Investigation of long non-coding RNAs in extracellular vesicles from low-volume blood serum specimens of colorectal cancer patients.

Colorectal cancer (CRC) is the second most prevalent cancer type worldwide, which highlights the urgent need for non-invasive biomarkers for its early detection and improved prognosis. We aimed to investigate the patterns of long non-coding RNAs (lncRNAs) in small extracellular vesicles (sEVs) collected from low-volume blood serum specimens of CRC patients, focusing on their potential as diagnostic biomarkers. Our research comprised two phases: an initial exploratory phase involving RNA sequencing of sEVs from 76 CRC patients and 29 healthy controls, and a subsequent validation phase with a larger cohort of 159 CRC patients and 138 healthy controls. Techniques such as dynamic light scattering, transmission electron microscopy, and Western blotting were utilized for sEV characterization. Optimized protocol for sEV purification, RNA isolation and preamplification was applied to successfully sequence the RNA content of sEVs and validate the results by RT-qPCR. We successfully isolated sEVs from blood serum and prepared sequencing libraries from a low amount of RNA. High-throughput sequencing identified differential levels of 460 transcripts between CRC patients and healthy controls, including mRNAs, lncRNAs, and pseudogenes, with approximately 20% being lncRNAs, highlighting several tumor-specific lncRNAs that have not been associated with CRC development and progression. The validation phase confirmed the upregulation of three lncRNAs (NALT1, AL096828, and LINC01637) in blood serum of CRC patients. This study not only identified lncRNA profiles in a population of sEVs from low-volume blood serum specimens of CRC patients but also highlights the value of innovative techniques in biomolecular research, particularly for the detection and analysis of low-abundance biomolecules in clinical samples. The identification of specific lncRNAs associated with CRC provides a foundation for future research into their functional roles in cancer development and potential clinical applications.

16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling.

16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1-V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1-V2M primers. Moreover, the V1-V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1-V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.

Does Pathological Complete Response after Neoadjuvant Therapy Influence Postoperative Morbidity in Rectal Cancer after Transanal Total Mesorectal Excision?

PURPOSE: It is still unclear if pathological complete response (pCR) after neoadjuvant chemoradiotherapy (CRT) in patients treated for rectal cancer causes worse postoperative outcomes, especially after transanal total mesorectal excision (TaTME). Worse postoperative outcomes might be an argument for an organ preserving watch and wait strategy in fragile patients and patients with comorbidities. The aim of this study is to evaluate whether patients treated for rectal cancer who had pCR to neoadjuvant therapy develop worse postoperative outcomes after TaTME than patients without complete response. METHODS: Comparative retrospective analysis (with nearest neighbor matching algorithm) of postoperative outcomes in two groups of patients, with pCR, n = 15 and without pCR (non-pCR), n = 57. All patients were operated on only by one surgical approach, TaTME, for middle and distal rectal tumors. All procedures were performed by one surgical team between 2014 and 2020 at the University Hospital Brno in Czech Republic. RESULTS: Overall morbidity was comparable between the groups (pCR group - 53.8% vs. non-pCR - 38.6%, p = 0.381). Anastomotic leak (AL) was observed in 33.3% of patients with pCR and in 17.5% of patients in the non-pCR group without statistical significance (p = 0.281). CONCLUSION: In conclusion, pathological complete response after neoadjuvant therapy does not appear to affect postoperative morbidity in rectal cancer after TaTME. Therefore, in patients with complete response who are not adherent to W&W surveillance, surgical resection can be perform without increased postoperative complications.

Malignant complications of celiac disease: a case series and review of the literature.

BACKGROUND: Celiac disease is an immune-mediated enteropathy triggered by gluten in genetically susceptible individuals. Diagnosis is based on evaluating specific autoantibodies and histopathologic findings of duodenal biopsy specimens. The only therapy for celiac disease is a gluten-free diet. Celiac disease can be complicated by malnutrition, other autoimmune diseases, refractoriness to treatment, and gastrointestinal tumors. This article presents seven cases of malignancies in patients with celiac disease. Its objective is to raise awareness of the malignant complications of celiac disease, leading to earlier diagnosis and improved outcomes. CASE PRESENTATION: Seven cases of malignant complications of celiac disease occurred among 190 patients followed at the Department of Internal Medicine and Gastroenterology, University Hospital Brno from 2014 to 2021. We describe these cases and the presentation, diagnostic process, course, management, and outcomes for each, along with proposed potential risk factors of malignant complications. There was one Caucasian man who was 70 years old and six Caucasian women who were 36, 46, 48, 55, 73, and 82 years old in our cohort. Of the seven cases of malignancies in our cohort, four patients were diagnosed with small bowel adenocarcinoma, one with diffuse large B-cell lymphoma, one with carcinoma of the tongue, and one with colorectal carcinoma. CONCLUSIONS: Malignancies occurred in 3.7% of patients followed up for celiac disease. Awareness of the malignant complications of celiac disease, risk factors, presentation, and disease course could lead to earlier diagnosis and improved outcomes.

Lack of Association between Epidermal Growth Factor or Its Receptor and Reflux Esophagitis, Barrett's Esophagus, and Esophageal Adenocarcinoma: A Case-Control Study.

The epidermal growth factor (EGF) and its receptor (EGFR) gene-gene interactions were shown to increase the susceptibility to esophageal cancer. However, the role of the EGF/EGFR pathway in the development of gastroesophageal reflux disease (GERD) and its complications (reflux esophagitis (RE), Barrett's esophagus (BE), and esophageal adenocarcinoma (EAC)) remains unclear. This association study is aimed at investigating functional EGF and EGFR gene polymorphisms, their mRNA expression in esophageal tissues, and EGF plasma levels in relation to RE, BE, and EAC development in the Central European population. 301 patients with RE/BE/EAC (cases) as well as 98 patients with nonerosive reflux disease (NERD) and 8 healthy individuals (controls) were genotyped for +61 A>G EGF (rs4444903) and +142285 G>A EGFR (rs2227983) polymorphisms using the TaqMan quantitative polymerase chain reaction (qPCR). In random subgroups, the EGF and EGFR mRNA expressions were analyzed by reverse transcription qPCR in esophageal tissue with and without endoscopically visible pathological changes; and the EGF plasma levels were determined by enzyme-linked immunosorbent assay. None of the genotyped SNPs nor EGF-EGFR genotype interactions were associated with RE, BE, or EAC development (p > 0.05). Moreover, mRNA expression of neither EGF nor EGFR differed between samples of the esophageal tissue with and without endoscopically visible pathology (p > 0.05) nor between samples from patients with different diagnoses, i.e., RE, BE, or EAC (p > 0.05). Nevertheless, the lower EGF mRNA expression in carriers of combined genotypes AA +61 EGF (rs4444903) and GG +142285 EGFR (rs2227983; p < 0.05) suggests a possible direct/indirect effect of EGF-EGFR gene interactions on EGF gene expression. In conclusion, EGF and EGFR gene variants and their mRNA/protein expression were not associated with RE, BE or EAC development in the Central European population.

The Use of Confocal Laser Endomicroscopy in Diagnosing Barrett's Esophagus and Esophageal Adenocarcinoma.

Confocal laser endomicroscopy (CLE) is a diagnostic technique that enables real-time microscopic imaging during microscopic examination and evaluation of epithelial structures with 1000-fold magnification. CLE can be used in the diagnosis of various pathologies, in pneumology, and in urology, and it is very widely utilized in gastroenterology, most importantly in the diagnosis of Barrett's esophagus (BE), esophageal adenocarcinoma (EAC), biliary strictures, and cystic pancreatic lesions. A literature search was made in MEDLINE/PubMed and Google Scholar databases while focusing on diagnostics using CLE of BE and EAC. We then examined randomized and observational studies, systematic reviews, and meta-analyses relating to the utilization of CLE in BE and EAC diagnostics. Here, we discuss whether CLE can be a suitable diagnostic method for surveillance of BE. Even though many studies have proven that CLE increases diagnostic accuracy in detecting neoplastic transformation of BE, CLE is still not used as a standard diagnostic tool in BE surveillance due to a deficiency of scientific evidence. More studies and data are needed if CLE is to find a place as a new technique in BE surveillance.

Small bowel adenocarcinoma diagnosed by video capsule endoscopy in a patient with celiac disease: a case report and review of literature.

Celiac disease is an immune mediated entheropathy triggered by gluten in genetically predisposed individuals. Patients with celiac disease are at a higher risk of gastrointestinal malignancies. Diagnosis at an advance stage is one of the factors of an unfavorable prognosis of these complications. Our patient is a woman who was diagnosed with celiac disease at 53 years of age. After two years on a gluten-free diet she developed sideropenic anemia. No source of bleeding was found on the esophagogastroduodenoscopy or colonoscopy. Video capsule endoscopy revealed exulcerated bleeding stenosis in the jejunum, in front of which the capsule lodged. There were no signs of infiltration on simultaneous CT enterography. The patient was operated on and the infiltration of the jejunum was resected. The specimen was evaluated by a histopathologist as a moderately differentiated adenocarcinoma. Due to the risk factors, the patient received adjuvant chemotherapy. The knowledge of the malignant complications of celiac disease, their risk factors and the possibilities of modern enteroscopic methods could help in the early diagnosis and improvement of the prognosis of these diseases. Due to a lack of data and an absence of guidelines, treatment of a small bowel adenocarcinoma is based on an expert agreement and guidelines for colon cancer. Surgical treatment is the only potentially curative option. For stage II with risk factors and stage III adjuvant chemotherapy should be considered.

Confocal laser endomicroscopy in the diagnostics of esophageal diseases: a pilot study.

BACKGROUND: Probebased confocal laser endomicroscopy (pCLE) is a novel diagnostic technique for endoscopy which enables a microscopic view at a cellular resolution in realtime. Endoscopic detection of early neoplasia in the distal esophagus is difficult and often these lesions can be missed. The aim of the pilot study was to obtain characteristic pCLE figures in esophageal diseases for following studies, and to evaluate the possible future role of pCLE in the diagnostics of dysplastic Barretts esophagus (BE) or early esophageal adenocarcinoma (EAC). METHODS: A review of the current literature was performed and previously published pCLE images and classifications of esophageal diseases were searched and studied first. In phase two of the pilot study patients with esophageal diseases such as reflux esophagitis, BE and EAC were enrolled and scheduled for upper endoscopy with pCLE. A healthy cohort was also included. RESULTS: From January 2019 to July 2019, a total of 14 patients were enrolled in this prospective pilot study: 3 patients with reflux esophagitis, 4 with BE, 3 with EAC and 4 persons were included in the healthy cohort. The endoscopy with pCLE was performed and characteristic pCLE figures were obtained. The correct diagnoses based on realtime pCLE were evaluated by an endoscopist in 11 of the 14 cases (78.6 %). CONCLUSION: It was possible to obtain typical pCLE images of esophageal diseases during a standard capassisted endoscopic procedure. pCLE seems to be a feasible new technique in BE surveillance and early neoplastic lesion detection. However, more studies and data on larger number of patients are needed.

Identification and Validation of Circulating Micrornas as Prognostic Biomarkers in Pancreatic Ductal Adenocarcinoma Patients Undergoing Surgical Resection.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and aggressive cancers with a less than 6% five-year survival rate. Circulating microRNAs (miRNAs) are emerging as a useful tool for non-invasive diagnosis and prognosis estimation in the various cancer types, including PDAC. Our study aimed to evaluate whether miRNAs in the pre-operative blood plasma specimen have the potential to predict the prognosis of PDAC patients. In total, 112 PDAC patients planned for surgical resection were enrolled in our prospective study. To identify prognostic miRNAs, we used small RNA sequencing in 24 plasma samples of PDAC patients with poor prognosis (overall survival (OS) < 16 months) and 24 plasma samples of PDAC patients with a good prognosis (OS > 20 months). qPCR validation of selected miRNA candidates was performed in the independent cohort of PDAC patients (n = 64). In the discovery phase of the study, we identified 44 miRNAs with significantly different levels in the plasma samples of the group of good and poor prognosis patients. Among these miRNAs, 23 showed lower levels, and 21 showed higher levels in plasma specimens from PDAC patients with poor prognosis. Eleven miRNAs were selected for the validation, but only miR-99a-5p and miR-365a-3p were confirmed to have significantly lower levels and miR-200c-3p higher levels in plasma samples of poor prognosis cases. Using the combination of these 3-miRNA levels, we were able to identify the patients with poor prognosis with sensitivity 85% and specificity 80% (Area Under the Curve = 0.890). Overall, 3-miRNA prognostic score associated with OS was identified in the pre-operative blood plasma samples of PDAC patients undergoing surgical resection. Following further independent validations, the detection of these miRNA may enable identification of PDAC patients who have no survival benefit from the surgical treatment, which is associated with the high morbidity rates.

Tumor microRNAs Identified by Small RNA Sequencing as Potential Response Predictors in Locally Advanced Rectal Cancer Patients Treated With Neoadjuvant Chemoradiotherapy.

BACKGROUND/AIM: Rectal cancer accounts for approximately one-third of all colorectal cancers. Currently, the standard treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (CRT) with capecitabine or 5-fluorouracil followed by curative surgery. Unfortunately, only 20% of patients with LARC present complete pathological response after CRT, whereas in 20-40% cases the response is poor or absent. The aim of our study was to evaluate whether microRNAs (miRNAs) in tumor biopsy specimen have the potential to predict therapeutic response in LARC patients. PATIENTS AND METHODS: In total 87 LARC patients treated by CRT were enrolled in our prospective study. To identify predictive miRNAs, we used small RNA sequencing in 40 tumor biopsy samples of LARC patients (20 responders, 20 non-responders) and qPCR validation of selected miRNA candidates. RESULTS: In the discovery phase of the study, we identified 69 miRNAs to have significantly different expression between the group of responders (TRG 1,2) and a group of non-responders (TRG 4,5) to neoadjuvant CRT. Among these miRNAs, 48 showed a lower expression and 21 showed higher expression in tumor tissues from poorly responding LARC patients. Five miRNAs were selected for validation, but only miR-487a-3p was confirmed to have a significantly higher expression in the tumor biopsy specimens of non-responders to neoadjuvant CRT (p<0.0006, AUC=0.766). Gene Ontology (GO) clustering and pathway enrichment analysis of the miR-487a-3p mRNA targets, revealed potential mechanisms behind miR-487a-3p roles in chemoradioresistance (e.g. TGF-beta signaling pathway, protein kinase activity, double-stranded DNA binding, or microRNAs in cancer). CONCLUSION: By combination of miRNA expression profiling and integrative computational biology we identified miR-487a-3p as a potential predictive biomarker of CRT response in LARC patients.

MicroRNA Biogenesis Pathway Genes Are Deregulated in Colorectal Cancer.

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Each step of their production and maturation has to be strictly regulated, as any disruption of control mechanisms may lead to cancer. Thus, we have measured the expression of 19 genes involved in miRNAs biogenesis pathway in tumor tissues of 239 colorectal cancer (CRC) patients, 17 CRC patients with liver metastases and 239 adjacent tissues using real-time PCR. Subsequently, the expression of analyzed genes was correlated with the clinical-pathological features as well as with the survival of patients. In total, significant over-expression of all analyzed genes was observed in tumor tissues as well as in liver metastases except for LIN28A/B. Furthermore, it was shown that the deregulated levels of some of the analyzed genes significantly correlate with tumor stage, grade, location, size and lymph node positivity. Finally, high levels of DROSHA and TARBP2 were associated with shorter disease-free survival, while the over-expression of XPO5, TNRC6A and DDX17 was detected in tissues of patients with shorter overall survival and poor prognosis. Our data indicate that changed levels of miRNA biogenesis genes may contribute to origin as well as progression of CRC; thus, these molecules could serve as potential therapeutic targets.

Serum-based microRNA signatures in early diagnosis and prognosis prediction of colon cancer.

Early detection of colorectal cancer is the main prerequisite for successful treatment and reduction of mortality. Circulating microRNAs were previously identified as promising diagnostic, prognostic and predictive biomarkers. The purpose of this study was to identify serum microRNAs enabling early diagnosis and prognosis prediction of colon cancer. In total, serum samples from 427 colon cancer patients and 276 healthy donors were included in three-phase biomarker study. Large-scale microRNA expression profiling was performed using Illumina small RNA sequencing. Diagnostic and prognostic potential of identified microRNAs was validated on independent training and validation sets of samples using RT-qPCR. Fifty-four microRNAs were found to be significantly deregulated in serum of colon cancer patients compared to healthy donors (P < 0.01). A diagnostic four-microRNA signature consisting of miR-23a-3p, miR-27a-3p, miR-142-5p and miR-376c-3p was established (AUC = 0.917), distinguishing colon cancer patients from healthy donors with sensitivity of 89% and specificity of 81% (AUC = 0.922). This panel of microRNAs exhibited high diagnostic performance also when analyzed separately in colon cancer patients in early stages of the disease (T1-4N0M0; AUC = 0.877). Further, a prognostic panel based on the expression of miR-23a-3p and miR-376c-3p independent of TNM stage was established (HR 2.30; 95% CI 1.44-3.66; P < 0.0004). In summary, highly sensitive signatures of circulating microRNAs enabling non-invasive early detection and prognosis prediction of colon cancer were identified.

Self-expandable biodegradable biliary stents in porcine model.

BACKGROUND: Treatment or prevention of a benign biliary tree stricture is an unresolved problem. A novel self-expandable biodegradable polydioxanon biliary stent in a porcine model was studied. MATERIALS AND METHODS: This new stent was used in 23 pigs. Feasibility and safety of surgical stenting, time of biodegradation, and histologic reaction in 2, 8, 13, and 20 wk of a follow-up were studied. All stents were inserted into a common bile duct through a duodenal papilla following small dilatation. After surgical evaluation of abdominal cavities, the pigs were sacrificed to remove common bile ducts with the stents. All bile ducts were assessed by macroscopic and histopathologic examination. RESULTS: Self-expansion was correct in all cases. Neither bile duct obstruction nor postsurgical complications were observed. Macroscopic evaluation indicated lightening of the stent color in 2 wk, a partial disintegration in 8 wk, and a complete absorption in 13 and 20 wk. Histologic evaluation in general substantiated a mild-to-moderate inflammatory reaction in the lamina propria during the whole follow up and had no clinical consequences. No cholangitis, necrosis, abscess, or excessive fibroplasia was found in a hepatoduodenal ligament. CONCLUSIONS: Our results suggest that polydioxanon biodegradable self-expanding stents seem to be useful for biliary system implantation, offer a good biocompatibility, and completely degrade within 13 wk.

Surgical treatment of Clostridium colitides.

INTRODUCTION: Infection with Clostridium difficile (CDI) is the most frequent cause of nosocomial diarrhoeas. Most cases are successfully treated by antibiotic therapy, but nearly 10% may progress to the fulminative form of this condition. The objective of the work is retrospective evaluation of the results of surgical treatment in patients with the fulminative form of Clostridium colitis with revealing of risk factors leading to serious post-operative morbidity and mortality. PATIENTS AND METHODOLOGY: Retrospective evaluation of the results of surgical treatment in patients with the fulminative form of Clostridium colitis between 2008 and 4/2012. RESULTS: Between 2008 and 4/2012 Clostridium toxins were positively detected in 1,088 patients in total, 21 of whom underwent operations due to the fulminative form of Clostridium colitis. The operations included 4 total colectomies with terminal ileostomy, 15 subtotal colectomies with terminal ileostomy, 1 caecostomy and 1 axial ileostomy. The 30-day mortality was 23.8%, and morbidity reached 66.6%. High leukocytosis is a statistically significant predictor of post-operative mortality and morbidity (p = 0.008). CONCLUSION: Early indication for a colectomy operation with terminal ileostomy in patients with the fulminative form of Clostridium colitis leads to lower morbidity and mortality.