Optimization of Genomewide CRISPR Screens Using AsCas12a and Multi-Guide Arrays

Genomewide loss-of-function (LOF) screening using clustered regularly interspaced short palindromic repeats (CRISPR) has facilitated the discovery of novel gene functions across diverse physiological and pathophysiological systems. A challenge with conventional genomewide CRISPR-Cas9 libraries is the unwieldy size (60,000-120,000 constructs), which is resource intensive and prohibitive in some experimental contexts. One solution to streamlining CRISPR screening is by multiplexing two or more guides per gene on a single construct, which enables functional redundancy to compensate for suboptimal gene knockout by individual guides. In this regard, AsCas12a (Cpf1) and its derivatives, for example, enhanced AsCas12a (enAsCas12a), have enabled multiplexed guide arrays to be specifically and efficiently processed for genome editing. Prior studies have established that multiplexed CRISPR-Cas12a libraries perform comparably to the larger equivalent CRISPR-Cas9 libraries, yet the most efficient CRISPR-Cas12a library design remains unresolved. In this study, we demonstrate that CRISPR-Cas12a genomewide LOF screening performed optimally with three guides arrayed per gene construct and could be adapted to robotic cell culture without noticeable differences in screen performance. Thus, the conclusions from this study provide novel insight to streamlining genomewide LOF screening using CRISPR-Cas12a and robotic cell culture.

Detecting personal microbiota signatures at artificial crime scenes

When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real residences. We demonstrate that humans (n = 30) leave behind microbial signatures that can be used to track interaction with various surfaces within a building, but the likelihood of accurately detecting the specific burglar for a given home was between 20-25%. Also, the human microbiome contains rare microbial taxa that can be combined to create a unique microbial profile, which when compared to 600 other individuals can improve our ability to link an individual 'burglar' to a residence. In total, 5512 discriminating, non-singleton unique exact sequence variants (uESVs) were identified as unique to an individual, with a minimum of 1 and a maximum of 568, suggesting some people maintain a greater degree of unique taxa compared to our population of 600. Approximate 60-77% of the unique exact sequence variants originated from the hands of participants, and these microbial discriminators spanned 36 phyla but were dominated by the Proteobacteria (34%). A fitted regression generated to determine whether an intruder's uESVs found on door handles in an office decayed over time in the presence or absence of office workers, found no significant shift in proportion of uESVs over time irrespective of the presence of office workers. While it was possible to detect the correct burglars' microbiota as having contributed to the invaded space, the predictions were very weak in comparison to accepted forensic standards. This suggests that at this time 16S rRNA amplicon sequencing of the built environment microbiota cannot be used as a reliable trace evidence standard for criminal investigations.

An alternative system for cerebrovascular reconstructions: non-penetrating arcuate-legged clips

Non-penetrating, arcuate-legged titanium clips (VCS) have been utilized successfully over the past five years for a variety of cerebrovascular reconstructions. These applications, including both micro and macrovascular reconstructions, their clinical outcomes and technical considerations are described. Applications include patch angioplasty of cervical carotid endarterectomies, superficial temporal to middle cerebral artery 'bypass' procedures, Takayasu's arteritis and cavernous carotid reconstructions. The non-penetrating clip has proven to be a safe and reliable alternative to suture for these demanding reconstructions. Clips provide the advantages of improved anastomotic compliance, reduced operative time, and reduced incidence of post-operative anastomotic intimal hyperplasia and stenosis. Clip related pitfalls are discussed with recommendations regarding usage.

Dural closure with nonpenetrating clips prevents meningoneural adhesions: an experimental study in dogs

OBJECTIVE

Meningospinal and cranial dural adhesions were compared in a canine model, after duraplasty using nonpenetrating clips or penetrating needles and sutures.

METHODS

Fourteen dogs underwent bilateral craniotomies and duraplasties, with implantation of dural prostheses (DuraGuard; Biovascular Corp., Minneapolis, MN), using either 6-0 silk sutures or titanium clips (DuraClose; Surgical Dynamics, Norwalk, CT). Fourteen other dogs underwent L3-L4 laminectomies; three longitudinal dural incisions were closed with 6-0 silk sutures, 6-0 polyglactin 910 (Vicryl) sutures, or clips. Groups of eight dogs (four cranially treated and four spinally treated) were killed 6, 12, 24, and 52 weeks after surgery, and specimens were collected for study after perfusion and fixation (two cranial and two spinal dural reconstructions at 52 wk). Evaluations included assessment of the appearance of approximated dural margins and responses to clips, sutures, and dural prostheses (inflammation, foreign body reaction, fibrosis, and severity of meningospinal/meningocerebral adhesions). Data were evaluated using the Wilcoxon signed-rank and McNemar tests.

RESULTS

Duraplasties with clips displayed significantly less extensive acute and chronic inflammation, foreign body reaction, and meningoneural adhesions than did repairs with needles and sutures.

CONCLUSION

This report is the first long-term experimental study comparing two fundamentally different methods for dural repair in a relevant animal model.

Facilitated vascular anastomoses: the one-shot device

BACKGROUND

A mechanical system for facilitating vascular anastomosis (end-to-side, end-to-end) is described that enables the rapid construction of nonpenetrated, compliant junctions. The instrument (United States Surgical One-Shot system) simultaneously applies either 10 or 12 nonpenetrating, arcuate-legged titanium clips to everted vessel or prosthetic conduit edges.

METHODS AND RESULTS

The instrument has been tested in animals (jugular and femoral vein jump grafts in carotid and femoral arteries, interpositional grafts, 20 pigs) and human cadaveric constructs (saphenous veins to left anterior descending coronary arteries, 20 cases, 5 brachiocephalic access fistulas) as end-to-side constructs. Clipped constructs have equivalent or superior physical properties to control sutured constructs (6-0 polypropylene) as gauged by burst and tensile strength. All studies were performed under Food and Drug Administration Good Laboratory Practice standards, and the device has been approved for marketing by the Food and Drug Administration.

CONCLUSIONS

The device enables rapid and reproducible vascular anastomotic constructs with vessels as small as 1.8 mm outer diameter. The constructs are flanged, interrupted, and nonpenetrated.

Nonpenetrating clips for coronary anastomosis

BACKGROUND

A nonsuture clip technique (nonpenetrating titanium clips applied to everted tissue edges at high compressive forces) was used to perform coronary anastomoses in a clinical setting.

METHODS

Clipped coronary anastomoses were performed in 10 patients. The anastomoses incorporated the left internal mammary artery to the left anterior descending artery (n = 1) and the saphenous vein to the right coronary artery (n = 5), the posterior descending artery (n = 2), the diagonal artery (n = 2), and one vein-to-vein proximal anastomosis (n = 1).

RESULTS

The mean duration for completion of the anastomoses was 15 minutes (range, 7 to 20 minutes). This time was reduced from 20 minutes at the beginning of the clinical experience to 7 minutes for the last 3 patients. No technical complication was related to clip application and all patients had uneventful outcomes. Three anastomoses studied by coronary angiography were patent without stenosis.

CONCLUSION

The clipped anastomotic technique has a rapid learning curve, the same safety as suture methods, and the potential for facilitating endoscopic vascular reconstructions.