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.

Accuracy of Computer-aided Diagnosis in Colonoscopy Varies According to Polyp Location: A Systematic Review and Meta-analysis.

BACKGROUND & AIMS: Computer-aided diagnosis (CADx) assists endoscopists in differentiating between neoplastic and non-neoplastic polyps during colonoscopy. This study aimed to evaluate the impact of polyp location (proximal vs. distal colon) on the diagnostic performance of CADx for ≤5 mm polyps. METHODS: We searched for studies evaluating the performance of real-time CADx alone (ie, independently of endoscopist judgement) for predicting the histology of colorectal polyps ≤5 mm. The primary endpoints were CADx sensitivity and specificity in the proximal and distal colon. Secondary outcomes were the negative predictive value (NPV), positive predictive value (PPV), and the accuracy of the CADx alone. Distal colon was limited to the rectum and sigmoid. RESULTS: We included 11 studies for analysis with a total of 7782 polyps ≤5 mm. CADx specificity was significantly lower in the proximal colon compared with the distal colon (62% vs 85%; risk ratio (RR), 0.74; 95% confidence interval [CI], 0.72-0.84). Conversely, sensitivity was similar (89% vs 87%); RR, 1.00; 95% CI, 0.97-1.03). The NPV (64% vs 93%; RR, 0.71; 95% CI, 0.64-0.79) and accuracy (81% vs 86%; RR, 0.95; 95% CI, 0.91-0.99) were significantly lower in the proximal than distal colon, whereas PPV was higher in the proximal colon (87% vs 76%; RR, 1.11; 95% CI, 1.06-1.17). CONCLUSION: The diagnostic performance of CADx for polyps in the proximal colon is inadequate, exhibiting significantly lower specificity compared with its performance for distal polyps. Although current CADx systems are suitable for use in the distal colon, they should not be employed for proximal polyps until more performant systems are developed specifically for these lesions.

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.

BACKGROUND: The role of endoscopic submucosal dissection (ESD) in the treatment of Barrett esophagus-associated neoplasia (BEN) has been evolving. We examined the efficacy and safety of ESD and endoscopic mucosal resection (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, 5 comparative) were included. The mean lesion sizes for ESD and EMR were 22.5 mm and 15.8 mm, respectively; most lesions were Paris type IIa. For ESD, pooled analysis showed rates of en bloc, R0, and curative resection, and local recurrence of 98%, 78%, 65%, and 2%, respectively. Complete eradication of dysplasia and intestinal metaplasia were achieved in 94% and 59% of cases, respectively. Pooled rates of perforation, intraprocedural bleeding, delayed bleeding, and stricture were 1%, 1%, 2%, and 10%, respectively. For EMR, pooled analysis showed rates of en bloc, R0, and curative resection, and local recurrence of 37%, 67%, 62%, and 6%, respectively. Complete eradication of dysplasia and intestinal metaplasia were achieved in 94% and 75% of cases. Pooled rates of perforation, intraprocedural bleeding, delayed bleeding, and stricture were 0.1%, 1%, 0.4%, and 8%, respectively. The mean procedure times for ESD and EMR were 113 and 22 minutes, respectively. Comparative analysis showed higher en bloc and R0 resection rates with ESD compared with EMR, with comparable adverse events. CONCLUSION: ESD and EMR can both be employed to treat BEN depending on lesion type and size, and center expertise.