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1. A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples

Author

Chao Zhang, Prashant V. Thakkar, Sarah Ellen Powell, Prateek Sharma, Sreekar Vennelaganti, Doron Betel, and Manish A. Shah

Subjects
gastrointestinal tract, whole genome sequencing, quantitative PCR, microbiome, clinical biopsy, metagenomics, Microbiology, QR1-502
Abstract

Identification of the human microbiome has proven to be of utmost importance with the emerging role of bacteria in various physiological and pathological processes. High throughput sequencing strategies have evolved to assess the composition of the microbiome. To identify possible bias that may exist in the processing of tissue for whole genome sequencing (WGS), it is important to evaluate the extraction method on the overall microbial content and composition. Here we compare two different methods of extraction, homogenization vs. enzymatic lysis, on gastric, esophageal and colorectal biopsies and survey the microbial content and composition using WGS and quantitative PCR (qPCR). We examined total bacterial content using universal 16S rDNA qPCR as well as the abundance of three phyla (Actinobacter, Firmicutes, Bacteroidetes) and one genus (Fusobacterium). We found minimal differences between the two extraction methods in the overall community structure. Furthermore, based on our qPCR analysis, neither method demonstrated preferential extraction of any particular clade of bacteria, nor significantly altered the detection of Gram-positive or Gram-negative organisms. However, although the overall microbial composition remained very similar and the most prevalent bacteria could be detected effectively using either method, the precise community structure and microbial abundances between the two methods were different, primarily due to variations in detection of low abundance genus. We also demonstrate that the homogenization extraction method provides higher microbial DNA content and higher read counts from human tissue biopsy samples of the gastrointestinal tract.

Published
2019
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2. Progression from low-grade dysplasia to malignancy in patients with Barrett's esophagus diagnosed by two or more pathologists

Author

Prashanth Vennelaganti, Sowmya Dharmapuri, Jaymon Patel, Harsha Moole, Achuta Uppu, Zohair Ahmed, Naveen Bondalapati, Srinivas R. Puli, Raghuveer R. Boddireddy, Abhiram Duvvuri, Vishnu Moole, Pratyusha Yedama, and Sreekar Vennelaganti

Subjects
Male, medicine.medical_specialty, Esophageal Neoplasms, education, Esophageal adenocarcinoma, Adenocarcinoma, Malignancy, digestive system, Gastroenterology, 03 medical and health sciences, Barrett Esophagus, 0302 clinical medicine, Internal medicine, otorhinolaryngologic diseases, Medicine, Barrett’s esophagus, Humans, In patient, Esophagus, Low grade dysplasia, neoplasms, Aged, Observer Variation, Hyperplasia, High grade dysplasia, business.industry, Annual incidence of progression, General Medicine, Middle Aged, medicine.disease, digestive system diseases, Pathologists, surgical procedures, operative, medicine.anatomical_structure, Dysplasia, 030220 oncology & carcinogenesis, Barrett's esophagus, Systematic review, Disease Progression, 030211 gastroenterology & hepatology, Female, business, Precancerous Conditions, Meta-Analysis
Abstract

AIM To evaluate annual incidence of low grade dysplasia (LGD) progression to high grade dysplasia (HGD) and/or esophageal adenocarcinoma (EAC) when diagnosis was made by two or more expert pathologists. METHODS Studies evaluating the progression of LGD to HGD or EAC were included. The diagnosis of LGD must be made by consensus of two or more expert gastrointestinal pathologists. Articles were searched in Medline, Pubmed, and Embase. Pooled proportions were calculated using fixed and random effects model. Heterogeneity among studies was assessed using the I2 statistic. RESULTS Initial search identified 721 reference articles, of which 53 were selected and reviewed. Twelve studies (n = 971) that met the inclusion criteria were included in this analysis. Among the total original LGD diagnoses in the included studies, only 37.49% reached the consensus LGD diagnosis after review by two or more expert pathologists. Total follow up period was 1532 patient-years. In the pooled consensus LGD patients, the annual incidence rate (AIR) of progression to HGD and or EAC was 10.35% (95%CI: 7.56-13.13) and progression to EAC was 5.18% (95%CI: 3.43-6.92). Among the patients down staged from original LGD diagnosis to No-dysplasia Barrett’s esophagus, the AIR of progression to HGD and EAC was 0.65% (95%CI: 0.49-0.80). Among the patients down staged to Indefinite for dysplasia, the AIR of progression to HGD and EAC was 1.42% (95%CI: 1.19-1.65). In patients with consensus HGD diagnosis, the AIR of progression to EAC was 28.63% (95%CI: 13.98-43.27). CONCLUSION When LGD is diagnosed by consensus agreement of two or more expert pathologists, its progression towards malignancy seems to be at least three times the current estimates, however it could be up to 20 times the current estimates. Biopsies of all Barrett’s esophagus patients with LGD should be reviewed by two expert gastroenterology pathologists. Follow-up strict surveillance programs should be in place for these patients.

Published
2016

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