Background: High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still exists considerable discrepancy on gene expression measurements and DEG results between the two platforms. The objective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-azadeoxy-cytidine (5-Aza) treated HT-29 colon cancer cells with an additional simulation study.Methods: We first performed general correlation analysis comparing gene expression profiles on both platforms. An Errors-In-Variables (EIV) regression model was subsequently applied to assess proportional and fixed biases between the two technologies. Then several existing algorithms, designed for DEG identification in RNA-Seq and microarray data, were applied to compare the cross-platform overlaps with respect to DEG lists, which were further validated using qRT-PCR assays on selected genes. Functional analyses were subsequently conducted using Ingenuity Pathway Analysis (IPA).Results: Pearson and Spearman correlation coefficients between the RNA-Seq and microarray data each exceeded 0.80, with 66%~68% overlap of genes on both platforms. The EIV regression model indicated the existence of both fixed and proportional biases between the two platforms. The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets. DESeq method exhibited a better control on the false discovery rate than baySeq on the simulated dataset although it performed slightly inferior to baySeq in the sensitivity test. RNA-Seq and qRT-PCR, but not microarray data, confirmed the expected reversal ofSPARCgene suppression after treating HT-29 cells with 5-Aza. Thirty-three IPA canonical pathways were identified by both microarray and RNA-Seq data, 152 pathways by RNA-Seq data only, and none by microarray data only.Conclusions: These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods. The EIV regression model reveals both fixed and proportional biases between RNA-Seq and microarray. This may explain in part the lower cross-platform overlap in DEG lists compared to those in detectable genes.

Postoperative ileus is a prolonged impairment of gastrointestinal motility following surgical procedures. This often leads to increased morbidity, extended hospital stays, and high healthcare expenditures. In this review, we discuss the pathophysiology underlying postoperative ileus, its epidemiology, and perioperative management strategies. Patient characteristics, as well as expected perioperative course, could be used to stratify the risks of postoperative ileus. Preventive measures hinge upon a multimodal approach, minimally invasive surgical techniques, fluid management, early postoperative ambulation, and opioid-sparing analgesia strategies. Adjuvant interventions such as alvimopan, caffeine, and chewing gum have demonstrated efficacy in modulating the neurogenic and inflammatory components of postoperative ileus. Minimally invasive approaches, comprehensive perioperative management, and adjuvant therapies hold promise for prevention. Current management relies heavily on supportive care, underscoring the need for research into the underlying neurogenic and inflammatory mechanisms to guide the development of targeted treatments.

Background: Intestinal aspergillosis (IA) is a rare entity primarily discovered in immunocompromised patients. Because of its low incidence, IA is not considered routinely in the differential of abdominal pain, distension, and diarrhea. A systematic characterization of demographics, comorbidities, clinical presentations, and outcomes can help surgeons recognize and manage IA in critically ill patients. Methods: Two independent authors carried out the literature search using PubMed, MEDLINE, and Scopus databases. The Mesh terms utilized were: ‘intestinal’ and ‘aspergillosis’ combined with the Boolean operator ‘AND’ (synonyms were combined with the Boolean operator ‘OR’). Intestinal aspergillosis was defined as inflammation of the gastrointestinal tract (duodenum to rectum) caused by Aspergillus spp. All articles reporting IA were included. Articles describing aspergillosis of the esophagus or stomach were excluded. Statistical analysis was performed using SPSS software (version 18; SPSS Inc., Chicago, IL). Results: Forty-two articles reporting 56 cases were included in the study. Mean age was 44.9 ± 20.5 years. Male to female ratio was 29:27. The most common condition in patients who developed IA was transplantation (19 patients; 34%). The most common clinical presentations of IA were abdominal pain (21 patients; 38%) and diarrhea 12 patients; 21%). Sixty-six percent of patients had primary IA whereas 34% developed IA secondarily to systemic infection. Diagnostic modalities included exploratory laparotomy (35 patients; 63%) and endoscopy (7 patients; 13%). Mean time to diagnosis was 8.6 ± 11.3 days. Intestinal aspergillosis was limited to the small bowel in 61% of patients. In 43 (77%) patients, bowel resection is the definitive treatment, whereas 13 (23%) patients underwent antifungal therapy alone. Mortality rate was 39%. Sixty-three percent of patients treated with surgery survived, compared with 46% treated with antifungal therapy alone (p = 0.34). Conclusion: Intestinal aspergillosis is a life-threatening condition with a mortality rate of 39%. Extrapulmonary IA is seen in patients with neutropenia, sepsis, inflammatory conditions, and immunosuppression. Patients who undergo surgery are more likely to survive this infection.

Bacteria are believed to play an important role in intestinal tumorigenesis and contribute to both gut luminal and circulating metabolites. Celecoxib, a selective cyclooxygenase-2 inhibitor, alters gut bacteria and metabolites in association with suppressing the development of intestinal polyps in mice. The current study sought to evaluate whether celecoxib exerts its chemopreventive effects, in part, through intestinal bacteria and metabolomic alterations. Using ApcMin/+ mice, we demonstrated that treatment with broad-spectrum antibiotics (ABx) reduced abundance of gut bacteria and attenuated the ability of celecoxib to suppress intestinal tumorigenesis. Use of ABx also impaired celecoxib's ability to shift microbial populations and gut luminal and circulating metabolites. Treatment with ABx alone markedly reduced tumor number and size in ApcMin/+ mice, in conjunction with profoundly altering the metabolite profiles of the intestinal lumen and blood. Many of the metabolite changes in the gut and circulation overlapped and included shifts in microbially derived metabolites. To complement these findings in mice, we evaluated the effects of ABx on circulating metabolites in patients with colon cancer. This showed that ABx treatment led to a shift in blood metabolites, including several that were of bacterial origin. Importantly, changes in metabolites in patients given ABx overlapped with alterations found in mice that also received ABx. Taken together, these findings suggest a potential role for bacterial metabolites in mediating both the chemopreventive effects of celecoxib and intestinal tumor growth. Prevention Relevance: This study demonstrates novel mechanisms by which chemopreventive agents exert their effects and gut microbiota impact intestinal tumor development. These findings have the potential to lead to improved cancer prevention strategies by modulating microbes and their metabolites.

In the United States, individuals of Black/African Ancestry (AA) have a higher incidence and mortality from colorectal cancer (CRC) compared to individuals of White/European Ancestry (EA). In order to develop an approach towards disentangling the complex effects of associated race and socioeconomic factors on CRC outcome, we have conducted a manual chart review of sporadic CRC pathological diagnoses (total n = 334) at an urban public hospital (UH) and a suburban university hospital (SH). There were significant differences between the SH and UH CRC patients with respect to Black/AA race (4.2% vs. 89.1%, p < 0.0001) and Medicaid/Self-pay insurance status (14.9% vs. 85.0%, p < 0.0001). While a higher proportion of newly diagnosed CRC patients presented with metastatic stage 4 CRC at the UH (21%) than the SH (12.5%), only the presence of symptoms was significantly associated with stage 4 CRC (odds ratio, OR 7.94, 95% confidence interval, CI 1.83- 34.54, p = 0.0057) in a multivariable generalized linear model (GLM). The proportion of asymptomatic CRC patients was ~20% at both institutions, suggesting that the UH has contributed to reducing CRC disparities. Initiation of CRC screening at the recommended age at both institutions could reduce the proportion of CRC patients presenting with metastatic spread.