticoids for increased aminotransferase levels or decreased factor IX levels (or both) starting between 11 and 123 days. No infusion-related serious adverse events, thrombotic events, development of factor IX inhibitors, or malignant conditions were observed. Fidanacogene elaparvovec was superior to prophylaxis for the treatment of participants with hemophilia B, leading to reduced bleeding and stable factor IX expression. (Funded by Pfizer; BENEGENE-2 ClinicalTrials.gov number, NCT03861273.).

Through drug exposure, a rare, transient transcriptional program characterized by high levels of expression of known resistance drivers can get ‘burned in’, leading to the selection of cells endowed with a transcriptional drug resistance and thus more chemoresistant cancers. Therapies that target signalling molecules that are mutated in cancers can often have substantial short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures 1 , 2 . Resistance can result from secondary mutations 3 , 4 , but in other cases there is no clear genetic cause, raising the possibility of non-genetic rare cell variability 5 , 6 , 7 , 8 , 9 , 10 , 11 . Here we show that human melanoma cells can display profound transcriptional variability at the single-cell level that predicts which cells will ultimately resist drug treatment. This variability involves infrequent, semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The addition of drug then induces epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming begins with a loss of SOX10-mediated differentiation followed by activation of new signalling pathways, partially mediated by the activity of the transcription factors JUN and/or AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics in single cells. We find that other cell types also exhibit sporadic expression of many of these same marker genes, suggesting the existence of a general program in which expression is displayed in rare subpopulations of cells.

Neovascular, or wet, age-related macular degeneration causes central vision loss and represents a major health problem in elderly people, and is currently treated with frequent intraocular injections of anti-VEGF protein. Gene therapy might enable long-term anti-VEGF therapy from a single treatment. We tested the safety of rAAV.sFLT-1 in treatment of wet age-related macular degeneration with a single subretinal injection. In this single-centre, phase 1, randomised controlled trial, we enrolled patients with wet age-related macular degeneration at the Lions Eye Institute and the Sir Charles Gairdner Hospital (Nedlands, WA, Australia). Eligible patients had to be aged 65 years or older, have age-related macular degeneration secondary to active subfoveal choroidal neovascularisation, with best corrected visual acuity (BCVA) of 3/60–6/24 and 6/60 or better in the other eye. Patients were randomly assigned (3:1) to receive either 1 × 1010 vector genomes (vg; low-dose rAAV.sFLT-1 group) or 1 × 1011 vg (high-dose rAAV.sFLT-1 group), or no gene-therapy treatment (control group). Randomisation was done by sequential group assignment. All patients and investigators were unmasked. Staff doing the assessments were masked to the study group at study visits. All patients received ranibizumab at baseline and week 4, and rescue treatment during follow-up based on prespecified criteria including BCVA measured on the Early Treatment Diabetic Retinopathy Study (EDTRS) scale, optical coherence tomography, and fluorescein angiography. The primary endpoint was ocular and systemic safety. This trial is registered with ClinicalTrials.gov, number NCT01494805. From Dec 16, 2011, to April 5, 2012, we enrolled nine patients of whom eight were randomly assigned to receive either intervention (three patients in the low-dose rAAV.sFLT-1 group and three patients in the high-dose rAAV.sFLT-1 group) or no treatment (two patients in the control group). Subretinal injection of rAAV.sFLT-1 was highly reproducible. No drug-related adverse events were noted; procedure-related adverse events (subconjunctival or subretinal haemorrhage and mild cell debris in the anterior vitreous) were generally mild and self-resolving. There was no evidence of chorioretinal atrophy. Clinical laboratory assessments generally remained unchanged from baseline. Four (67%) of six patients in the treatment group required zero rescue injections, and the other two (33%) required only one rescue injection each. rAAV.sFLT-1 was safe and well tolerated. These results support ocular gene therapy as a potential long-term treatment option for wet age-related macular degeneration. National Health and Medical Research Council of Australia, Richard Pearce Bequest, Lions Save Sight Foundation, Brian King Fellowship, and Avalanche Biotechnologies, Inc.

Studies of the singlet oxygen (¹O₂)-overproducing flu and chlorina1 (ch1) mutants of Arabidopsis (Arabidopsis thaliana) have shown that ¹O₂-induced changes in gene expression can lead to either programmed cell death (PCD) or acclimation. A transcriptomic analysis of the ch1 mutant has allowed the identification of genes whose expression is specifically affected by each phenomenon. One such gene is OXIDATIVE SIGNAL INDUCIBLE1 (OXI1) encoding an AGC kinase that was noticeably induced by excess light energy and ¹O₂ stress conditions leading to cell death. Photo-induced oxidative damage and cell death were drastically reduced in the OXI1 null mutant (oxi1) and in the double mutant ch1*oxi1 compared with the wild type and the ch1 single mutant, respectively. This occurred without any changes in the production rate of ¹O₂ but was cancelled by exogenous applications of the phytohormone jasmonate. OXI1-mediated ¹O₂ signaling appeared to operate through a different pathway from the previously characterized OXI1-dependent response to pathogens and H₂O₂ and was found to be independent of the EXECUTER proteins. In high-light-stressed plants, the oxi1 mutation was associated with reduced jasmonate levels and with the up-regulation of genes encoding negative regulators of jasmonate signaling and PCD. Our results show that OXI1 is a new regulator of ¹O₂-induced PCD, likely acting upstream of jasmonate.

As a natural flavonol, fisetin has significant inhibitory effects on many cancers. Although fisetin can inhibit kidney cancer, its effects on kidney renal stem cells (HuRCSCs) remain unknown. Our study found that renal cancer tissues and CD44+/CD105+ HuRCSCs both show high TET1 protein expression. Both in vivo and in vitro experiments showed that fisetin can effectively inhibit HuRCSC cell division and proliferation, invasion, in vivo tumourigenesis and angiogenesis. Our findings showed that fisetin can significantly decrease TET1 expression levels in HuRCSCs and overall 5hmC levels in the genomes of these cells. At the same time, ChIP‐PCR results showed that fisetin can effectively inhibit 5hmC modification levels at the CpG islands in cyclin Y (CCNY) and CDK16 and reduce their transcription and activity. Thus, we conclude that fisetin inhibits the epigenetic mechanism in renal cancer stem cells, that is, fisetin inhibits TET1 expression and reduces 5hmC modification in specific loci in the promoters of CCNY/CDK16 in HuRSCs. This in turn inhibits transcription of these genes, causing cell cycle arrest and ultimately inhibiting renal cancer stem cell activity.

Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high‐quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well‐defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation. Synopsis A systematic analysis of how genetic variation in a yeast cross affects the transcriptome, the proteome and the phosphoproteome reveals multi‐layered changes in regulatory networks that ultimately have an impact on hundreds of cellular traits. Genetic effects on transcripts are transmitted to protein abundance changes for most genes. Phosphorylation states are crucial for unraveling genetic effects on signaling networks and cell physiology. Phosphorylation QTLs tend to co‐occur with missense variants. Overall, the study indicates complex post‐transcriptional QTL effects on signaling networks, for example in the mating pheromone pathway. Graphical Abstract A systematic analysis of how genetic variation in a yeast cross affects the transcriptome, the proteome and the phosphoproteome reveals multi‐layered changes in regulatory networks that ultimately have an impact on hundreds of cellular traits.

A multicenter clinical study demonstrated the presence of a loss-of-function HSP110 mutation in about 15% of colorectal cancers, which resulted from an alternative splicing and was produced at the detriment of wild-type HSP110. Patients expressing low levels of wild-type HSP110 had excellent outcomes (i.e. response to an oxaliplatin-based chemotherapy). Here, we show in vitro, in vivo, and in patients' biopsies that HSP110 co-localizes with DNA damage (γ-H2AX). In colorectal cancer cells, HSP110 translocates into the nucleus upon treatment with genotoxic chemotherapy such as oxaliplatin. Furthermore, we show that HSP110 interacts with the Ku70/Ku80 heterodimer, an essential element of the non-homologous end joining (NHEJ) repair machinery. We also demonstrate by evaluating the resolved 53BP1 foci that depletion in HSP110 impairs repair steps of the NHEJ pathway, which is associated with an increase in DNA double-strand breaks and in the cells' sensitivity to oxaliplatin. HSP110-depleted cells sensitization to oxaliplatin-induced DNA damage is abolished upon re-expression of HSP110. Confirming a role for HSP110 in DNA non-homologous repair, SCR7 and NU7026, two inhibitors of the NHEJ pathway, circumvents HSP110-induced resistance to chemotherapy. In conclusion, HSP110 through its interaction with the Ku70/80 heterodimer may participate in DNA repair, thereby inducing a protection against genotoxic therapy.

Intercropping is both a well-established and yet novel agricultural practice, depending on one’s perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., “trait-based” breeding) or quantitative genetics-driven (i.e., “product-based” breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.

The cytidine analogues azacytidine and 5-aza-2’-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect. Chronic myelomonocytic leukaemia is treated with agents that modify DNA methylation but whether they have direct cytotoxic effects is unclear. Here, the authors show that cells from treated patients show marked methylation changes without altered somatic mutation burden, suggesting that cytotoxicity is not a major factor in therapeutic efficacy.