Precision RNAi using synthetic shRNAmir target sites.

Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

Impact of Changing Regulations and the Dynamic Nature of European Risk Management Plans for Human Medicines on the Lifecycle of Safety Concerns.

INTRODUCTION: The European Risk Management Plan (EU-RMP) is a proactive planning tool for identification, characterisation and management of important risks and missing information throughout the lifecycle of a medicinal product. Over the past 15 years the EU-RMP has been a part of the pharmacovigilance practice in Europe, but there are no published studies assessing impact of the growing experience and evolving regulatory framework on the content and focus of the EU-RMP. OBJECTIVES: The objectives were to study the real-world impact of evolving pharmacovigilance guidelines on the proactive lifecycle management of important risks and missing information through EU-RMPs, and to further explore the impact of different resources on the management of the benefit-risk profile. METHODS: A retrospective study based on the review of 64 EU-RMPs dated between 01 January 2006 and 01 October 2020 for seven human medicinal products for which Boehringer Ingelheim holds the Marketing Authorisation in the European Union. Data on the timing and rational behind changes (i.e., inclusion, reclassification, removal) to the safety concerns (Important Identified Risks, Important Potential Risks, Missing Information) and associated additional Pharmacovigilance activities and/or Risk Minimisation measures were collected and assessed. RESULTS: The analysed EU-RMPs included a total of 197 safety concerns, 129 of which were removed and 19 were reclassified during the observation period. The implementation of the Guidelines on Good Pharmacovigilance Practices Module V in 2012 and Revision 2 in 2017 resulted in a noticeable decrease in the number of safety concerns. Clinical trial, non-clinical and routine post-marketing data were common sources that influenced the safety concern dynamics, and results from dedicated post-authorisation studies lead to the removal of 21 important risks and missing information. Many safety concerns were related to pharmacological class effect (n = 55) and target population characteristics (n = 37). CONCLUSIONS: This study demonstrated that the growing knowledge regarding benefit-risk of approved products and the introduction of new or revised regulatory guidelines influenced the EU-RMP lifecycle of safety concerns, and moreover, the results emphasise that exchange of knowledge about the pharmacological class and target population between stakeholders are important for keeping an up-to-date understanding of a medicinal product's safety profile. The aim of improving the efficiency of risk management has leveraged the accumulation of knowledge leading to revision of regulatory guidelines and increasingly, proactive Risk Management Plans focused on safety concerns that are important for patients and public health.

APC/CCdh1 is required for the termination of chromosomal passenger complex activity upon mitotic exit.

During mitosis, the chromosomal passenger complex (CPC) ensures the faithful transmission of the genome. The CPC is composed of the enzymatic component Aurora B (AURKB) and the three regulatory and targeting components borealin, INCENP, and survivin (also known as BIRC5). Although the CPC is known to be involved in diverse mitotic events, it is still unclear how CPC function terminates after mitosis. Here we show that borealin is ubiquitylated by the anaphase promoting complex/cyclosome (APC/C) and its cofactor Cdh1 (also known as FZR1) and is subsequently degraded in G1 phase. Cdh1 binds to regions within the N terminus of borealin that act as a non-canonical degron. Aurora B has also been shown previously to be degraded by the APC/CCdh1 from late mitosis to G1. Indeed, Cdh1 depletion sustains an Aurora B activity with stable levels of borealin and Aurora B throughout the cell cycle, and causes reduced efficiency of DNA replication after release from serum starvation. Notably, inhibition of Aurora B kinase activity improves the efficiency of DNA replication in Cdh1-depleted cells. We thus propose that APC/CCdh1 terminates CPC activity upon mitotic exit and thereby contributes to proper control of DNA replication.

Chromokinesin KIF4A teams up with stathmin 1 to regulate abscission in a SUMO-dependent manner.

Cell division ends when two daughter cells physically separate via abscission, the cleavage of the intercellular bridge. It is not clear how the anti-parallel microtubule bundles bridging daughter cells are severed. Here, we present a novel abscission mechanism. We identified chromokinesin KIF4A, which is adjacent to the midbody during cytokinesis, as being required for efficient abscission. KIF4A is regulated by post-translational modifications. We evaluated modification of KIF4A by the ubiquitin-like protein SUMO. We mapped lysine 460 in KIF4A as the SUMO acceptor site and employed CRISPR-Cas9-mediated genome editing to block SUMO conjugation of endogenous KIF4A. Failure to SUMOylate this site in KIF4A delayed cytokinesis. SUMOylation of KIF4A enhanced the affinity for the microtubule destabilizer stathmin 1 (STMN1). We here present a new level of abscission regulation through the dynamic interactions between KIF4A and STMN1 as controlled by SUMO modification of KIF4A.

Borealin-nucleosome interaction secures chromosome association of the chromosomal passenger complex.

Chromosome association of the chromosomal passenger complex (CPC; consisting of Borealin, Survivin, INCENP, and the Aurora B kinase) is essential to achieve error-free chromosome segregation during cell division. Hence, understanding the mechanisms driving the chromosome association of the CPC is of paramount importance. Here using a multifaceted approach, we show that the CPC binds nucleosomes through a multivalent interaction predominantly involving Borealin. Strikingly, Survivin, previously suggested to target the CPC to centromeres, failed to bind nucleosomes on its own and requires Borealin and INCENP for its binding. Disrupting Borealin-nucleosome interactions excluded the CPC from chromosomes and caused chromosome congression defects. We also show that Borealin-mediated chromosome association of the CPC is critical for Haspin- and Bub1-mediated centromere enrichment of the CPC and works upstream of the latter. Our work thus establishes Borealin as a master regulator determining the chromosome association and function of the CPC.

Two Interlinked Bistable Switches Govern Mitotic Control in Mammalian Cells.

Distinct protein phosphorylation levels in interphase and M phase require tight regulation of Cdk1 activity [1, 2]. A bistable switch, based on positive feedback in the Cdk1 activation loop, has been proposed to generate different thresholds for transitions between these cell-cycle states [3-5]. Recently, the activity of the major Cdk1-counteracting phosphatase, PP2A:B55, has also been found to be bistable due to Greatwall kinase-dependent regulation [6]. However, the interplay of the regulation of Cdk1 and PP2A:B55 in vivo remains unexplored. Here, we combine quantitative cell biology assays with mathematical modeling to explore the interplay of mitotic kinase activation and phosphatase inactivation in human cells. By measuring mitotic entry and exit thresholds using ATP-analog-sensitive Cdk1 mutants, we find evidence that the mitotic switch displays hysteresis and bistability, responding differentially to Cdk1 inhibition in the mitotic and interphase states. Cdk1 activation by Wee1/Cdc25 feedback loops and PP2A:B55 inactivation by Greatwall independently contributes to this hysteretic switch system. However, elimination of both Cdk1 and PP2A:B55 inactivation fully abrogates bistability, suggesting that hysteresis is an emergent property of mutual inhibition between the Cdk1 and PP2A:B55 feedback loops. Our model of the two interlinked feedback systems predicts an intermediate but hidden steady state between interphase and M phase. This could be verified experimentally by Cdk1 inhibition during mitotic entry, supporting the predictive value of our model. Furthermore, we demonstrate that dual inhibition of Wee1 and Gwl kinases causes loss of cell-cycle memory and synthetic lethality, which could be further exploited therapeutically.

HP1α targets the chromosomal passenger complex for activation at heterochromatin before mitotic entry.

The chromosomal passenger complex (CPC) is directed to centromeres during mitosis via binding to H3T3ph and Sgo1. Whether and how heterochromatin protein 1α (HP1α) influences CPC localisation and function during mitotic entry is less clear. Here, we alter HP1α dynamics by fusing it to a CENP-B DNA-binding domain. Tethered HP1 strongly recruits the CPC, destabilising kinetochore-microtubule interactions and activating the spindle assembly checkpoint. During mitotic exit, the tethered HP1 traps active CPC at centromeres. These HP1-CPC clusters remain catalytically active throughout the subsequent cell cycle. We also detect interactions between endogenous HP1 and the CPC during G2 HP1α and HP1γ cooperate to recruit the CPC to active foci in a CDK1-independent process. Live cell tracking with Fab fragments reveals that H3S10ph appears well before H3T3 is phosphorylated by Haspin kinase. Our results suggest that HP1 may concentrate and activate the CPC at centromeric heterochromatin in G2 before Aurora B-mediated phosphorylation of H3S10 releases HP1 from chromatin and allows pathways dependent on H3T3ph and Sgo1 to redirect the CPC to mitotic centromeres.

Quantifying drylands' drought resistance and recovery: the importance of drought intensity, dominant life history and grazing regime.

Projected global change will increase the level of land-use and environmental stressors such as drought and grazing, particularly in drylands. Still, combined effects of drought and grazing on plant production are poorly understood, thus hampering adequate projections and development of mitigation strategies. We used a large, cross-continental database consisting of 174 long-term datasets from >30 dryland regions to quantify ecosystem responses to drought and grazing with the ultimate goal to increase functional understanding in these responses. Two key aspects of ecosystem stability, resistance to and recovery after a drought, were evaluated based on standardized and normalized aboveground net primary production (ANPP) data. Drought intensity was quantified using the standardized precipitation index. We tested effects of drought intensity, grazing regime (grazed, ungrazed), biome (grassland, shrubland, savanna) or dominant life history (annual, perennial) of the herbaceous layer to assess the relative importance of these factors for ecosystem stability, and to identify predictable relationships between drought intensity and ecosystem resistance and recovery. We found that both components of ecosystem stability were better explained by dominant herbaceous life history than by biome. Increasing drought intensity (quasi-) linearly reduced ecosystem resistance. Even though annual and perennial systems showed the same response rate to increasing drought intensity, they differed in their general magnitude of resistance, with annual systems being ca. 27% less resistant. In contrast, systems with an herbaceous layer dominated by annuals had substantially higher postdrought recovery, particularly when grazed. Combined effects of drought and grazing were not merely additive but modulated by dominant life history of the herbaceous layer. To the best of our knowledge, our study established the first predictive, cross-continental model between drought intensity and drought-related relative losses in ANPP, and suggests that systems with an herbaceous layer dominated by annuals are more prone to ecosystem degradation under future global change regimes.

Are there consistent grazing indicators in Drylands? Testing plant functional types of various complexity in South Africa's Grassland and Savanna Biomes.

Despite our growing knowledge on plants' functional responses to grazing, there is no consensus if an optimum level of functional aggregation exists for detecting grazing effects in drylands. With a comparative approach we searched for plant functional types (PFTs) with a consistent response to grazing across two areas differing in climatic aridity, situated in South Africa's grassland and savanna biomes. We aggregated herbaceous species into PFTs, using hierarchical combinations of traits (from single- to three-trait PFTs). Traits relate to life history, growth form and leaf width. We first confirmed that soil and grazing gradients were largely independent from each other, and then searched in each biome for PFTs with a sensitive response to grazing, avoiding confounding with soil conditions. We found no response consistency, but biome-specific optimum aggregation levels. Three-trait PFTs (e.g. broad-leaved perennial grasses) and two-trait PFTs (e.g. perennial grasses) performed best as indicators of grazing effects in the semi-arid grassland and in the arid savanna biome, respectively. Some PFTs increased with grazing pressure in the grassland, but decreased in the savanna. We applied biome-specific grazing indicators to evaluate if differences in grazing management related to land tenure (communal versus freehold) had effects on vegetation. Tenure effects were small, which we mainly attributed to large variability in grazing pressure across farms. We conclude that the striking lack of generalizable PFT responses to grazing is due to a convergence of aridity and grazing effects, and unlikely to be overcome by more refined classification approaches. Hence, PFTs with an opposite response to grazing in the two biomes rather have a unimodal response along a gradient of additive forces of aridity and grazing. The study advocates for hierarchical trait combinations to identify localized indicator sets for grazing effects. Its methodological approach may also be useful for identifying ecological indicators in other ecosystems.

different Roles for the axin interactions with the SAMP versus the second twenty amino acid repeat of adenomatous polyposis coli.

Wnt signalling is prevented by the proteosomal degradation of ß-catenin, which occurs in a destruction complex containing adenomatous polyposis coli (APC), APC-like (APCL), Axin and Axin2. Truncating mutations of the APC gene result in the constitutive stabilisation of ß-catenin and the initiation of colon cancer, although tumour cells tolerate the expression of wild-type APCL. Using the colocalisation of overexpressed Axin, APC and APCL constructs as a readout of interaction, we found that Axin interacted with the second twenty amino acid repeat (20R2) of APC and APCL. This interaction involved a domain adjacent to the C-terminal DIX domain of Axin. We identified serine residues within the 20R2 of APCL that were involved in Axin colocalisation, the phosphorylation of truncated APCL and the down-regulation of ß-catenin. Our results indicated that Axin, but not Axin2, displaced APC, but not APCL, from the cytoskeleton and stimulated its incorporation into bright cytoplasmic dots that others have recognised as ß-catenin destruction complexes. The SAMP repeats in APC interact with the N-terminal RGS domain of Axin. Our data showed that a short domain containing the first SAMP repeat in truncated APC was required to stimulate Axin oligomerisation. This was independent of Axin colocalisation with 20R2. Our data also suggested that the RGS domain exerted an internal inhibitory constraint on Axin oligomerisation. Considering our data and those from others, we discuss a working model whereby ß-catenin phosphorylation involves Axin and the 20R2 of APC or APCL and further processing of phospho-ß-catenin occurs upon the oligomerisation of Axin that is induced by binding the SAMP repeats in APC.

Adenomatous polyposis coli (APC) membrane recruitment 3, a member of the APC membrane recruitment family of APC-binding proteins, is a positive regulator of Wnt-ß-catenin signalling.

The adenomatous polyposis coli (APC) membrane recruitment (Amer) family proteins Amer1/Wilms tumour gene on the X chromosome and Amer2 are binding partners of the APC tumour suppressor protein, and act as negative regulators in the Wnt signalling cascade. So far, nothing has been known about the third member of the family, Amer3. Here we show that Amer3 binds to the armadillo repeat domain of APC, similarly to Amer1 and Amer2. Amer3 also binds to the Wnt pathway regulator conductin/axin2. Furthermore, we identified Amer1 as binding partner of Amer3. Whereas Amer1 and Amer2 are linked to the plasma membrane by an N-terminal membrane localization domain, Amer3 lacks this domain. Amer3 localizes to the cytoplasm and nucleus of epithelial cells, and this is dependent on specific nuclear import and export sequences. Functionally, exogenous Amer3 enhances the expression of a ß-catenin/T-cell factor-dependent reporter gene, and knockdown of endogenous Amer3 reduces Wnt target gene expression in colorectal cancer cells. Thus, Amer3 acts as an activator of Wnt signalling, in contrast to Amer1 and Amer2, which are inhibitors, suggesting a nonredundant role of Amer proteins in the regulation of this pathway. Our data, together with those of previous studies, provide a comprehensive picture of similarities and differences within the Amer protein family.

Cytokeratin 8-MHC class I interactions: a potential novel immune escape phenotype by a lymph node metastatic carcinoma cell line.

Defective human leukocyte antigen (HLA) class I expression in malignant cells facilitates their escape from destruction by CD8(+) cytotoxic T lymphocytes. In this study, a post-translational mechanism of HLA class I abnormality that does not involve defects in the HLA subunits and antigen processing machinery components was identified and characterized. The marked HLA class I downregulation phenotype of a metastatic carcinoma cell line can be readily reversed by trypsin, suggesting a masking effect by serine protease-sensitive HLA class I-interacting factors. Co-immunoprecipitation, combined with LC-tandem mass spectrometry and immunoblotting identified these factors as cytokeratin (CK) 8 and its heterodimeric partners CK18 and CK19. Ectopic CK8/18 or CK8/19 expression in HEK293 cells resulted in surface CK8 expression with an HLA class I downregulation phenotype, while redirecting CK8/18 and CK8/19 to the endoplasmic reticulum (ER) had no such effect. This observation and the failure to constrain CK8/18 and CK8/19 membrane trafficking by an ER-Golgi transport inhibitor suggested an ER-independent route for CK8 access to HLA class I molecules. Monoclonal antibody mapping revealed a potential CK8 blockade of HLA class I-CD8 and -TCR contacts. These findings, along with the emerging role of cell surface CK8 in cancer metastasis, may imply a dual strategy for tumor cell survival in the host.

Functional comparison of human adenomatous polyposis coli (APC) and APC-like in targeting beta-catenin for degradation.

Truncating mutations affect the adenomatous polyposis coli (APC) gene in most cases of colon cancer, resulting in the stabilization of ß-catenin and uncontrolled cell proliferation. We show here that colon cancer cell lines express also the paralog APC-like (APCL or APC2). RNA interference revealed that it controls the level and/or the activity of ß-catenin, but it is less efficient and binds less well to ß-catenin than APC, thereby providing one explanation as to why the gene is not mutated in colon cancer. A further comparison indicates that APCL down-regulates the ß-catenin level despite the lack of the 15R region known to be important in APC. To understand this discrepancy, we performed immunoprecipitation experiments that revealed that phosphorylated ß-catenin displays a preference for binding to the 15 amino acid repeats (15R) rather than the first 20 amino acid repeat of APC. This suggests that the 15R region constitutes a gate connecting the steps of ß-catenin phosphorylation and subsequent ubiquitination/degradation. Using RNA interference and domain swapping experiments, we show that APCL benefits from the 15R of truncated APC to target ß-catenin for degradation, in a process likely involving heterodimerization of the two partners. Our data suggest that the functional complementation of APCL by APC constitutes a substantial facet of tumour development, because the truncating mutations of APC in colorectal tumours from familial adenomatous polyposis (FAP) patients are almost always selected for the retention of at least one 15R.