Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex.

Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3.4 Å. The structure explains the molecular mechanism for immune system suppression, and structure-guided mutations show that the Acr proteins bind to residues essential for crRNA-mediated detection of DNA. Collectively, these data provide a snapshot of an ongoing molecular arms race between viral suppressors and the immune system they target.

RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2.

Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided, sequence-nonspecific degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA following recognition of a complementary RNA target, culminating in abortive infection1. Here we report structures of Cas12a2 in binary, ternary and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of 'aromatic clamp' residues that are crucial for double-stranded DNA degradation and in vivo immune system function. Our work provides a structural basis for this mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.

Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA.

Bacterial abortive-infection systems limit the spread of foreign invaders by shutting down or killing infected cells before the invaders can replicate1,2. Several RNA-targeting CRISPR-Cas systems (that is, types III and VI) cause abortive-infection phenotypes by activating indiscriminate nucleases3-5. However, a CRISPR-mediated abortive mechanism that leverages indiscriminate DNase activity of an RNA-guided single-effector nuclease has yet to be observed. Here we report that RNA targeting by the type V single-effector nuclease Cas12a2 drives abortive infection through non-specific cleavage of double-stranded DNA (dsDNA). After recognizing an RNA target with an activating protospacer-flanking sequence, Cas12a2 efficiently degrades single-stranded RNA (ssRNA), single-stranded DNA (ssDNA) and dsDNA. Within cells, the activation of Cas12a2 induces an SOS DNA-damage response and impairs growth, preventing the dissemination of the invader. Finally, we harnessed the collateral activity of Cas12a2 for direct RNA detection, demonstrating that Cas12a2 can be repurposed as an RNA-guided RNA-targeting tool. These findings expand the known defensive abilities of CRISPR-Cas systems and create additional opportunities for CRISPR technologies.

Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC.

The NFE2L2 (NRF2) oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion, and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry-based targeted proteomics assay based on internal standard-triggered parallel reaction monitoring to quantify 69 NRF2 pathway components and targets, as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved an existing internal standard-triggered parallel reaction monitoring acquisition algorithm, called SureQuant, to increase throughput, sensitivity, and precision. Testing the optimized platform on 27 lung and upper aerodigestive cancer cell models revealed 35 NRF2 responsive proteins. In formalin-fixed paraffin-embedded HNSCCs, NRF2 signaling intensity positively correlated with NRF2-activating mutations and with SOX2 protein expression. Protein markers of T-cell infiltration correlated positively with one another and with human papilloma virus infection status. CDKN2A (p16) protein expression positively correlated with the human papilloma virus oncogenic E7 protein and confirmed the presence of translationally active virus. This work establishes a clinically actionable HNSCC protein biomarker assay capable of quantifying over 600 peptides from frozen or formalin-fixed paraffin-embedded archived tissues in under 90 min.

CasDinG is a 5'-3' dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity.

CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5'-3' DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5'-GNAWN-3' on the 5'-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.

A Conserved Structural Chassis for Mounting Versatile CRISPR RNA-Guided Immune Responses.

Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for targeted elimination of foreign nucleic acids. These immune systems have been divided into three main types, and the first atomic-resolution structure of a type III RNA-guided immune complex provides new insights into the mechanisms of nucleic acid degradation. Here we compare the crystal structure of a type III complex to recently determined structures of DNA-targeting type I CRISPR complexes. Structural comparisons support previous assertions that type I and type III systems share a common ancestor and reveal how a conserved structural chassis is used to support RNA-, DNA-, or both RNA- and DNA-targeting mechanisms.

Specimen-Based Resection Margins and Local Control during Transoral Robotic Surgery for Oropharyngeal HPV-Mediated Squamous Cell Carcinoma.

OBJECTIVES: The aim of the study was to investigate the association of surgical margin conditions, including positive specimen margins revised to negative relative to local recurrence, disease-free survival, and overall survival (OS) within a cohort of HPV-mediated oropharyngeal squamous cell carcinoma (OPSCC) who underwent en bloc resection via transoral robotic surgery (TORS). MATERIALS AND METHODS: Retrospective cohort of patients with untreated HPV-mediated OPSCC cT1 or T2 undergoing TORS resection between October 2014 and March 2020. The methodologic description of our interdisciplinary institutional approach, number of cut-through margins (CTMs) during intraoperative consultation, percentage of final positive margin cases, and disease-free survival and OS stratified by margin status and margin tumor-free distance is identified. RESULTS: 135 patients with primary cT1/T2 HPV-mediated OPSCC met inclusion criteria. Twenty-eight of 135 (20.7%) specimens revealed CTM and were revised during the same operative setting. Three of 135 (2.2%) surgical cases had positive final margin status. Local control rate was 97%. On univariate analysis, margin distance did not impact OS. CTM and final positive margins had lower OS than initially negative margins (p = 0.044). Pathologic N-stage significantly impacted OS (p < 0.001). CONCLUSIONS: High local control rate and low final positive margin status confound the study of specimen margin-based techniques in HPV-mediated OPSCC resected en bloc with TORS. Pathologic N-stage may impact OS more than margin status. Larger numbers are needed to confirm differences.

National analysis of positive surgical margins in oropharyngeal salivary gland malignancies.

OBJECTIVE: Positive surgical margins (PSM) are associated with worse survival in oropharyngeal salivary gland malignancies (OPSGM), but existing literature is limited to small series. Our objective was to identify risk factors for PSM using the national cancer database (NCDB), including a transoral robotic surgical (TORS) approach. METHODS: NCDB was queried for patients with T1-T4a OPSGM undergoing resection between 2010 and 2017. Risk factors for PSM were determined using logistic regression. Overall survival (OS) was analyzed using Kaplan-Meier and Cox proportional hazards models. RESULTS: Of 785 patients, 165 (21.0 %) had PSM. Age, stage T4a tumors (OR 2.00, 95 % Confidence Interval [CI]: 1.03-3.88), adenoid cystic carcinoma (OR 2.02, 95 % CI: 1.29-3.18), and treatment at lower volume institutions (OR 1.68, 95 % CI: 1.09-2.59) were all independently associated with PSM. TORS versus a non-robotic approach was not associated with PSM (23.9 % vs 20.4 %, p 0.358), respectively. Positive margins were independently associated with a worse OS than negative margins (HR 1.63, 95 % CI: 1.03-2.59). Adjuvant radiation therapy was associated with improved survival in high grade tumors with positive margins. CONCLUSION: This study represents the largest review assessing risk factors for positive margins in OPSGM. Histologic type (adenoid cystic carcinoma), age, T4a tumor stage and treatment at a lower volume institution were all predictive of positive margins. With increasing use of TORS over the last decade, there does not appear to be a greater risk of positive margins using this modality in select patients. LEVEL OF EVIDENCE: N/A.

Practice patterns of virtual surgical planning: Survey of the reconstructive section of the American Head and Neck Society.

PURPOSE: Virtual surgical planning (VSP), with custom made implants and guides represents a recent major advance. Nonetheless, knowledge related to practice patterns is limited. The purpose of this study was to provide data from the AHNS Reconstruction Section related to practice patterns, perceived value of VSP, as well as elucidate specific situations which represent high value for the application of VSP. MATERIALS AND METHODS: A multi-center web-based survey consisting of 30 questions regarding practice patterns related to VSP practices delivered via email to 203 members of the AHNS Reconstructive Surgery Section at institutions across North America. RESULTS: There was a 34% response rate (70/203). A majority of the respondents (96%) used VSP in approximately 50% of their mandibular reconstruction cases, and in 42% of maxillary cases. 46% reported using patient specific implants >75% of cases. Respondents estimated that ~17% of patients received dental implant reconstruction. The majority of respondents (71.0%) did not know the cost of VSP at their institution. The remaining respondents indicated the average cost was $6680 per case. VSP was felt to be necessary as a teaching tool by 55.9%. CONCLUSIONS: Our results demonstrate that a majority of respondents frequently utilize VSP in their practice for head and neck reconstruction. Complex, multi-unit reconstructions were felt to offer the greatest value when utilizing VSP. Future work should focus on increasing the rates of dental implant reconstruction in this population, optimizing value of VSP with careful case selection, and understanding the educational value and costs of these platforms.

Lateral diffusion of single poly(ethylene oxide) chains on the surfaces of glassy and molten polymer films.

Fluorescence correlation spectroscopy was used to show that the temperature-dependent diffusion coefficient of poly(ethylene oxide) (PEO) adsorbed on polystyrene and different poly(alkyl methacrylate) (PAMA) films in aqueous solution exhibited a maximum close to (but below) the surface glass transition temperature, Tgs, of the film. This elevated diffusion was observed over a small range of temperatures below Tgs for these surfaces, and at other temperatures, the diffusion was similar to that on silicon, although the diffusion coefficient for PEO on polystyrene at temperatures above Tgs did not completely decrease to that on silicon, in contrast to the PAMA surfaces. It is concluded that the enhanced surface mobility of the films near the surface glass transition temperature induces conformational changes in the adsorbed PEO. The origin of this narrow and dramatic increase in diffusion coefficient is not clear, but it is proposed that it is caused by a coupling of a dominant capillary mode in the liquid surface layer with the polymer. Friction force microscopy experiments also demonstrate an unexpected increase in friction at the same temperature as the increase in diffusion coefficient.

20 pack-year smoking history as strongest smoking metric predictive of HPV-positive oropharyngeal cancer outcomes.

OBJECTIVES: While smoking is associated with worse outcomes in HPV-positive oropharyngeal squamous cell carcinoma (OPSCC), the magnitude of this association is unclear given the heterogenous smoking definitions and outcomes. Our objective was to investigate the association between smoking, survival, and recurrence in HPV-related OPSCC using multiple smoking metrics reported in the literature. MATERIALS AND METHODS: This was a retrospective cohort study of 375 adults with p16+ OPSCC undergoing surgical resection (n = 272) or definitive chemoradiation (n = 103) at a tertiary academic institution from 2006 to 2017. The primary outcome was overall survival (OS). Secondary outcomes included disease-free survival (DFS), disease-specific survival (DSS), and recurrence. We used multiple smoking metrics commonly cited in previous studies, including ever versus never smokers, current versus former/never smokers, ≤10 versus >10 pack-year, ≤20 versus >20 pack-year, and continuous pack-year. RESULTS: There were 375 patients, median age 58 years, with 326 (87%) males, and median follow-up of 52 months. Of all smoking metrics, >20 pack-year history was the strongest predictor of both OS (HR 2.24, 95% CI: 1.19-4.20) and DFS (HR 1.67, 95% CI: 1.04-2.66) on univariable and multivariable analysis after adjusting for age, overall stage, and comorbidities. Patients with >20 pack-year smoking history were also more likely to have recurrence (HR 1.59, 95% CI: 0.95-2.67) after adjusting for overall stage. CONCLUSION: Heavier smoking >20 pack-years was the strongest smoking metric associated with 2-times worse survival and recurrence. Our findings suggest that >20 pack-year smoking history may be a more useful cutoff for risk stratification models but requires further validation.

Role of nucleotide identity in effective CRISPR target escape mutations.

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR-Cas systems.

The association of smoking and outcomes in HPV-positive oropharyngeal cancer: A systematic review.

PURPOSE: While smoking is linked to worse outcomes for human papillomavirus (HPV)-related oropharyngeal squamous cell cancer (OPSCC), the magnitude of this association and the amount of smoking exposure necessary to confer clinically significant differences in outcomes is unclear. Recent studies suggested that greater tobacco exposure results in higher risk of cancer progression and death. Our study objective was to perform a systematic review of the association between smoking and HPV-related OPSCC outcomes. MATERIALS AND METHODS: A literature search was conducted in April 2019 to identify relevant articles using Embase, Medline, Scopus, CENTRAL, and Cochrane databases. All studies were independently screened by two investigators to identify studies that assessed HPV-positive patients as an independent cohort, specified smoking measures, and reported locoregional recurrence (LRR), overall survival (OS), disease-specific survival (DSS), or disease-free survival (DFS) in association with smoking. RESULTS: Of 1130 studies identified, 10 met final inclusion criteria with 2321 total patients, mean age 57.5 years. Smoking measures included ever vs never, current vs never/former smokers, ≤10 vs >10 pack-year, and continuous pack-years. Of these studies, 8 (80%) showed a significant effect of smoking on increasing recurrence and mortality. Adjusted HRs for LRR ranged from 0.6 to 5.2, OS from 1.3 to 4.0, DSS from 2.3 to 7.2, and DFS from 1.02 to 4.2 among heavier smokers compared to lighter/non-smokers. CONCLUSIONS: While there was significant variability in smoking metrics and reported outcomes, all studies reporting statistically significant HRs showed that smoking was associated with worse outcomes. Further studies using uniform smoking measures are necessary to better understand this association.

Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease.

Prokaryotic CRISPR-Cas adaptive immune systems rely on small non-coding RNAs derived from CRISPR loci to recognize and destroy complementary nucleic acids. However, the mechanism of Type IV CRISPR RNA (crRNA) biogenesis is poorly understood. To dissect the mechanism of Type IV CRISPR RNA biogenesis, we determined the x-ray crystal structure of the putative Type IV CRISPR associated endoribonuclease Cas6 from Mahella australiensis (Ma Cas6-IV) and characterized its enzymatic activity with RNA cleavage assays. We show that Ma Cas6-IV specifically cleaves Type IV crRNA repeats at the 3' side of a predicted stem loop, with a metal-independent, single-turnover mechanism that relies on a histidine and a tyrosine located within the putative endonuclease active site. Structure and sequence alignments with Cas6 orthologs reveal that although Ma Cas6-IV shares little sequence homology with other Cas6 proteins, all share common structural features that bind distinct crRNA repeat sequences. This analysis of Type IV crRNA biogenesis provides a structural and biochemical framework for understanding the similarities and differences of crRNA biogenesis across multi-subunit Class 1 CRISPR immune systems.

The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers.

Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity.

Carbodiimide cross-linking counteracts the detrimental effects of gamma irradiation on the physical properties of collagen-hyaluronan sponges.

Collagen-based scaffolds are extensively used in biomaterials and tissue engineering applications. These scaffolds have shown great biocompatibility and versatility, but their relatively low mechanical properties may limit use in orthopaedic load-bearing applications. Moreover, terminal sterilization with gamma irradiation, as is commonly performed with commercial devices, presents concerns over structural integrity and enzymatic stability. Therefore, the goal of this study was to test the hypothesis that EDC/NHS cross-linking (10 mM/5 mM) can protect collagen-hyaluronan sponges from the damaging effects of gamma irradiation. Specifically, we evaluated compressive and tensile mechanical properties, enzymatic stability, porosity and pore size, and swelling ratio. Ultimate tensile strength and elastic modulus exhibited increases (168.5 and 245.8%, respectively) following irradiation, and exhibited over tenfold increases (1049.2 and 1270.6%, respectively) following cross-linking. Irradiation affected pore size (38.4% decrease), but cross-linking prior to irradiation resulted in only a 17.8% decrease. Cross-linking also showed an offsetting effect on the equilibrium modulus, enzymatic stability, and swelling ratio of sponges. These results suggest that carbodiimide cross-linking of collagen-hyaluronan sponges can mitigate the structural damage typically experienced during gamma irradiation, warranting their use in tissue engineering applications.

Intraoperative imaging during minimally invasive transoral robotic surgery using near-infrared light.

PURPOSE: The purpose of this study was to determine if the use of the FIREFLY imaging system could be an asset in transoral robotic surgery (TORS) for oropharyngeal squamous cell carcinoma (OPSCC). The system uses indocyanine green dye (ICG), which fluoresces when illuminated by near-infrared light from the Da Vinci robot. The system may improve visualization of tumor margins, highlight important vascular structures, and help identify the location of tumors and unknown primary head and neck cancers. METHODS: Six patients with OPSCC were enrolled in the study. Two of these cases were unknown primaries, one was base of tongue, and three were palatine tonsils. Each patient was given two 3ml doses of ICG, one at the beginning of the surgical case and one during resection of the tumor. The oropharynx was then visualized using the near-infrared light of the Da Vinci robot for a minute after injection. RESULTS: The FIREFLY system was unable to detect gross tumors, positive margins, unknown primaries, or vascular structures in any of the six subjects in the study. In addition, there were no adverse events or side effects in any of the subjects. CONCLUSION: The use of the FIREFLY system with indocyanine green fluorescence did not identify tumor boundaries, unknown primary head and neck cancers, or vascular structures in the oropharynx.

Transoral Resection of Human Papillomavirus (HPV)-Positive Squamous Cell Carcinoma of the Oropharynx: Outcomes with and Without Adjuvant Therapy.

BACKGROUND: With the rise of oropharyngeal squamous cell carcinoma associated with human papillomavirus (HPV), appropriate treatment strategies continue to be tailored toward minimizing treatment while preserving oncologic outcomes. This study aimed to compare the outcomes for those undergoing transoral resection with or without adjuvant therapy for HPV-related oropharyngeal carcinoma. METHODS: A case-match cohort analysis was performed at two institutions on patients with HPV-related oropharyngeal squamous cell carcinoma. All the subjects underwent transoral surgery and neck dissection. The patients treated with surgery alone were matched 1:1 to those treated with surgery and adjuvant therapy using two groups identified as confounders: T-stage (T1/2 or T3/4) and number of pathologically positive lymph nodes (≤4 or >4). RESULTS: The study identified 105 matched pairs, with a median follow-up period of 42 months (range 3.1-102.3 months). The patients were staged as T1/T2 (86%) or T3/4 (14%). Each group had five patients with more than four positive lymph nodes. Adjuvant therapy significantly improved disease-free survival (hazard ratio [HR] 0.067; 95% confidence interval [CI] 0.01-0.62) and was associated with a lower risk of local and regional recurrence (risk ratio [RR] 0.096; 95% CI 0.02-0.47). No difference in disease-specific survival (HR 0.22; 95% CI 0.02-2.57) or overall survival (HR 0.18; 95% CI 0.01-2.4) was observed with the addition of adjuvant therapy. The risk of the gastrostomy tube was higher for those receiving adjuvant therapy (RR 7.3; 95% CI 2.6-20.6). CONCLUSIONS: Transoral surgery is an effective approach for the treatment of HPV-related oropharyngeal carcinoma. The addition of adjuvant therapy appears to decrease the risk of recurrence and improve disease-free survival but may not significantly improve overall survival.

Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.

In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro. Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.