High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility.

Genome-wide association studies (GWASs) have identified numerous lung cancer risk-associated loci. However, decoding molecular mechanisms of these associations is challenging since most of these genetic variants are non-protein-coding with unknown function. Here, we implemented massively parallel reporter assays (MPRAs) to simultaneously measure the allelic transcriptional activity of risk-associated variants. We tested 2,245 variants at 42 loci from 3 recent GWASs in East Asian and European populations in the context of two major lung cancer histological types and exposure to benzo(a)pyrene. This MPRA approach identified one or more variants (median 11 variants) with significant effects on transcriptional activity at 88% of GWAS loci. Multimodal integration of lung-specific epigenomic data demonstrated that 63% of the loci harbored multiple potentially functional variants in linkage disequilibrium. While 22% of the significant variants showed allelic effects in both A549 (adenocarcinoma) and H520 (squamous cell carcinoma) cell lines, a subset of the functional variants displayed a significant cell-type interaction. Transcription factor analyses nominated potential regulators of the functional variants, including those with cell-type-specific expression and those predicted to bind multiple potentially functional variants across the GWAS loci. Linking functional variants to target genes based on four complementary approaches identified candidate susceptibility genes, including those affecting lung cancer cell growth. CRISPR interference of the top functional variant at 20q13.33 validated variant-to-gene connections, including RTEL1, SOX18, and ARFRP1. Our data provide a comprehensive functional analysis of lung cancer GWAS loci and help elucidate the molecular basis of heterogeneity and polygenicity underlying lung cancer susceptibility.

The Environmental Impact of Gastrointestinal Procedures: A Prospective Study of Waste Generation, Energy Consumption, and Auditing in an Endoscopy Unit.

BACKGROUND & AIMS: Gastrointestinal (GI) endoscopy procedures are critical for screening, diagnosis, and treatment of a variety of GI disorders. However, like the procedures in other medical disciplines, they are a source of environmental waste generation and energy consumption. METHODS: We prospectively collected data on total waste generation, energy consumption, and the role of intraprocedural inventory audit of a single tertiary care academic endoscopy unit over a 2-month period (May-June 2022). Detailed data on items used were collected, including procedure type (esophagogastroduodenoscopy or colonoscopy), accessories, intravenous tubing, biopsy jars, linen, and personal protective equipment use. Data on endoscope reprocessing-related waste generation and energy use in the endoscopy unit (equipment, lights, and computers) were also collected. We used an endoscopy staff-guided auditing and review of the items used during procedures to determine potentially recyclable items going to landfill waste. The waste generated was stratified into biohazardous, nonbiohazardous, or potentially recyclable items. RESULTS: A total of 450 consecutive procedures were analyzed for total waste management (generation and reprocessing) and energy consumption. The total waste generated during the study period was 1398.6 kg (61.6% directly going to landfill, 33.3% biohazard waste, and 5.1% sharps), averaging 3.03 kg/procedure. The average waste directly going to landfill was 219 kg per 100 procedures. The estimated total annual waste generation approximated the size of 2 football fields (1-foot-high layered waste). Endoscope reprocessing generated 194 gallons of liquid waste per day, averaging 13.85 gallons per procedure. Total energy consumption in the endoscopy unit was 277.1 kW·h energy per day; for every 100 procedures, amounting to 1200 miles of distance traveled by an average fuel efficiency car. The estimated carbon footprint for every 100 GI procedures was 1501 kg carbon dioxide (CO2) equivalent (= 1680 lbs of coal burned), which would require 1.8 acres of forests to sequester. The recyclable waste audit and review demonstrated that 20% of total waste consisted of potentially recyclable items (8.6 kg/d) that could be avoided by appropriate waste segregation of these items. CONCLUSIONS: On average, every 100 GI endoscopy procedures (esophagogastroduodenoscopy/colonoscopy) are associated with 303 kg of solid waste and 1385 gallons of liquid waste generation, and 1980 kW·h energy consumption. Potentially recyclable materials account for 20% of the total waste. These data could serve as an actionable model for health systems to reduce total waste generation and decrease landfill waste and water waste toward environmentally sustainable endoscopy units.

Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India.

BACKGROUND: Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS: 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION: We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Computer-Aided Diagnosis for Leaving Colorectal Polyps In Situ : A Systematic Review and Meta-analysis.

BACKGROUND: Computer-aided diagnosis (CADx) allows prediction of polyp histology during colonoscopy, which may reduce unnecessary removal of nonneoplastic polyps. However, the potential benefits and harms of CADx are still unclear. PURPOSE: To quantify the benefit and harm of using CADx in colonoscopy for the optical diagnosis of small (≤5-mm) rectosigmoid polyps. DATA SOURCES: Medline, Embase, and Scopus were searched for articles published before 22 December 2023. STUDY SELECTION: Histologically verified diagnostic accuracy studies that evaluated the real-time performance of physicians in predicting neoplastic change of small rectosigmoid polyps without or with CADx assistance during colonoscopy. DATA EXTRACTION: The clinical benefit and harm were estimated on the basis of accuracy values of the endoscopist before and after CADx assistance. The certainty of evidence was assessed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) framework. The outcome measure for benefit was the proportion of polyps predicted to be nonneoplastic that would avoid removal with the use of CADx. The outcome measure for harm was the proportion of neoplastic polyps that would be not resected and left in situ due to an incorrect diagnosis with the use of CADx. Histology served as the reference standard for both outcomes. DATA SYNTHESIS: Ten studies, including 3620 patients with 4103 small rectosigmoid polyps, were analyzed. The studies that assessed the performance of CADx alone (9 studies; 3237 polyps) showed a sensitivity of 87.3% (95% CI, 79.2% to 92.5%) and specificity of 88.9% (CI, 81.7% to 93.5%) in predicting neoplastic change. In the studies that compared histology prediction performance before versus after CADx assistance (4 studies; 2503 polyps), there was no difference in the proportion of polyps predicted to be nonneoplastic that would avoid removal (55.4% vs. 58.4%; risk ratio [RR], 1.06 [CI, 0.96 to 1.17]; moderate-certainty evidence) or in the proportion of neoplastic polyps that would be erroneously left in situ (8.2% vs. 7.5%; RR, 0.95 [CI, 0.69 to 1.33]; moderate-certainty evidence). LIMITATION: The application of optical diagnosis was only simulated, potentially altering the decision-making process of the operator. CONCLUSION: Computer-aided diagnosis provided no incremental benefit or harm in the management of small rectosigmoid polyps during colonoscopy. PRIMARY FUNDING SOURCE: European Commission. (PROSPERO: CRD42023402197).

Utilizing human cerebral organoids to model breast cancer brain metastasis in culture.

BACKGROUND: Metastasis, the spread, and growth of malignant cells at secondary sites within a patient's body, accounts for over 90% of cancer-related mortality. Breast cancer is the most common tumor type diagnosed and the leading cause of cancer lethality in women in the United States. It is estimated that 10-16% breast cancer patients will have brain metastasis. Current therapies to treat patients with breast cancer brain metastasis (BCBM) remain palliative. This is largely due to our limited understanding of the fundamental molecular and cellular mechanisms through which BCBM progresses, which represents a critical barrier for the development of efficient therapies for affected breast cancer patients. METHODS: Previous research in BCBM relied on co-culture assays of tumor cells with rodent neural cells or rodent brain slice ex vivo. Given the need to overcome the obstacle for human-relevant host to study cell-cell communication in BCBM, we generated human embryonic stem cell-derived cerebral organoids to co-culture with human breast cancer cell lines. We used MDA-MB-231 and its brain metastatic derivate MDA-MB-231 Br-EGFP, other cell lines of MCF-7, HCC-1806, and SUM159PT. We leveraged this novel 3D co-culture platform to investigate the crosstalk of human breast cancer cells with neural cells in cerebral organoid. RESULTS: We found that MDA-MB-231 and SUM159PT breast cancer cells formed tumor colonies in human cerebral organoids. Moreover, MDA-MB-231 Br-EGFP cells showed increased capacity to invade and expand in human cerebral organoids. CONCLUSIONS: Our co-culture model has demonstrated a remarkable capacity to discern the brain metastatic ability of human breast cancer cells in cerebral organoids. The generation of BCBM-like structures in organoid will facilitate the study of human tumor microenvironment in culture.

Functional studies of lung cancer GWAS beyond association.

Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately 45 genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of the current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.

Effect of a phthalate derivative purified from Bacillus zhangzhouensis SK4 on quorum sensing regulated virulence factors of Pseudomonas aeruginosa.

Pseudomonas aeruginosa causes life-threatening diseases and is resistant to almost all conventional antibiotics. The quorum sensing (QS) system of P. aeruginosa contributes to many pathogenic factors some of which are pigment production, motility, and biofilm. The disruption of quorum sensing system may be an impactful strategy to deal with infections. The present study investigates the anti-quorum sensing property of a bioactive molecule extracted from marine epibiotic bacteria present on the surface of seaweeds. Among all the isolates tested against monitor strain Chromobacterium violaceum (MTCC 2656), the one with the highest activity was identified as Bacillus zhangzhouensis SK4. The culture supernatant was extracted with chloroform which was then partially purified by TLC and column chromatography. The probable anti-QS compound was identified as 1,2-benzenedicarboxylic acid, bis (2-methylpropyl ester) by GC-MS and NMR analysis. The treatment of P. aeruginosa MCC 3457 with the lead compound resulted in the reduced production of pyocyanin, rhamnolipids, exopolysaccharide, biofilm, and motility. The observations of light and scanning electron microscopy also supported the biofilm inhibition. The lead compound showed synergism with the meropenem antibiotic and significantly reduced MIC. The molecular docking and pharmacokinetics study predicted 1, 2-benzenedicarboxylic acid, bis (2-methylpropyl ester), a phthalate derivative as a good drug candidate. The molecular dynamics study was also performed to check the stability of the lead compound and LasR complex. Further, lead compounds did not exhibit any cytotoxicity when tested on human embryonic kidney cells. As per our knowledge, this is the first report on the anti-QS activity of B. zhangzhouensis SK4, indicating that epibiotic bacteria can be a possible source of novel compounds to deal with the multidrug resistance phenomenon.

Analyzing methods for reducing recurrence rates after EMR of large nonpedunculated colorectal polyps: an indirect pairwise comparison.

BACKGROUND AND AIMS: Despite advances in EMR techniques, a high polyp recurrence rate remains a challenge. Due to the scarcity of direct comparisons, we performed an indirect comparison of conventional EMR (EMR alone), underwater EMR (U-EMR), and EMR + adjuvant thermal ablation of polypectomy margins to assess polyp recurrence rates. METHODS: Electronic databases were searched from inception to January 12, 2023, for studies reporting polyp recurrence rates after EMR for large nonpedunculated polyps (>15 mm) with or without adjuvant techniques (snare tip soft coagulation [STSC]/argon plasma coagulation [APC]). An indirect comparison was performed by using the frequentist method. The p-score was calculated to identify preferred intervention. Publication bias was assessed by using a comparison-adjusted funnel plot. RESULTS: A total of 9 full articles were identified. On direct comparisons, EMR + STSC had 82% reduced odds (odds ratio, .18; 95% confidence interval, .13-.26; P < .001), whereas U-EMR alone had 77% reduced odds (odds ratio, .23; 95% confidence interval, .08-.67; P = .007) of polyp recurrence compared with EMR alone. On indirect comparison, all interventions had significantly lower odds of polyp recurrence compared with EMR alone. The p-score ranking showed that EMR + STSC seems a potential first method in reducing the odds of polyp recurrence, followed by U-EMR, EMR + APC, and EMR alone. CONCLUSIONS: EMR + STSC seems to provide favorable odds for reducing polyp recurrence postresection for large nonpedunculated polyps. Standardization of methods to detect residual polyp and prevent polyp recurrence at the time of EMR are required.

Endoscopic Submucosal Dissection and Endoscopic Mucosal Resection for Barrett's Associated Neoplasia: A Systematic Review and Meta-analysis of the Published Literature.

Introduction The role of endoscopic submucosal dissection (ESD) in the treatment of Barrett's associated neoplasia (BEN) has been evolving. We examined the efficacy and safety of ESD and EMR for BEN. Methods A database search was performed for studies reporting efficacy and safety outcomes of ESD and EMR for BEN. Pooled proportional and comparative meta-analyses were performed. Results 47 studies (23 ESD, 19 EMR, and 5 comparative) were included. Mean lesion size for ESD and EMR were 22.5 mm and 15.8 mm respectively. Majority of lesions were Paris type IIa. Pooled analysis for ESD showed en-bloc resection, R0 resection, curative resection, and local recurrence rates of 98%, 78%, 65%, and 2%, respectively. Complete eradication of dysplasia (CE-D) and complete eradication of intestinal metaplasia (CE-IM) were achieved in 94% and 59% of cases. Pooled rates of perforation, intraprocedural bleeding (IPB), delayed bleeding (DB), and stricture were 1%, 1%, 2%, and 10%, respectively. Pooled analysis for EMR showed en-bloc resection, R0 resection, curative resection, and local recurrence rates of 37%, 67%, 62%, and 6%, respectively. CE-D and CE-IM were achieved in 94% and 76% of cases. Pooled rates of perforation, IPB, DB, and stricture were 0.1%, 1%, 0.4%, and 7.7%, respectively. The mean procedure time for ESD and EMR were 111.3 and 22.3 mins respectively. Comparative analysis showed higher en-bloc and R0 resection rates with ESD compared to EMR, with comparable adverse events. Conclusion ESD and EMR both can be employed to treat BEN depending on the lesion type, size, and expertise.

Dizziness and vertigo in patients with tension-type headache: A case-control study.

BACKGROUND: A few studies have demonstrated dizziness and vertigo in patients with tension-type headache (TTH). However, the prevalence and other characteristics of vestibular symptoms in TTH has not been studied in a systemic manner so far. The aim of the study was to see the prevalence of vestibular symptoms in patients with tension-type headache as compared with controls. METHODS: This case-control study included 100 TTH patients and 100 controls who do not have significant history of headaches. RESULTS: Vestibular symptoms (Vertigo, dizziness, vestibulovisual or postural symptom) were experienced by 25% of patients with TTH and 10% in the control group (Odd Ratio = 3.0 [95% CI, 1.4-6.6], P = .006). The vestibular symptoms were statistically more in patients with chronic tension-type headache (CTTH) than episodic TTH (67% vs 9%. 9, P5 = < 0.005). Hospital Anxiety and Depression score (HAD-A and HAD-D) scores in patients with TTH with vestibular symptoms were significantly higher than TTH without vestibular symptoms- HAD-A (5.1 ± 1.7 vs 4.0 ± 1.5, P = 0.002) and HAD-D(5.8 ± 2.1 vs 4.2 ± 1.9, P = < 0.001). Phonophobia was also more frequent in TTH patients with vertigo (42% vs.13%, P5 = 0.005). CONCLUSION: Vestibular symptoms may be more common in patients TTH than control. The prevalence of vestibular symptoms depends on the frequency of TTH.

Microwave-induced one-pot synthesis of 3-imidazolyl indole clubbed 1,2,3-triazole hybrids as antiproliferative agents and density functional theory study.

Herein, we outline a highly efficient PEG-4000-mediated one-pot three-component reaction for the synthesis of 3-imidazolyl indole clubbed 1,2,3-triazole derivatives (5a-r) at up to 96% yield as antiproliferative agents. This three-component protocol offers the advantages of an environmentally benign reaction, excellent yield, quick response time, and operational simplicity triggered by the copper catalyst under microwave irradiation. All the synthesized compounds were tested for antiproliferative activity against six human solid tumor cell lines, that is, A549 and SW1573 (nonsmall cell lung), HBL100 and T-47D (breast), HeLa (cervix), and WiDr (colon). Among them, six compounds, 5g-j, 5m, and 5p, demonstrated effective antiproliferative action with GI50 values under 10 µM. Furthermore, density functional theory (DFT) calculations were performed for all the synthesized molecules through geometry optimizations, frontier molecular orbital approach, and molecular electrostatic potential (MESP). The theoretical DFT calculation was performed using the DFT/B3LYP/6-31+G (d,p) basis set. Moreover, the biological reactivity of all the representative synthesized molecules was compared with the theoretically calculated quantum chemical descriptors and MESP 3D plots. We also investigated the drug-likeness characteristic and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction. In general, our approach enables environmentally friendly access to 3-imidazolyl indole clubbed 1,2,3-triazole derivatives as prospective antiproliferative agents.

ECRG2/SPINK7 Tumor Suppressor as Modulator of DNA Damage Response.

Esophageal Cancer-Related Gene 2 (ECRG2), also known as Serine Peptidase Inhibitor Kazal type 7 (SPINK7), is a novel tumor suppressor gene from the SPINK family of genes that exhibits anticancer potential. ECRG2 was originally identified during efforts to discover genes involved in esophageal tumorigenesis. ECRG2 was one of those genes whose expression was absent or reduced in primary human esophageal cancers. Additionally, absent or reduced ECRG2 expression was also noted in several other types of human malignancies. ECRG2 missense mutations were identified in various primary human cancers. It was reported that a cancer-derived ECRG2 mutant (valine to glutamic acid at position 30) failed to induce cell death and caspase activation triggered by DNA-damaging anticancer drugs. Furthermore, ECRG2 suppressed cancer cell proliferation in cultured cells and grafted tumors in animals and inhibited cancer cell migration/invasion and metastasis. ECRG2 also was identified as a negative regulator of Hu-antigen R (HuR), an oncogenic RNA-binding protein that is known to regulate mRNA stability and the expression of transcripts corresponding to many cancer-related genes. ECRG2 function is important also for the regulation of inflammatory responses and the maintenance of epithelial barrier integrity in the esophagus. More recently, ECRG2 was discovered as one of the newest members of the pro-apoptotic transcriptional targets of p53. Two p53-binding sites (BS-1 and BS-2) were found within the proximal region of the ECRG2 gene promoter; the treatment of DNA-damaging agents in cancer cells significantly increased p53 binding to the ECRG2 promoter and triggered a strong ECRG2 promoter induction following DNA damage. Further, the genetic depletion of ECRG2 expression significantly impeded apoptotic cell death induced by DNA damage and wild-type p53 in cancer cells. These findings suggest that the loss of ECRG2 expression, commonly observed in human cancers, could play important roles in conferring anticancer drug resistance in human cancers. Thus, ECRG2 is a novel regulator in DNA damage-induced cell death that may also be a potential target for anticancer therapeutics.

Using landfill leachate to indicate the chemical and biochemical activities in elevated temperature landfills.

Landfill leachate properties contain important information and can be a unique indicator for the chemical and biochemical activities in landfills. In the recent decade, more landfills are experiencing elevated temperature, causing an imbalance in the decomposition of solid waste and affecting the properties of the landfill leachate. This study analyzes the properties of leachate from two landfills that were experiencing elevated temperature (ETLFs), samples were collected from both elevated temperature impacted and non-impacted areas in each landfill. The accumulation of volatile fatty acids (VFA) in leachates from elevated temperature impacted areas of both landfill sites revealed that methanogenesis was inhibited by the elevated temperature, which was further confirmed by the more acidic pH, higher H/C elemental ratio, and lower degree of aromaticity of the elevated temperature impacted leachates. Also, carbohydrates depletion indicated possible enhancement of hydrolysis and acidogenesis by elevated temperature, which was supported by compositional comparison of isolated acidic species by negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) at 21 T derived from both elevated temperature impacted and non-impacted areas in the same landfill site. Furthermore, leachate organics fractionation showed that leachates not impacted by elevated temperature contain less hydrophilic fraction and more humic fraction than elevated temperature-impacted leachates for both ETLFs.

Intraoperative navigation system use increases accuracy of glenoid component inclination but not functional outcomes in reverse total shoulder arthroplasty: a prospective comparative study.

BACKGROUND: While the use of computer-assisted navigation systems in prosthetic implantation is steadily increasing, its utility in reverse shoulder arthroplasty (RSA) remains unclear. The purpose of this study was to evaluate the clinical utility of an intraoperative navigation system in patients undergoing RSA. MATERIALS AND METHODS: Patients undergoing navigated or standard RSA at a single institution between September 2020 and December 2021 were prospectively enrolled. Exclusion criteria included noncompliance with study procedures or humeral fracture. Outcome measures included postoperative version and inclination, range of motion (ROM), complications, and patient-reported outcome measurements (PROMs: American Shoulder and Elbow Surgeons score [ASES], Disabilities of the Arm, Shoulder, and Hand score [DASH], Simple Shoulder Test [SST], and Visual Analog Scale [VAS]) at final follow-up. RESULTS: The final cohort contained 16 patients with navigation and 17 with standard RSA at a mean follow-up of 16 months (range 12-18 months). Average age was 72 years (range 66-80 years), 8 male (24%) and 25 female (76%). There were no differences in demographics between groups (p > 0.05). At baseline, the navigated group had a greater proportion of Walch B1 and B2 glenoids (p = 0.04). There were no differences between groups regarding baseplate type and native/planned/postoperative glenoid version and inclination. In both groups, planned and postoperative versions were not significantly different (p = 0.76). Patients who did not have navigation demonstrated significant differences between planned and postoperative inclination (p = 0.04), while those with navigation did not (p = 0.09). PROM scores did not differ between groups at final follow-up for SST (p = 0.64), DASH (p = 0.38), ASES (p = 0.77), or VAS (p = 0.1). No difference in final ROM was found between groups (p > 0.05). Over 50% of all screws in both groups were positioned outside the second cortex (p = 0.37), albeit with no complications. CONCLUSIONS: There were no statistically significant differences in ROM, PROMs, and satisfaction between patients receiving computer-navigated and standard RSA at a short-term follow-up. Despite more severe preoperative glenoid erosion in the navigated group, all patients were able to achieve an appropriate neutral axis postoperatively. The cost effectiveness and appropriate use of computer-navigated RSA warrant specific investigation in future studies. LEVEL OF EVIDENCE: II, prospective cohort study. TRIAL REGISTRATION: 9/1/2020 to 12/31/2021.

Evaluation of the efficiency of thermostable L-asparaginase from B. licheniformis UDS-5 for acrylamide mitigation during preparation of French fries.

A thermostable L-asparaginase was produced from Bacillus licheniformis UDS-5 (GenBank accession number, OP117154). The production conditions were optimized by the Plackett Burman method, followed by the Box Behnken method, where the enzyme production was enhanced up to fourfold. It secreted L-asparaginase optimally in the medium, pH 7, containing 0.5% (w/v) peptone, 1% (w/v) sodium chloride, 0.15% (w/v) beef extract, 0.15% (w/v) yeast extract, 3% (w/v) L-asparagine at 50 °C for 96 h. The enzyme, with a molecular weight of 85 kDa, was purified by ion exchange chromatography and size exclusion chromatography with better purification fold and percent yield. It displayed optimal catalysis at 70 °C in 20 mM Tris-Cl buffer, pH 8. The purified enzyme also exhibited significant salt tolerance too, making it a suitable candidate for the food application. The L-asparaginase was employed at different doses to evaluate its ability to mitigate acrylamide, while preparing French fries without any prior treatment. The salient attributes of B. licheniformis UDS-5 L-asparaginase, such as greater thermal stability, salt stability and acrylamide reduction in starchy foods, highlights its possible application in the food industry.

Epigenetic modification of m6A regulator proteins in cancer.

Divergent N6-methyladenosine (m6A) modifications are dynamic and reversible posttranscriptional RNA modifications that are mediated by m6A regulators or m6A RNA methylation regulators, i.e., methyltransferases ("writers"), demethylases ("erasers"), and m6A-binding proteins ("readers"). Aberrant m6A modifications are associated with cancer occurrence, development, progression, and prognosis. Numerous studies have established that aberrant m6A regulators function as either tumor suppressors or oncogenes in multiple tumor types. However, the functions and mechanisms of m6A regulators in cancer remain largely elusive and should be explored. Emerging studies suggest that m6A regulators can be modulated by epigenetic modifications, namely, ubiquitination, SUMOylation, acetylation, methylation, phosphorylation, O-GlcNAcylation, ISGylation, and lactylation or via noncoding RNA action, in cancer. This review summarizes the current roles of m6A regulators in cancer. The roles and mechanisms for epigenetic modification of m6A regulators in cancer genesis are segregated. The review will improve the understanding of the epigenetic regulatory mechanisms of m6A regulators.

Lack of Effectiveness of Computer Aided Detection for Colorectal Neoplasia: A Systematic Review and Meta-Analysis of Nonrandomized Studies.

BACKGROUND AND AIMS: Benefits of computer-aided detection (CADe) in detecting colorectal neoplasia were shown in many randomized trials in which endoscopists' behavior was strictly controlled. However, the effect of CADe on endoscopists' performance in less-controlled setting is unclear. This systematic review and meta-analyses were aimed at clarifying benefits and harms of using CADe in real-world colonoscopy. METHODS: We searched MEDLINE, EMBASE, Cochrane, and Google Scholar from inception to August 20, 2023. We included nonrandomized studies that compared the effectiveness between CADe-assisted and standard colonoscopy. Two investigators independently extracted study data and quality. Pairwise meta-analysis was performed utilizing risk ratio for dichotomous variables and mean difference (MD) for continuous variables with a 95% confidence interval (CI). RESULTS: Eight studies were included, comprising 9782 patients (4569 with CADe and 5213 without CADe). Regarding benefits, there was a difference in neither adenoma detection rate (44% vs 38%; risk ratio, 1.11; 95% CI, 0.97 to 1.28) nor mean adenomas per colonoscopy (0.93 vs 0.79; MD, 0.14; 95% CI, -0.04 to 0.32) between CADe-assisted and standard colonoscopy, respectively. Regarding harms, there was no difference in the mean non-neoplastic lesions per colonoscopy (8 studies included for analysis; 0.52 vs 0.47; MD, 0.14; 95% CI, -0.07 to 0.34) and withdrawal time (6 studies included for analysis; 14.3 vs 13.4 minutes; MD, 0.8 minutes; 95% CI, -0.18 to 1.90). There was a substantial heterogeneity, and all outcomes were graded with a very low certainty of evidence. CONCLUSION: CADe in colonoscopies neither improves the detection of colorectal neoplasia nor increases burden of colonoscopy in real-world, nonrandomized studies, questioning the generalizability of the results of randomized trials.

Prolonged Gastrointestinal Manifestations After Recovery From COVID-19.

BACKGROUND & AIMS: Acute enteric infections are well known to result in long-term gastrointestinal (GI) disorders. Although COVID-19 is principally a respiratory illness, it demonstrates significant GI tropism, possibly predisposing to prolonged gut manifestations. We aimed to examine the long-term GI impact of hospitalization with COVID-19. METHODS: Nested within a large-scale observational cohort study of patients hospitalized with COVID-19 across North America, we performed a follow-up survey of 530 survivors 12-18 months later to assess for persistent GI symptoms and their severity, and for the development of disorders of gut-brain interaction (DGBIs). Eligible patients were identified at the study site level and surveyed electronically. The survey instrument included the Rome IV Diagnostic Questionnaire for DGBI, a rating scale of 24 COVID-related symptoms, the Gastrointestinal Symptoms Rating Scale, and the Impact of Events-Revised trauma symptom questionnaire (a measure of posttraumatic stress associated with the illness experience). A regression analysis was performed to explore the factors associated with GI symptom severity at follow-up. RESULTS: Of the 530 invited patients, 116 responded (52.6% females; mean age, 55.2 years), and 73 of those (60.3%) met criteria for 1 or more Rome IV DGBI at follow-up, higher than the prevalence in the US general population (P < .0001). Among patients who experienced COVID-related GI symptoms during the index hospitalization (abdominal pain, nausea, vomiting, or diarrhea), 42.1% retained at least 1 of these symptoms at follow-up; in comparison, 89.8% of respondents retained any (GI or non-GI) COVID-related symptom. The number of moderate or severe GI symptoms experienced during the initial COVID-19 illness by self-report correlated with the development of DGBI and severity of GI symptoms at follow-up. Posttraumatic stress disorder (Impact of Events-Revised score ≥33) related to the COVID-19 illness experience was identified in 41.4% of respondents and those individuals had higher DGBI prevalence and GI symptom severity. Regression analysis revealed that higher psychological trauma score (Impact of Events-Revised) was the strongest predictor of GI symptom severity at follow-up. CONCLUSIONS: In this follow-up survey of patients 12-18 months after hospitalization with COVID-19, there was a high prevalence of DGBIs and persistent GI symptoms. Prolonged GI manifestations were associated with the severity of GI symptoms during hospitalization and with the degree of psychological trauma related to the illness experience.

Impact of withdrawal time on adenoma detection rate: results from a prospective multicenter trial.

BACKGROUND AND AIMS: Performing a high-quality colonoscopy is critical for optimizing the adenoma detection rate (ADR). Colonoscopy withdrawal time (a surrogate measure) of ≥6 minutes is recommended; however, a threshold of a high-quality withdrawal and its impact on ADR are not known. METHODS: We examined withdrawal time (excluding polyp resection and bowel cleaning time) of subjects undergoing screening and/or surveillance colonoscopy in a prospective, multicenter, randomized controlled trial. We examined the relationship of withdrawal time in 1-minute increments on ADR and reported odds ratio (OR) with 95% confidence intervals. Linear regression analysis was performed to assess the maximal inspection time threshold that impacts the ADR. RESULTS: A total of 1142 subjects (age, 62.3 ± 8.9 years; 80.5% men) underwent screening (45.9%) or surveillance (53.6%) colonoscopy. The screening group had a median withdrawal time of 9.0 minutes (interquartile range [IQR], 3.3) with an ADR of 49.6%, whereas the surveillance group had a median withdrawal time of 9.3 minutes (IQR, 4.3) with an ADR of 63.9%. ADR correspondingly increased for a withdrawal time of 6 minutes to 13 minutes, beyond which ADR did not increase (50.4% vs 76.6%, P < .01). For every 1-minute increase in withdrawal time, there was 6% higher odds of detecting an additional subject with an adenoma (OR, 1.06; 95% confidence interval, 1.02-1.10; P = .004). CONCLUSIONS: Results from this multicenter, randomized controlled trial underscore the importance of a high-quality examination and efforts required to achieve this with an incremental yield in ADR based on withdrawal time. (Clinical trial registration number: NCT03952611.).

Long-term outcomes of peroral endoscopic myotomy for achalasia: a systematic review and meta-analysis.

BACKGROUND: The long-term outcomes of esophageal peroral endoscopic myotomy (POEM) are still unknown. METHODS: We searched electronic databases (MEDLINE/PubMed, EMBASE, Scopus) for studies assessing outcomes after POEM for esophageal achalasia with a minimum median follow-up duration of 36 months. Pooled rates of clinical success and postoperative reflux were calculated and compared with the same values at 12/24/36 months when available. Subgroup analyses were performed to explore the interstudy heterogeneity. RESULTS: From 1528 initial records, 11 studies (2017-2021) were included. A total of 2342 patients (age 48.1 [SD 6.8] years; 50.1 % males) with a median follow-up of 48 months (interquartile range 45-60) were analyzed. The pooled clinical success rate was 87.3 % (95 %CI 83.6 %-91.0 %; I2  = 73.1 %). The symptomatic reflux pooled rate was 22.0 % (95 %CI 14.4 %-29.5 %; I2  = 92.7 %). Three cases of peptic strictures and one Barrett's esophagus were reported. The pooled rate of severe adverse events was 1.5 % (95 %CI 0.5 %-2.5 %; I2  = 52.8 %). CONCLUSIONS: Long-term clinical efficacy of POEM persisted in 87 % of patients with achalasia. Post-POEM symptomatic reflux remained stable over time. The risk for Barrett's esophagus and peptic strictures appeared minimal.