A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs

While CRISPR interference (CRISPRi) systems have been widely implemented in pooled lentiviral screening, there has been limited use with synthetic guide RNAs for the complex phenotypic readouts enabled by experiments in arrayed format. Here we describe a novel deactivated Cas9 fusion protein, dCas9-SALL1-SDS3, which produces greater target gene repression than first or second generation CRISPRi systems when used with chemically modified synthetic single guide RNAs (sgRNAs), while exhibiting high target specificity. We show that dCas9-SALL1-SDS3 interacts with key members of the histone deacetylase and Swi-independent three complexes, which are the endogenous functional effectors of SALL1 and SDS3. Synthetic sgRNAs can also be used with in vitro-transcribed dCas9-SALL1-SDS3 mRNA for short-term delivery into primary cells, including human induced pluripotent stem cells and primary T cells. Finally, we used dCas9-SALL1-SDS3 for functional gene characterization of DNA damage host factors, orthogonally to small interfering RNA, demonstrating the ability of the system to be used in arrayed-format screening.

ErCas12a CRISPR-MAD7 for Model Generation in Human Cells, Mice, and Rats

MAD7 is an engineered class 2 type V-A CRISPR-Cas (Cas12a/Cpf1) system isolated from Eubacterium rectale. Analogous to Cas9, it is an RNA-guided nuclease with demonstrated gene editing activity in Escherichia coli and yeast cells. Here, we report that MAD7 is capable of generating indels and fluorescent gene tagging of endogenous genes in human HCT116 and U2OS cancer cell lines, respectively. In addition, MAD7 is highly proficient in generating indels, small DNA insertions (23 bases), and larger integrations ranging from 1 to 14 kb in size in mouse and rat embryos, resulting in live-born transgenic animals. Due to the different protospacer adjacent motif requirement, small-guide RNA, and highly efficient targeted gene disruption and insertions, MAD7 can expand the CRISPR toolbox for genome enginnering across different systems and model organisms.

Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity

The discovery that the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) acquired immune system can be utilized to create double-strand breaks (DSBs) in eukaryotic genomes has resulted in the ability to create genomic changes more easily than with other genome engineering techniques. While there is significant potential for the CRISPR-Cas9 system to advance basic and applied research, several unknowns remain, including the specificity of the RNA-directed DNA cleavage by the small targeting RNA, the CRISPR RNA (crRNA). Here we describe a novel synthetic RNA approach that allows for high-throughput gene editing experiments. This was used with a functional assay for protein disruption to perform high-throughput analysis of crRNA activity and specificity. We performed a comprehensive test of target cleavage using crRNAs that contain one and two nucleotide mismatches to the DNA target in the 20mer targeting region of the crRNA, allowing for the evaluation of hundreds of potential mismatched target sites without the requirement for the off-target sequences and their adjacent PAMs to be present in the genome. Our results demonstrate that while many crRNAs are functional, less than 5% of crRNAs with two mismatches to their target are effective in gene editing; this suggests an overall high level of functionality but low level of off-targeting.

Lung fibroblasts accelerate wound closure in human alveolar epithelial cells through hepatocyte growth factor/c-Met signaling

There are 190,600 cases of acute lung injury/acute respiratory distress syndrome (ALI/ARDS) each year in the United States, and the incidence and mortality of ALI/ARDS increase dramatically with age. Patients with ALI/ARDS have alveolar epithelial injury, which may be worsened by high-pressure mechanical ventilation. Alveolar type II (ATII) cells are the progenitor cells for the alveolar epithelium and are required to reestablish the alveolar epithelium during the recovery process from ALI/ARDS. Lung fibroblasts (FBs) migrate and proliferate early after lung injury and likely are an important source of growth factors for epithelial repair. However, how lung FBs affect epithelial wound healing in the human adult lung has not been investigated in detail. Hepatocyte growth factor (HGF) is known to be released mainly from FBs and to stimulate both migration and proliferation of primary rat ATII cells. HGF is also increased in lung tissue, bronchoalveolar lavage fluid, and serum in patients with ALI/ARDS. Therefore, we hypothesized that HGF secreted by FBs would enhance wound closure in alveolar epithelial cells (AECs). Wound closure was measured using a scratch wound-healing assay in primary human AEC monolayers and in a coculture system with FBs. We found that wound closure was accelerated by FBs mainly through HGF/c-Met signaling. HGF also restored impaired wound healing in AECs from the elderly subjects and after exposure to cyclic stretch. We conclude that HGF is the critical factor released from FBs to close wounds in human AEC monolayers and suggest that HGF is a potential strategy for hastening alveolar repair in patients with ALI/ARDS.

Endocytic transport and cytokinesis: from regulation of the cytoskeleton to midbody inheritance

Abscission is the last step of cytokinesis that leads to the physical separation of two daughter cells. An emerging picture is that abscission is a complex event that relies on changes in both lipid composition and cytoskeletal dynamics. These subcellular processes lead to the establishment of the abscission site and recruitment of the ESCRT-III protein complex to mediate the final separation event. It has become apparent that endocytic transport to the cleavage furrow during late cytokinesis mediates and coordinates lipid and cytoskeleton dynamics, thus playing a key role in abscission. Furthermore, new evidence suggests that endosomes may have additional roles in post-mitotic cellular events such as midbody inheritance and degradation. Here, we highlight recent findings regarding the function of these endosomes in the regulation of cell division.

ESCRT or endosomes?: Tales of the separation of two daughter cells

The final abscission event of cytokinesis is necessary for daughter cells to part ways from one another. Failure to properly divide has been indicated as a potential cancer initiating event due to an increase in cellular aneuploidy. However, the exact mechanisms of abscission have remained obscured by our inability to properly discern the spatiotemporal regulation of the various proteins and organelles required for cytokinesis. Three recent publications have taken slightly varied high resolution imaging approaches to visualize cytokinesis and abscission. As a result of this work, two differing, but not necessarily mutually exclusive, models have emerged. One model is ESCRT-dependent and the other, recycling endosome-dependent, each describing the steps leading up to the final abscission event. Presently these models describe late cytokinesis events leading to abscission in greater detail than previously known.

Endocytic membrane fusion and buckling-induced microtubule severing mediate cell abscission

Cytokinesis and abscission are complicated events that involve changes in membrane transport and cytoskeleton organization. We have used the combination of time-lapse microscopy and correlative high-resolution 3D tomography to analyze the regulation and spatio-temporal remodeling of endosomes and microtubules during abscission. We show that abscission is driven by the formation of a secondary ingression within the intracellular bridge connecting two daughter cells. The initiation and expansion of this secondary ingression requires recycling endosome fusion with the furrow plasma membrane and nested central spindle microtubule severing. These changes in endosome fusion and microtubule reorganization result in increased intracellular bridge plasma membrane dynamics and abscission. Finally, we show that central spindle microtubule reorganization is driven by localized microtubule buckling and breaking, rather than by spastin-dependent severing. Our results provide a new mechanism for mediation and regulation of the abscission step of cytokinesis.

Making the final cut - mechanisms mediating the abscission step of cytokinesis

Cytokinesis is the final stage of mitotic cell division that results in a physical separation of two daughter cells. Cytokinesis begins in the early stages of anaphase after the positioning of the cleavage plane and after the chromosomes segregate. This involves the recruitment and assembly of an actomyosin contractile ring, which constricts the plasma membrane and compacts midzone microtubules to form an electron-dense region, termed the midbody, located within an intracellular bridge. The resolution of this intracellular bridge, known as abscission, is the last step in cytokinesis that separates the two daughter cells. While much research has been done to delineate the mechanisms mediating actomyosin ring formation and contraction, the machinery that is responsible for abscission remains largely unclear. Recent work from several laboratories has demonstrated that dramatic changes occur in cytoskeleton and endosome dynamics, and are a prerequisite for abscission. However, the mechanistic details that regulate the final plasma membrane fusion during abscission are only beginning to emerge and are the subject of considerable controversy. Here we review recent studies within this field and discuss the proposed models of cell abscission.