PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics

The clinical success of CRISPR therapies hinges on the safety and efficacy of Cas proteins. The Cas9 from Francisella novicida (FnCas9) is highly precise, with a negligible affinity for mismatched substrates, but its low cellular targeting efficiency limits therapeutic use. Here, we rationally engineer the protein to develop enhanced FnCas9 (enFnCas9) variants and broaden their accessibility across human genomic sites by ~3.5-fold. The enFnCas9 proteins with single mismatch specificity expanded the target range of FnCas9-based CRISPR diagnostics to detect the pathogenic DNA signatures. They outperform Streptococcus pyogenes Cas9 (SpCas9) and its engineered derivatives in on-target editing efficiency, knock-in rates, and off-target specificity. enFnCas9 can be combined with extended gRNAs for robust base editing at sites which are inaccessible to PAM-constrained canonical base editors. Finally, we demonstrate an RPE65 mutation correction in a Leber congenital amaurosis 2 (LCA2) patient-specific iPSC line using enFnCas9 adenine base editor, highlighting its therapeutic utility.

Facial nerve communication with ansa cervicalis - An unusual anatomical variation

Neural connections of the seventh cranial nerve with its neighboring nerves are common and well documented; however, communication with ansa cervicalis is as yet unknown. We present a case with such a connection found during cadaveric dissection, with hitherto unknown consequences. In this specimen, after giving the marginal mandibular and cervical branches, the cervicofacial division continued distally to communicate with the distal loop of ansa cervicalis. Presence of such connection may result in facial muscle paralysis on injury to the ansa or strap muscle paralysis on injury to the facial nerve, depending on the direction of nerve fibers. Such unusual connections bring to light the need for extreme care during surgeries in the neck to safeguard any such connections and when using the ansa as donor.

Bone anchor as fixation method for abdominal wall reconstruction. A case report about a ten times recurred inguinal hernia

INTRODUCTION

While the use of bone anchor fixation for abdominal wall reconstruction for supra-pubic incisional hernia is well described (Yee et al., 2008 [1]), we show in this case report, written in line with the SCARE criteria (Agha et al., 2020 [2]), a novel use of this tool as an adjunct in the repair of a ten time recurrent inguinal hernia.

CASE REPORT

A 65 years old multiparous, diabetic non-obese female, with previous abdominoplasty was submitted for left inguinal hernia for ten times, between multiples complications between infection, more than one mesh excision by anterior approach and laparoscopic approach. The wide range of procedures culminated in a destruction of the abdominal wall, making it impossible for a usual fixation of mesh in the region. Therefore, a multidisciplinary approach was planned for the patient with a bone anchor as a mesh fixation method. With a year follow up we did not observe a local hernia recurrence.

CLINICAL DISCUSSION

Hernia itself is a multifactorial disease. As a anatomical defect, surgery is the only effective treatment. Our report brings a novel approach to a challenging case with many previous unsuccessful applications of conventional surgeries. Hence, we stimulate the multidisciplinary discussion for enhancing post operatory outcomes and a better point of care for the patient.

Public attitude toward and perceptions of dairy cattle welfare in cow-calf management systems differing in type of social and maternal contact

Early cow-calf separation followed by individual housing of calves is standard practice on dairy farms. However, a growing body of evidence suggests that as awareness grows the public will oppose these practices, which could compromise the dairy industry's social license. Despite disagreement among different stakeholders over weighting and evaluations of effects of early separation (e.g., distress response, disease risk), recent systematic reviews indicate that there is little scientific evidence supporting this practice. The acceptability of alternative cow-calf management systems is unknown. We used a mixed methods survey with a convenience sample of 307 Canadians plus a representative sample of 1,487 Americans to investigate perceptions of these systems, examining the effects of providing social or foster cow contact following early separation or not separating cow-calf pairs. Attitudes and perceptions of animal welfare were more positive (on a 7-point scale where 1 is most negative, 7 is most positive, and 4 is a neutral midpoint) toward the system where calves were not separated from the cow (mean ± SE; 5.8 ± 0.07; 5.7 ± 0.07), compared with systems in which the calf was separated and individually housed (3.6 ± 0.07; 3.4 ± 0.07), separated and group housed (3.7 ± 0.07; 3.4 ± 0.07), or separated and kept with a foster cow (3.8 ± 0.07; 3.6 ± 0.07). Participants were consistent in their attitudes toward and perceptions of animal welfare within the system, suggesting that participants took a holistic and value-oriented approach to cow-calf management regarding separation. These results, in combination with many participants' concern for the importance of the mother cow-calf relationship and perceptions that severing of this bond was a breach of standard of care, suggest that there may be low acceptance of any cow-calf management system involving early separation as such systems are unlikely to resonate with underlying values.

FnCas9 Editor Linked Uniform Detection Assay for COVID-19

The recent COVID-19 outbreak and pandemic of 2020 and its surveillance were implemented by quickly adapting the existing diagnostic methods to detect the SARS-CoV-2 RNA. While traditional methods for detecting pathogenic DNA and RNA have relied heavily on gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and sequencing-based methods, their shortcomings under resource-limited settings have emphasized the need of developing point-of-care (POC) diagnostics. Clustered regularly interspaced short palindromic repeats (CRISPR)-based detection systems provide a rapid and accurate alternative. Here, we describe a CRISPR-Cas9-based detection system FnCas9 Editor Linked Uniform Detection Assay (FELUDA) using a lateral flow test that can detect nucleobase and nucleotide sequences depending upon the stoichiometric-based binding of FnCas9 ribonucleoprotein complex (RNP)-target sequences. The assay has been optimized to be conducted within 1 h and shows 100% sensitivity and 97% specificity in clinical samples across a range of viral loads. The lateral strip results are read using the True Outcome Predicted via Strip Evaluation (TOPSE) smartphone application. This assay is versatile and can be optimized and adjusted to target various diseases.

Histopathological features for coexistent invasive cancer in large colorectal adenomatous polyps

Background

Histopathological features associated with coexistent invasive adenocarcinoma in large colorectal adenomas have not been described. This study aimed to determine the association of histopathological features in areas of low-grade dysplasia with coexistent invasive adenocarcinoma.

Methods

High-grade lesions (containing high-grade dysplasia or adenocarcinoma) from a cohort of large (at least 20 mm) colorectal adenomas removed by endoscopic resection were subjected to detailed histopathological analysis. The histopathological features in low-grade areas with coexistent adenocarcinoma were reviewed and their diagnostic performance was evaluated.

Results

Seventy-four high-grade lesions from 401 endoscopic resections of large adenomas were included. In the low-grade dysplastic areas, a coexistent invasive adenocarcinoma was associated significantly with a cribriform or trabecular growth pattern (P < 0.001), high nuclear grade (P < 0.001), multifocal intraluminal necrosis (P < 0.001), atypical mitotic figures (P = 0.006), infiltrative lesion edges (P < 0.001), a broad fibrous band (P = 0.001), ulceration (P < 0.001), expansile nodules (P < 0.001) and an extensive tumour-infiltrating lymphocyte pattern (P = 0.04). Lesions with coexistent invasive adenocarcinoma harboured at least one of these features. The area under the receiver operating characteristic curve (AUROC) for coexistent invasive adenocarcinoma, using frequencies of adverse histopathological factors in low-grade areas, was 0.92. The presence of two or more of these adverse histopathological features in low-grade areas had a sensitivity of 86 per cent and a specificity of 84 per cent for coexistent invasive adenocarcinoma.

Conclusion

Several histopathological features in low-grade dysplastic areas of adenomas could be predictive of coexistent adenocarcinoma.

FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip

The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral load and prognostic complexities. Several of these variants are point mutations that are difficult to diagnose using the gold standard quantitative real-time PCR (qRT-PCR) method and necessitates widespread sequencing which is expensive, has long turn-around times, and requires high viral load for calling mutations accurately. Here, we repurpose the high specificity of Francisella novicida Cas9 (FnCas9) to identify mismatches in the target for developing a lateral flow assay that can be successfully adapted for the simultaneous detection of SARS-CoV-2 infection as well as for detecting point mutations in the sequence of the virus obtained from patient samples. We report the detection of the S gene mutation N501Y (present across multiple variant lineages of SARS-CoV-2) within an hour using lateral flow paper strip chemistry. The results were corroborated using deep sequencing on multiple wild-type (n = 37) and mutant (n = 22) virus infected patient samples with a sensitivity of 87% and specificity of 97%. The design principle can be rapidly adapted for other mutations (as shown also for E484K and T716I) highlighting the advantages of quick optimization and roll-out of CRISPR diagnostics (CRISPRDx) for disease surveillance even beyond COVID-19. This study was funded by Council for Scientific and Industrial Research, India.

Association of clinical factors and recent anticancer therapy with COVID-19 severity among patients with cancer: a report from the COVID-19 and Cancer Consortium

BACKGROUND

Patients with cancer may be at high risk of adverse outcomes from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We analyzed a cohort of patients with cancer and coronavirus 2019 (COVID-19) reported to the COVID-19 and Cancer Consortium (CCC19) to identify prognostic clinical factors, including laboratory measurements and anticancer therapies.

PATIENTS AND METHODS

Patients with active or historical cancer and a laboratory-confirmed SARS-CoV-2 diagnosis recorded between 17 March and 18 November 2020 were included. The primary outcome was COVID-19 severity measured on an ordinal scale (uncomplicated, hospitalized, admitted to intensive care unit, mechanically ventilated, died within 30 days). Multivariable regression models included demographics, cancer status, anticancer therapy and timing, COVID-19-directed therapies, and laboratory measurements (among hospitalized patients).

RESULTS

A total of 4966 patients were included (median age 66 years, 51% female, 50% non-Hispanic white); 2872 (58%) were hospitalized and 695 (14%) died; 61% had cancer that was present, diagnosed, or treated within the year prior to COVID-19 diagnosis. Older age, male sex, obesity, cardiovascular and pulmonary comorbidities, renal disease, diabetes mellitus, non-Hispanic black race, Hispanic ethnicity, worse Eastern Cooperative Oncology Group performance status, recent cytotoxic chemotherapy, and hematologic malignancy were associated with higher COVID-19 severity. Among hospitalized patients, low or high absolute lymphocyte count; high absolute neutrophil count; low platelet count; abnormal creatinine; troponin; lactate dehydrogenase; and C-reactive protein were associated with higher COVID-19 severity. Patients diagnosed early in the COVID-19 pandemic (January-April 2020) had worse outcomes than those diagnosed later. Specific anticancer therapies (e.g. R-CHOP, platinum combined with etoposide, and DNA methyltransferase inhibitors) were associated with high 30-day all-cause mortality.

CONCLUSIONS

Clinical factors (e.g. older age, hematological malignancy, recent chemotherapy) and laboratory measurements were associated with poor outcomes among patients with cancer and COVID-19. Although further studies are needed, caution may be required in utilizing particular anticancer therapies.

CLINICAL TRIAL IDENTIFIER

NCT04354701.

Ultrasound-guided sacral multifidus plane block for analgesia following excision of sacrococcygeal teratoma in two neonates

Peri-operative pain management in the neonate with a sacrococcygeal teratoma poses significant challenges to the anaesthetist. Involvement of the sacrococcygeal area by the tumour often prevents the use of conventional regional anaesthetic techniques such as caudal or epidural analgesia, with a subsequent reliance on intravenous opioids and paracetamol. Since opioids are associated with respiratory depression, constipation and urinary retention, there is high incidence of opiophobia with consequent inappropriate dosage prescription, particularly in the paediatric population. We describe the use of an ultrasound-guided sacral multifidus plane block in two neonates undergoing surgical excision of sacrococcygeal teratoma. The block is technically easy to perform and also avoids traversing critical structures. Hence, it may be regarded as a promising analgesic technique for painful interventions in the sacrococcygeal area.

Surgery for chronic subdural hematoma in nonagenarians: A Scandinavian population-based multicenter study

OBJECTIVE

Chronic subdural hematoma (cSDH) is a prevalent condition often seen in the elderly, with surgery being the treatment of choice when symptomatic. So far, few have explored the surgical outcomes in patients 90 years or older. The aim of this study was to investigate outcome after cSDH surgery in nonagenarians (≥90 y/o group) compared to younger adult patients (<90 y/o group).

MATERIALS

In a Scandinavian population-based cohort we conducted a retrospective review of 1,254 patients undergoing primary burr-hole procedures for cSDH between January 1, 2005 and December 31, 2010 at three neurosurgical centers. In a comparative analysis, the primary end-point was difference in hematoma recurrence rates between the ≥90 y/o and <90 y/o groups. The secondary end-points were differences in perioperative morbidity and mortality between groups.

RESULTS

75 patients were 90 years or older. There was no significant difference in recurrences resulting in reoperation between the age groups (10.7% vs 13.6%, P=.47). There was also no significant difference in overall complication rate (4.1% vs 8.1%, P=.21) or severe complications (1.4% vs 2.0%, P=.68). There were three (4.0%) perioperative deaths within 30 days in the ≥90 y/o group and 40 (3.4%) in the <90 y/o group (P=.78).

CONCLUSION

Patients 90 years or older had similar rates of recurrence, perioperative morbidity and perioperative mortality as compared to younger patients. Age alone should not be a contraindication for surgery in patients with cSDH.

Identification of potential molecular associations between chikungunya virus non-structural protein 2 and human host proteins

Chikungunya virus (CHIKV) non-structural protein 2 (nsP2) is considered to be the master regulator of viral RNA replication and host responses generated during viral infection. This protein has two main functional domains: an N-terminal domain which exhibits NTPase, RNA triphosphatase and helicase activities and a C-terminal protease domain. Understanding how CHIKV nsP2 interacts with its host proteins is essential for elucidating all the required processes for viral replication and pathogenesis along with the identification of potential targets for antiviral therapy. In current study yeast two-hybrid (Y2H) screening of a human fetal brain cDNA library was performed using nsP2 protein as bait. The analysis identified seven host proteins (CCDC130, CPNE6, POLR2C, MAPK9, EIF4A2, EEF1A1 and EIF3I) as putative interactors of CHIKV nsP2 which were selected for further analysis based on their roles in host cellular machinery. The gene ontology analysis indicates that these proteins are mainly involved in apoptosis, transcription and translational mechanism of host cell. Domain mapping of nsP2 revealed that these associations are not random connections but instead they have functional significance. Further studies to identify the amino acid residues and their chemical interactions that may help in opening new possibilities for preventing these interactions, thus reducing chances of chikungunya infection were performed. This study expands the understanding of CHIKV-host interactions and is important for rational approaches of discovering new antiviral agents.

First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77

Arthrobacter agilis strain L77, is a plant growth promoting and cold active hydrolytic enzymes producing psychrotrophic bacterium, isolated from Pangong Lake, a subglacial lake in north western Himalayas, India. Genome analysis revealed metabolic versatility with genes involved in metabolism and cold shock adaptation, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of Arthrobacter agilis strain L77 consists of 3,608,439 bp (3.60 Mb) of a circular chromosome. The genome comprises of 3316 protein coding genes and 74 RNA genes, 725 hypothetical proteins, 25 pseudo-genes and 1404 unique genes.