Generation of an arrayed CRISPR-Cas9 library targeting epigenetic regulators: from high-content screens to in vivo assays

The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Screens employing genome-scale pooled small guide RNA (sgRNA) libraries are demanding, particularly when complex assays are used. Furthermore, pooled libraries are not suitable for microscopy-based high-content screens or for systematic interrogation of protein function. To overcome these limitations and exploit CRISPR-based technologies to comprehensively investigate epigenetic mechanisms, we have generated a focused sgRNA library targeting 450 epigenetic regulators with multiple sgRNAs in human cells. The lentiviral library is available both in an arrayed and pooled format and allows temporally-controlled induction of gene knock-out. Characterization of the library showed high editing activity of most sgRNAs and efficient knock-out at the protein level in polyclonal populations. The sgRNA library can be used for both selection and high-content screens, as well as for targeted investigation of selected proteins without requiring isolation of knock-out clones. Using a variety of functional assays we show that the library is suitable for both in vitro and in vivo applications, representing a unique resource to study epigenetic mechanisms in physiological and pathological conditions

Even odder after twenty-three years : the superconducting order parameter puzzle of Sr2RuO4

Funding: Max Planck Society.In this short review, we aim to provide a topical update on the status of efforts to understand the superconductivity of Sr2RuO4. We concentrate on the quest to identify a superconducting order parameter symmetry that is compatible with all the major pieces of experimental knowledge of the material, and highlight some major discrepancies that have become even clearer in recent years. As the pun in the title suggests, we have tried to start the discussion from scratch, making no assumptions even about fundamental issues such as the parity of the superconducting state. We conclude that no consensus is currently achievable in Sr2RuO4, and that the reasons for this go to the heart of how well some of the key probes of unconventional superconductivity are really understood. This is therefore a puzzle that merits continued in-depth study.Publisher PDFPeer reviewe

Epigenetics and Cancer Stem Cells: Unleashing, Hijacking, and Restricting Cellular Plasticity

Epigenetic regulators are one of the most commonly mutated classes of genes in cancer. During cancer initiation, mutated epigenetic regulators lead to oncogenic cellular reprogramming and promote the acquisition of uncontrolled self-renewal. The emergence of CSCs requires elaborate reorganization of the epigenome. During cancer growth, epigenetic mechanisms integrate the effect of cell-intrinsic (i.e., subclonal mutations) and cell-extrinsic (i.e., signaling from the microenvironment) changes and establish intratumoral heterogeneity, either promoting or inhibiting the CSC state. ‘Loose’ epigenetic constraints in cancer cells enhance cellular plasticity and allow reversible transitions between different phenotypic states. Enhanced cellular plasticity favors cancer cell adaptability and resistance to therapy. Modulation of epigenetic processes allows targeting of the most downstream determinants of the CSC state

Hydrodynamic electron flow and Hall viscosity

The authors acknowledge support from the Emergent Phenomena in Quantum Systems initiative of the Gordon and Betty Moore Foundation (T. S.) and NSF DMR-1507141 and a Simons Investigatorship (J. E. M.). We also acknowledge the support of the Max Planck Society and the UK Engineering and Physical Sciences Research Council under Grant No. EP/I032487/1.In metallic samples of small enough size and sufficiently strong momentum-conserving scattering, the viscosity of the electron gas can become the dominant process governing transport. In this regime, momentum is a long-lived quantity whose evolution is described by an emergent hydrodynamical theory. Furthermore, breaking time-reversal symmetry leads to the appearance of an odd component to the viscosity called the Hall viscosity, which has attracted considerable attention recently due to its quantized nature in gapped systems but still eludes experimental confirmation. Based on microscopic calculations, we discuss how to measure the effects of both the even and odd components of the viscosity using hydrodynamic electronic transport in mesoscopic samples under applied magnetic fields.PostprintPeer reviewe

Importance of molecular cell biology investigations in human medicine in the story of the Hutchinson-Gilford progeria syndrome

Ranged among laminopathies, Hutchinson–Gilford progeria syndrome is a syndrome that involves premature aging, leading usually to death at the age between 10 to 14 years predominatly due to a myocardial infarction or a stroke. In the lecture I shall overview the importance of molecular cell biology investigations that led to the discovery of the basic mechanism standing behind this rare syndrome. The genetic basis in most cases is a mutation at the nucleotide position 1824 of the lamin A gene. At this position, cytosine is substituted for thymine so that a cryptic splice site within the precursor mRNA for lamin A is generated. This results in a production of abnormal lamin A, termed progerin, its presence in cells having a deleterious dominant effect. Depending on the cell type and tissue, progerin induces a pleiotropy of defects that vary in different tissues. The present endeavour how to challenge this terrible disease will be also mentioned

Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia.

The evolution of established cancers is driven by selection of cells with enhanced fitness. Subclonal mutations in numerous epigenetic regulator genes are common across cancer types, yet their functional impact has been unclear. Here, we show that disruption of the epigenetic regulatory network increases the tolerance of cancer cells to unfavorable environments experienced within growing tumors by promoting the emergence of stress-resistant subpopulations. Disruption of epigenetic control does not promote selection of genetically defined subclones or favor a phenotypic switch in response to environmental changes. Instead, it prevents cells from mounting an efficient stress response via modulation of global transcriptional activity. This "transcriptional numbness" lowers the probability of cell death at early stages, increasing the chance of long-term adaptation at the population level. Our findings provide a mechanistic explanation for the widespread selection of subclonal epigenetic-related mutations in cancer and uncover phenotypic inertia as a cellular trait that drives subclone expansion

Strong peak in Tc of Sr2RuO4 under uniaxial pressure

Sr2RuO4 is an unconventional superconductor that has attracted widespread study because of its high purity and the possibility that its superconducting order parameter has odd parity. We study the dependence of its superconductivity on anisotropic strain. Applying uniaxial pressures of up to ~1 gigapascals along a 〈100〉 direction (a axis) of the crystal lattice results in the transition temperature (Tc) increasing from 1.5 kelvin in the unstrained material to 3.4 kelvin at compression by ≈0.6%, and then falling steeply. Calculations give evidence that the observed maximum Tc occurs at or near a Lifshitz transition when the Fermi level passes through a Van Hove singularity, and open the possibility that the highly strained, Tc = 3.4 K Sr2RuO4 has an even-parity, rather than an odd-parity, order parameter.PostprintPeer reviewe

Target-Specific Precision of CRISPR-Mediated Genome Editing

The CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict the editing outcome at specific sites is limited. Here, we examined indel profiles at over 1,000 genomic sites in human cells and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing (i.e., recurrence of a specific indel) varies considerably among sites, with some targets showing one highly preferred indel and others displaying numerous infrequent indels. Editing precision correlates with editing efficiency and a preference for single-nucleotide homologous insertions. Precise targets and editing outcome can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the protospacer adjacent motif (PAM). Indel profiles are robust, but they can be influenced by chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end joining that can provide insights into DNA repair mechanisms

The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

Tumors comprise functionally diverse subpopulations of cells with distinct proliferative potential. Here, we show that dynamic epigenetic states defined by the linker histone H1.0 determine which cells within a tumor can sustain the long-term cancer growth. Numerous cancer types exhibit high inter- and intratumor heterogeneity of H1.0, with H1.0 levels correlating with tumor differentiation status, patient survival, and, at the single-cell level, cancer stem cell markers. Silencing of H1.0 promotes maintenance of self-renewing cells by inducing derepression of megabase-sized gene domains harboring downstream effectors of oncogenic pathways. Self-renewing epigenetic states are not stable, and reexpression of H1.0 in subsets of tumor cells establishes transcriptional programs that restrict cancer cells’ long-term proliferative potential and drive their differentiation. Our results uncover epigenetic determinants of tumor-maintaining cells

Directional ballistic transport in the two-dimensional metal PdCoO2

In an idealized infinite crystal, the material properties are constrained by the symmetries of its unit cell. Naturally, the point-group symmetry is broken by the sample shape of any finite crystal, yet this is commonly unobservable in macroscopic metals. To sense the shape-induced symmetry lowering in such metals, long-lived bulk states originating from anisotropic Fermi surfaces are needed. Here we show how strongly facetted Fermi surfaces and long quasiparticle mean free paths present in microstructures of PdCoO2 yield an in-plane resistivity anisotropy that is forbidden by symmetry on an infinite hexagonal lattice. Bar shaped transport devices narrower than the mean free path are carved from single crystals using focused ion beam (FIB) milling, such that the ballistic charge carriers at low temperatures frequently collide with both sidewalls defining a channel. Two symmetry-forbidden transport signatures appear: the in-plane resistivity anisotropy exceeds a factor of 2, and transverse voltages appear in zero magnetic field. We robustly identify the channel direction as the source of symmetry breaking via ballistic Monte- Carlo simulations and numerical solution of the Boltzmann equation