Transient and tunable CRISPRa regulation of APOBEC/AID genes for targeting hepatitis B virus

APOBEC/AID cytidine deaminases play an important role in innate immunity and antiviral defenses and were shown to suppress hepatitis B virus (HBV) replication by deaminating and destroying the major form of HBV genome, covalently closed circular DNA (cccDNA), without toxicity to the infected cells. However, developing anti-HBV therapeutics based on APOBEC/AID is complicated by the lack of tools for activating and controlling their expression. Here, we developed a CRISPR-activation-based approach (CRISPRa) to induce APOBEC/AID transient overexpression (>4-800,000-fold increase in mRNA levels). Using this new strategy, we were able to control APOBEC/AID expression and monitor their effects on HBV replication, mutation, and cellular toxicity. CRISPRa prominently reduced HBV replication (∼90%-99% decline of viral intermediates), deaminated and destroyed cccDNA, but induced mutagenesis in cancer-related genes. By coupling CRISPRa with attenuated sgRNA technology, we demonstrate that APOBEC/AID activation can be precisely controlled, eliminating off-site mutagenesis in virus-containing cells while preserving prominent antiviral activity. This study untangles the differences in the effects of physiologically expressed APOBEC/AID on HBV replication and cellular genome, provides insights into the molecular mechanisms of HBV cccDNA mutagenesis, repair, and degradation, and, finally, presents a strategy for a tunable control of APOBEC/AID expression and for suppressing HBV replication without toxicity.

Contrast study after gastric repair: a review of incidence, outcomes and risk factors at an adult level 1 trauma center

PURPOSE

The role of contrast study after traumatic gastric repair, continues to be controversial. To that end, we aim to review the incidence, outcomes, and risk factors of patients undergoing contrast study after traumatic gastric repair.

METHODS

This was a retrospective review of all trauma patients admitted to a level 1 trauma center that sustained gastric injuries with subsequent repair between 2011 and 2018. Demographics, surgical interventions, complications, and clinical outcomes were evaluated. Statistical analysis included Chi-square/Fisher exact univariate analysis and multivariate logistic regression analysis with a 5% significance level.

RESULTS

A total of 233 patients received a gastric repair, of whom 49 (21%) had a contrast study performed. Out of 49 patients with a contrast study, one was found to have a gastric leak. Mean time to contrast study was 6.3 ± 2.7 days. There was no statistically significant difference in post-operative complications between non-contrast and contrast study groups. Multivariate logistic regression analysis demonstrated a lack of statistical significance in clinical risk factors that would lead to obtaining a contrast study.

CONCLUSION

Gastric leak after repair is rare and there is no statistically significant difference in clinical outcomes when comparing patients who underwent contrast study to those who did not. Routine contrast study after traumatic gastric repair may not be necessary and further evidence is warranted to determine the risk factors for a selective contrast study.

High expression of uracil DNA glycosylase determines C to T substitution in human pluripotent stem cells

Precise genome editing of human pluripotent stem cells (hPSCs) is crucial not only for basic science but also for biomedical applications such as ex vivo stem cell therapy and genetic disease modeling. However, hPSCs have unique cellular properties compared to somatic cells. For instance, hPSCs are extremely susceptible to DNA damage, and therefore Cas9-mediated DNA double-strand breaks (DSB) induce p53-dependent cell death, resulting in low Cas9 editing efficiency. Unlike Cas9 nucleases, base editors including cytosine base editor (CBE) and adenine base editor (ABE) can efficiently substitute single nucleotides without generating DSBs at target sites. Here, we found that the editing efficiency of CBE was significantly lower than that of ABE in human embryonic stem cells (hESCs), which are associated with high expression of DNA glycosylases, the key component of the base excision repair pathway. Sequential depletion of DNA glycosylases revealed that high expression of uracil DNA glycosylase (UNG) not only resulted in low editing efficiency but also affected CBE product purity (i.e., C to T) in hESCs. Therefore, additional suppression of UNG via transient knockdown would also improve C to T base substitutions in hESCs. These data suggest that the unique cellular characteristics of hPSCs could determine the efficiency of precise genome editing.

Efficacy of Postoperative Upper Gastrointestinal Series (UGI) and Computed Tomography (CT) Scan in Bariatric Surgery: a Meta-analysis on 7516 Patients

BACKGROUND

To demonstrate the lack of utility and efficacy of routine early postoperative upper gastrointestinal study (UGI) in obese patients undergoing bariatric surgery and to show the higher efficacy of CT scan in cases of clinical suspicion of a leakage, a meta-analysis was performed.

MATERIALS AND METHODS

A literature search including articles published in last 18 years was performed. For both UGI and CT scan, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. A first analysis considered overall patients, and a second analysis considered only symptomatic patients.

RESULTS

Starting from 1233 eligible citations, 18 articles, including 7516 patients, were left. The pooled sensitivity was 54% for UGI (95% CI 34-74) with a high heterogeneity (I² = 99.8%, p < .001), whereas CT scan showed a pooled sensitivity of 91% (95% CI 89-93) significantly higher than sensitivity of UGI series (p < 0.01), with a high heterogeneity (I² = 98.9%, p < .001). In symptomatic patients the pooled sensitivity of UGI series was significantly lower than sensitivity of CT scan [49% (95% CI 31-68) vs 94% (95% CI 92-96), p < 0.01]. PPV showed a significant difference between UGI series and CT scan (54 vs 100%, p < 0.01). Specificity for UGI series was 98.6%, and specificity for CT scan was 99.7% (p = ns); the mean NPV was 96 and 98% for UGI series and CT scan (p = ns).

CONCLUSIONS

According to our results, a CT scan triggered by clinical suspicion must be considered the first-line procedure to detect a postoperative leak following primary sleeve gastrectomy or Roux-en-Y gastric bypass.

Preoperative versus intraoperative diagnosis of hiatal hernia in bariatric population

BACKGROUND

Hiatal hernia is frequently encountered intraoperatively during bariatric surgery. There is scarce research pertaining to the diagnostic accuracy of a preoperative diagnostic modality in comparison to intraoperative diagnosis, along with patient characteristics and related factors contributing to hiatal hernia.

OBJECTIVE

To identify the prevalence and associations of hiatal hernia in the bariatric patient population, we compared the diagnostic accuracy of upper gastrointestinal series and esophagogastroduodenoscopy with the intraoperative findings across various patient characteristics.

SETTING

Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program, Teaching Hospital, New York, USA.

METHODS

Retrospective study of patients from 2015 to 2018 who met National Institutes of Health criteria for bariatric surgery.

RESULTS

There were 1094 patients included (135 males, 959 females), with an age range of 18 to 74 years. The diagnostic accuracy was determined by a sensitivity of 64.71% (95% confidence interval [CI] .55-.70), specificity of 74.38% (95% CI .71-.70), positive predictive value of 29.86% (95% CI .24-.30), negative predictive value of 92.59% (95%CI .89-90), likelihood ratio of 2.526, and P value < .0001 for esophagogastroduodenoscopy; a sensitivity of 14.02% (95% CI .08-0), specificity of 98.23% (95% CI .96-.90), positive predictive value of 71.43% (95% CI .50-.80), negative predictive value of 78.35% (95% CI .74-.80), likelihood ratio 7.921, and P value < .0001 were used for upper gastrointestinal series. Hiatal hernia with age <60 years was 17.09% versus 48.44% at >60 years (P < .0001). Hiatal hernia incidence was 17% in Hispanics, 22.5% in Caucasians, and 23.10% in blacks.

CONCLUSION

The prevalence of hiatal hernia is 18.92%. There is strong association between hiatal hernia and age and ethnicity and no association based on sex and body mass index. The diagnostic accuracy of upper gastrointestinal series is very low compared with that of esophagogastroduodenoscopy for hiatal hernia. Preoperative diagnosis of hiatal hernia in the bariatric population is not required based on our study. Not only does it lessen the economic burden, patient wait time, and discomfort of an additional study, but preoperative diagnosis does not change, alter, or aid in the intraoperative management of hiatal hernia considering the suboptimal accuracy of preoperative diagnostics, thus deeming them unwarranted.

The identification and treatment of intestinal malrotation in older children

PURPOSE

Intestinal malrotation is often diagnosed in infancy. The true incidence of malrotation outside of this age is unknown. These patients can present atypically or be asymptomatic and diagnosed incidentally. We evaluate the incidence, clinical presentation, ideal imaging, and intra-operative findings of patients with malrotation over 1 year of age.

METHODS

Retrospective review was conducted in patients older than 1 year, treated for malrotation at a single pediatric tertiary care center from 2000 to 2015. Data analyzed included demographics, presentation, imaging, intraoperative findings, and follow-up. Patients predisposed to malrotation were excluded.

RESULTS

246 patients were diagnosed with malrotation, of which 77 patients were older than 1 year of age. The most common presenting symptoms were vomiting (68%) and abdominal pain (57%). The most common method of diagnosis was UGI (61%). In 88%, the UGI revealed malrotation. 73 of 75 were confirmed to have malrotation at surgery. Intra-operatively, 60% were found to have a malrotated intestinal orientation and 33% with a non-rotated orientation. Obstruction was present in 22% with 12% having volvulus. Of those with follow-up, 58% reported alleviation of symptoms.

CONCLUSION

Despite age malrotation should be on the differential given a variable clinical presentation. UGI should be conducted to allow for prompt diagnosis and surgical intervention.

Retrospective study of etiology of non variceal acute gastrointestinal bleeding in Eastern Himalayan region of india in Sikkim

Upper gastrointestinal bleeding is one of the most commonly encountered emergencies in day-to-day practice. In the present retrospective study, the various causes of acute nonvariceal upper gastrointestinal bleeding (NVUGIB), its management modalities, and the final outcome of patients were studied.

Methods

A retrospective study of etiology of upper gastrointestinal (UGI) bleeding for a period of 13 months, January 2015 to February 2016 in Department of Gastroenterology, Central Referral Hospital, Gangtok, was conducted. There were a total of 127 upper gastrointestinal bleeding patients, out of which 70 patients were excluded due to endoscopically proven variceal bleeding. Of the 57 patients, the various causes were determined by investigations and were treated accordingly.

Conclusion

Hematemesis was the most common presentation and duodenal ulcers the most common etiology among the acute nonvariceal upper gastrointestinal bleed. The cause of bleeding was not identified in one patient. Majority (34 patients, 59.64%) of the patients was treated conservatively, some needed endoscopic interventions (23 patients, 40.35%) and there was no any mortality.

Perception of Urban Environmental Risks and the Effects of Urban Green Infrastructures (UGIs) on Human Well-being in Four Public Green Spaces of Guangzhou, China

Cities face many challenging environmental problems that affect human well-being. Environmental risks can be reduced by Urban Green Infrastructures (UGIs). The effects of UGIs on the urban environment have been widely studied, but less attention has been given to the public perception of these effects. This paper presents the results of a study in Guangzhou, China, on UGI users' perceptions of these effects and their relationship with sociodemographic variables. A questionnaire survey was conducted in four public green spaces. Descriptive statistics, a binary logistic regression model and cross-tabulation analysis were applied on the data from 396 valid questionnaires. The results show that UGI users were more concerned about poor air quality and high temperature than about flooding events. Their awareness of environmental risks was partly in accordance with official records. Regarding the perception of the impacts of environmental risks on human well-being, elderly and female respondents with higher education levels were the most sensitive to these impacts. The respondents' perceptions of these impacts differed among the different green spaces. The effects of UGIs were well perceived and directly observed by the UGI users, but were not significantly influenced by most sociodemographic variables. Moreover, tourists had a lower perception of the impacts of environmental risks and the effects of UGI than residents did. This study provides strong support for UGIs as an effective tool to mitigate environmental risks. Local governments should consider the role of UGIs in environmental risk mitigation and human well-being with regard to urban planning and policy making.

Routine versus selective upper gastrointestinal contrast series after omental patch repair for gastric or duodenal perforation

BACKGROUND

There are no guidelines on the routine or selective use of contrast upper gastrointestinal series (UGI) after omental patch repair (OPR) of a gastric (GP) or duodenal perforation (DP). This study aims to elucidate whether the use of selective versus routine contrast study will lead to worse clinical outcomes.

METHODS

A retrospective analysis of 115 (n = 115) patients with OPR of GP or DP was performed. Data were obtained from seven Florida Hospital campuses. Patients aged 18 and older from 2006 to 2016 were identified by ICD9 billing information. Patients were divided into two groups: UGI and no UGI. The UGI group was subdivided into selective versus routine. A selective UGI was defined as one or more of the following after post-operative day 3: WBC >12,000, peritonitis, fever >100.4 F, tachycardia >110 bpm on three or more assessments, and any UGI performed after POD 7. Perioperative symptoms, perforation location, size, abdominal contamination, laparoscopic or open, leak detection, length of stay, mortality, and reoperation within 2 weeks were also examined.

RESULTS

No differences between the UGI group and non-UGI group relating to preoperative symptoms, leak detection, death, and reoperation rate were revealed. Differences in length of stay were found to be statistically significant with the UGI group and non-UGI at a median of 15.5 and 8 days, respectively. In the UGI subgroup, 20 of the 29 patients received selective studies. There were no statistical differences identified in leak detection, death, and reoperation.

CONCLUSIONS

Rates of leak detection, reoperation, and death in patients with GP or DP repaired with omental patch utilizing an UGI study were not statistically significant. An increased length of stay was observed within the UGI group. There was no advantage demonstrated between a selective versus routine UGI; therefore, the use of selective UGI should be based upon clinical indications.

Life without dUTPase

Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair. Both dUTPase and the most efficient uracil-DNA glycosylase (UNG) is thought to be ubiquitous in free-living organisms. In the present work, we have systematically investigated the genotype of deposited fully sequenced bacterial and Archaeal genomes. We have performed bioinformatic searches in these genomes using the already well described dUTPase and UNG gene sequences. For dUTPases, we have included the trimeric all-beta and the dimeric all-alpha families and also, the bifunctional dCTP (deoxycytidine triphosphate) deaminase-dUTPase sequences. Surprisingly, we have found that in contrast to the generally held opinion, a wide number of bacterial and Archaeal species lack all of the previously described dUTPase gene(s). The dut– genotype is present in diverse bacterial phyla indicating that loss of this (or these) gene(s) has occurred multiple times during evolution. We discuss potential survival strategies in lack of dUTPases, such as simultaneous lack or inhibition of UNG and possession of exogenous or alternate metabolic enzymes involved in uracil-DNA metabolism. The potential that genes previously not associated with dUTPase activity may still encode enzymes capable of hydrolyzing dUTP is also discussed. Our data indicate that several unicellular microorganisms may efficiently cope with a dut– genotype lacking all of the previously described dUTPase genes, and potentially leading to an unusual uracil-enrichment in their genomic DNA.

Accuracy of radiographic estimation of small bowel dimensions in pediatric patients with short bowel syndrome

BACKGROUND

The decision to perform autologous intestinal lengthening in patients with short bowel syndrome (SBS) depends on total bowel length and the diameter and length of dilated segments. This study evaluated the accuracy of radiologic measurements of intestinal length and diameter.

METHODS

Patients who underwent an intestinal lengthening procedure with preoperative upper gastrointestinal study (UGI) were identified from 10/2012 through 1/2015. Measurements of total length and diameters and lengths of dilated segments on UGI were compared to intraoperative measurements using Spearman's rank correlation coefficients and Bland-Altman plots.

RESULTS

Fourteen patients underwent 15 lengthening procedures. Median age was 3.6years. Most common causes of SBS were complicated gastroschisis (43%) and small bowel atresia (36%). Intra-operative bowel lengths prior to performing lengthening procedures ranged from 21 to 170cm. The median measurements of radiographic and operative measurements (respectively) were total bowel lengths 77cm and 69cm (r=0.93, p<0.0001), maximum diameters 7.7cm and 7cm (r=0.86, p=0.001), and lengths of dilated segments 13cm and 14cm (r=0.41, p=0.36).

CONCLUSIONS

The correlation between UGI and operative measurements suggests that prediction of total bowel length and maximum diameter of dilation is accurate and can assist with operative planning.

Concordance Between Aspiration Detected on Upper Gastrointestinal Series and Videofluoroscopic Swallow Study in Bottle-Fed Children

The increasing incidence of pediatric dysphagia has raised questions about how to identify children at risk for aspiration. Multiple investigative imaging modalities are considered in diagnostic algorithms, since dysphagia may involve any or all phases of swallowing. Although upper gastrointestinal (UGI) series and videofluoroscopic swallow study (VFSS) are common procedures, the utility of UGI for detection of aspiration and the impact of oropharyngeal imaging during UGI on radiation exposure have not been well described. We hypothesized that diagnosis of aspiration on UGI would be predictive of aspiration on VFSS and screening swallows during UGI would increase radiation exposure. A retrospective review was completed of bottle-fed children undergoing UGI series within 1 month before/after standardized VFSS. UGI was imaged at 3 frames per second (fps) pulsed and VFSS at 30 fps continuous fluoroscopy. Cumulative radiation dose (CD) and dose area product (DAP) were recorded. VFSS and UGI were performed in 49 patients; however, only 21 (43 %) had documentation of swallow function on an UGI series. All children with aspiration on UGI demonstrated thin liquid aspiration on VFSS; however, 53 % without aspiration on UGI aspirated on VFSS. CD for UGI with versus without swallowing documentation was significantly higher (median = 0.33 vs. 0.21 mGy, p = 0.02) but within variability ranges reported for fluoroscopy equipment. DAP was not significantly higher for UGI with documentation of swallowing compared to without documentation of swallowing (median = 4.11 vs. 3.02 μGy cm(2), p = 0.09). UGI findings are specific but not sensitive markers for aspiration on VFSS. Imaging of swallowing on UGI may have an appreciable increase on radiation exposure.

Accuracy of routine postoperative swallow study in predicting leak or obstruction after gastric bypass

BACKGROUND

Many bariatric surgeons use a routine postoperative day 1 swallow study after Roux-en-Y gastric bypass to rule out leak or obstruction. The authors' practice adheres to this dictum, but the aim of this study was to determine how accurate this testing is in properly predicting complications.

METHODS

A retrospective chart review of all patients undergoing gastric bypass in the past 5 years (2008-2012) was performed; the results of their swallow study was examined and compared with their actual clinical outcome within 30 days of operation.

RESULTS

The records of 501 patients were reviewed, and there were 15 leaks and 29 obstructions for a total prevalence rate of 9%. When the swallow study was negative, 33 complications were missed and 433 reports were correct. When the swallow study was positive, only 11 complications were correctly identified and 24 of the reports were false positive. The sensitivity of the test was only 25%. The positive predictive value was only 31%. The result of the swallow study was incorrect 12% of the time.

CONCLUSION

Routine postoperative swallow study after gastric bypass was a poor method of accurately detecting clinically significant obstruction or leak. This test may be unnecessary for all patients and might best be used when clinically indicated.

Younger age at diagnosis is associated with panenteric, but not more aggressive, Crohn's disease

BACKGROUND & AIMS

Crohn's disease (CD) diagnosed in pediatric patients has been reported to have a more aggressive phenotype and course, with a greater prevalence of upper gastrointestinal involvement, than in adults. However, studies have not accounted for differences in diagnostic tests. We aimed to discern whether, in fact, CD diagnosed in childhood has a different outcome than CD diagnosed in adults.

METHODS

We performed comprehensive medical chart reviews of 571 patients with CD (451 with complete data) who were followed in a single referral inflammatory bowel disease clinic in Winnipeg, Canada, from 1993-2012. For specific time intervals, we determined types and numbers of imaging studies performed and parameters of disease phenotype, including age at diagnosis according to the Montreal classification (A1 diagnosed <17 years of age, A2 diagnosed 17-40 years, and A3 diagnosed >40 years).

RESULTS

Within 1 year of diagnosis, a higher proportion of A1 patients had upper gastrointestinal involvement and ileocolonic (L3) disease than A2 or A3 patients. These differences could be partly accounted for by the diagnostic tests performed during this time period. Although A1 patients underwent more extensive imaging studies, they had a lower prevalence of complicated disease, particularly compared with A3 patients. After a median follow-up period of 11.1 years, complicated disease behavior (B2 [structuring] or B3 [penetrating]) was similar among the 3 groups. Nonetheless, at the end of the study period, rates of inflammatory bowel disease-related abdominal surgery were significantly lower for A1 than A2 patients (odds ratio, 0.63; 95% confidence interval, 0.41-0.98) but not for A3 patients (odds ratio, 0.71; 95% confidence interval, 0.40-1.27).

CONCLUSIONS

On the basis of a database analysis of different age groups of patients with CD, studies of disease phenotypes among different cohorts should account for different patterns of diagnostic imaging evaluation. Our data show that although children are at increased risk of panenteric disease, they are not more likely to have more complicated disease or undergo surgery than adults.

Symptomatic duodenal Crohn's disease: is strictureplasty the right choice?

Primary duodenal localization of Crohn's disease (CD) is rare. Medical therapy can control symptoms, but surgery is required when progressive obstructive symptoms occur. Surgical options include bypass, resection, or strictureplasty, but it is still not clear which should be the treatment of choice. Reviewing the medical records of 1253 patients undergoing surgery for CD between January 1986 and December 2011 at the Digestive Surgery Unit of the Department of Clinical Physiopathology of the University of Florence, 10 patients (6 males and 4 females) underwent operations for duodenal CD. Four patients had only a duodenal localization, 6 patients had synchronous involvement of other intestinal tracts. Strictures were distributed in all the duodenal portions: in 7 patients there were single lesions, in 3 patients there were multiple lesions. Eight patients were treated with strictureplasty: 5 with the Heineke-Mikulicz technique, 2 with Jaboulay, and 1 with a pedunculated jejunal patch. Two patients were treated with resection: one with a B2 gastro-duodenal resection, and 1 with a duodenal-jejunal resection and an end to side duodeno-jejunal anastomosis. Follow up of the patients was from 2 to 18 years. No recurrence of duodenal CD was observed in the 2 patients treated with resection, while 2 of the 8 patients treated with strictureplasty had a recurrence. In our experience, strictureplasty is indicated when less than 2 strictures are present in the 2nd or 3rd duodenal portion. In cases with multiple strictures localized in the 1st or the distal duodenal portion, resection is preferable.

Index-based dietary patterns and risk of esophageal and gastric cancer in a large cohort study

BACKGROUND & AIMS

Diet could affect risk for esophageal and gastric cancers, but associations have been inconsistent. The diet is complex, so studies of dietary patterns, rather than studies of individual foods, might be more likely to identify cancer risk factors. There is limited research on index-based dietary patterns and esophageal and gastric cancers. We prospectively evaluated associations between the Healthy Eating Index-2005 (HEI-2005) and alternate Mediterranean Diet (aMED) scores and risk of esophageal and gastric cancers.

METHODS

We analyzed data from 494,968 participants in the National Institutes of Health-AARP Diet and Health study, in which AARP members (age, 51-70 y) completed a self-administered baseline food frequency questionnaire between 1995 and 1996. Their answers were used to estimate scores for each index.

RESULTS

During the follow-up period (1995-2006), participants developed 215 esophageal squamous cell carcinomas (ESCCs), 633 esophageal adenocarcinomas (EACs), 453 gastric cardia adenocarcinomas, and 501 gastric noncardia adenocarcinomas. Higher scores from the HEI-2005 were associated with a reduced risk of ESCC (comparing the highest quintile with the lowest quintile: hazard ratio, 0.51; 95% confidence interval, 0.31-0.86; Ptrend = .001) and EAC (hazard ratio, 0.75; 95% confidence interval, 0.57-0.98; Ptrend = .01). We observed an inverse association between ESCC, but not EAC, and a higher aMED score (meaning a higher-quality diet). HEI-2005 and aMED scores were not associated significantly with gastric cardia or noncardia adenocarcinomas.

CONCLUSIONS

By using data collected from 1995 through 2006 from the National Institutes of Health-AARP Diet and Health Study, HEI-2005 and aMED scores were associated inversely with risk for esophageal cancers, particularly ESCC. Adherence to dietary recommendations might help prevent esophageal cancers.