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BACKGROUND The Black/African Ancestry (AA) population has a higher prevalence of type 2 diabetes mellitus (T2DM) and a higher incidence and mortality rate for colorectal cancer (CRC) than all other races in the United States. T2DM has been shown to increase adenoma risk in predominantly white/European ancestry (EA) populations, but the effect of T2DM on adenoma risk in Black/AA individuals is less clear. We hypothesize that T2DM has a significant effect on adenoma risk in a predominantly Black/AA population. AIM To investigate the effect of T2DM and race on the adenoma detection rate (ADR) in screening colonoscopies in two disparate populations. METHODS A retrospective cohort study was conducted on ADR during index screening colonoscopies (age 45-75) performed at an urban public hospital serving a predominantly Black/AA population (92%) (2017-2018, n = 1606). Clinical metadata collected included basic demographics, insurance, body mass index (BMI), family history of CRC, smoking, diabetes diagnosis, and aspirin use. This dataset was combined with a recently reported parallel retrospective cohort data set collected at a suburban university hospital serving a predominantly White/EA population (87%) (2012-2015, n = 2882). RESULTS The ADR was higher in T2DM patients than in patients without T2DM or prediabetes (35.2% vs 27.9%, P = 0.0166, n = 981) at the urban public hospital. Multivariable analysis of the combined datasets showed that T2DM [odds ratio (OR) = 1.29, 95% confidence interval (CI): 1.08-1.55, P = 0.0049], smoking (current vs never OR = 1.47, 95%CI: 1.18-1.82, current vs past OR = 1.32, 95%CI: 1.02-1.70, P = 0.0026), older age (OR = 1.05 per year, 95%CI: 1.04-1.06, P < 0.0001), higher BMI (OR = 1.02 per unit, 95%CI: 1.01-1.03, P = 0.0003), and male sex (OR = 1.87, 95%CI: 1.62-2.15, P < 0.0001) were associated with increased ADR in the combined datasets, but race, aspirin use and insurance were not. CONCLUSION T2DM, but not race, is significantly associated with increased ADR on index screening colonoscopy while controlling for other factors.

Background Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors. Aim To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples. Methods Genomic DNA (gDNA) and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020. The 16S rRNA gene sequencing (V3V4 region, paired end, 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing (IPE, 125 bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores ≥ 6. Results PERMANOVA detected significant effects of tumor vs nontumor histology (P = 0.002) and antibiotics (P = 0.001) on microbial β-diversity, but CRC tumor location (left vs right), diabetes mellitus vs not diabetic and Black/African Ancestry (AA) vs not Black/AA, did not reach significance. Linear mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level taxa. QPCR confirmed increased Fusobacterium abundance in tumor vs nontumor groups, and detected significantly reduced bacterial load in the (+)antibiotics group. Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples. Differentially expressed genes obtained from separate analyses of tumor and nontumor samples, are presented for the antibiotics, CRC location, diabetes and Black/AA race groups. Conclusion Recent adoption of additional preoperative antibiotics as standard of care, has a measurable impact on -omics analysis of resected specimens. This study still confirmed increased Fusobacterium nucleatum in tumor.

Pancreatic ductal adenocarcinoma (PDAC) has one of the poorest prognoses of all malignancies, with a 5-year survival rate

Background and Aims Pancreatic cancer organoids are tumor models of individualized human pancreatic ductal adenocarcinoma (PDA), created from surgical specimens and used for personalized treatment strategies. Unfortunately, most patients with PDA are not operative candidates. Creation of human PDA organoids at the time of initial tumor diagnosis is therefore critical. Our aim was to assess the feasibility of creating human PDA organoids by EUS fine-needle biopsy (EUS-FNB) sampling in patients with PDA. Methods In this prospective clinical trial in patients referred to evaluate a pancreatic mass, EUS-FNA was performed for initial onsite diagnosis. Two additional needle passes were performed with a 22-gauge FNB needle for organoid creation. Primary outcome was successful isolation of organoids within 2 weeks of EUS-FNB sampling (P0, no passages), confirmed by organoid morphology and positive genotyping. Results Thirty-seven patients with 38 PDA tumors were enrolled. Successful isolation of organoids (P0) was achieved in 33 of 38 tumors (87%). Establishment of PDA organoid lines for ≥5 passages of growth (P5, five passages) was reached in 25 of 38 tumors (66%). In the single patient with successful P5 FNB sampling–derived and P5 surgically derived organoids, there was identical matching of specimens. There were no serious adverse events. Two patients developed bleeding at the EUS-FNB puncture site requiring hemostasis clips. Conclusions Pancreatic cancer organoids can be successfully and rapidly created by means of EUS-FNB sampling using a 22-gauge needle at the time of initial diagnosis. Successful organoid generation is essential for precision medicine in patients with pancreatic cancer in whom most are not surgically resectable. (Clinical trial registration number: NCT03140592.)

The combination therapy of lumacaftor and ivacaftor (Orkambi ® ) is approved for patients bearing the major cystic fibrosis (CF) mutation: ΔF508 . It has been predicted that Orkambi ® could treat patients with rarer mutations of similar “theratype”; however, a standardized approach confirming efficacy in these cohorts has not been reported. Here, we demonstrate that patients bearing the rare mutation: c.3700 A>G, causing protein misprocessing and altered channel function—similar to ΔF508‐CFTR, are unlikely to yield a robust Orkambi ® response. While in silico and biochemical studies confirmed that this mutation could be corrected and potentiated by lumacaftor and ivacaftor, respectively, this combination led to a minor in vitro response in patient‐derived tissue. A CRISPR/Cas9‐edited bronchial epithelial cell line bearing this mutation enabled studies showing that an “amplifier” compound, effective in increasing the levels of immature CFTR protein, augmented the Orkambi ® response. Importantly, this “amplifier” effect was recapitulated in patient‐derived nasal cultures—providing the first evidence for its efficacy in augmenting Orkambi ® in tissues harboring a rare CF‐causing mutation. We propose that this multi‐disciplinary approach, including creation of CRISPR/Cas9‐edited cells to profile modulators together with validation using primary tissue, will facilitate therapy development for patients with rare CF mutations.

Background: Diabetes is associated with an increased risk of colorectal cancer (CRC). We conducted a retrospective analysis of adenoma detection rates (ADR) in initial screening colonoscopies to further investigate the role of diabetes in adenoma detection. Methods: A chart review was performed on initial average risk screening colonoscopies (ages 45–75) during 2012–2015. Data collected included basic demographics, insurance, BMI, family history of CRC, smoking, diabetes, and aspirin use. Multivariable generalized linear mixed models for binary outcomes were used to examine the relationship between diabetes and variables associated with CRC risk and ADR. Results: Of 2865 screening colonoscopies, 282 were performed on patients with type 2 diabetes (T2DM). Multivariable analysis suggested that T2DM (OR = 1.49, 95% CI:1.13–1.97, p = 0.0047) was associated with an increased ADR, as well as smoking, older age, higher BMI and male sex (all p

Systemic autoinflammatory diseases (SAIDs) represent a spectrum of genetically heterogeneous inflammatory disorders. Some SAID-associated genes are located in chromosome 16, including familial Mediterranean fever gene (MEFV) and nucleotide-binding oligomerization domain 2 [NOD2] gene that are linked to Crohn's disease, Blau syndrome, and Yao syndrome. These disorders share overlapping clinical phenotypes, and genotyping is diagnostically helpful and distinctive. Using next generation sequencing in SAIDs, digenic variants or combinations of more genetic variants in different genes can be detected, and they may be related to the MEFV and NOD2 genes. These variants may contribute to heterogeneous phenotypes in an individual, complicating the diagnosis and therapy. An awareness of the clinical significance of the digenic or combined gene variants is important in the era of genomic medicine.

Background and Aims: The incidence and mortality of colorectal cancer is persistently highest in Black/African-Americans in the United States. While access to care, barriers to screening, and poverty might explain these findings, there in increased interest in examining biological factors that impact the colonic environment. Our group is examining biologic factors that contribute to disparities in development of adenomas prospectively. In preparation for this and to characterize a potential patient population, we conducted a retrospective review of initial screening colonoscopies in a cohort of patients. Methods: A retrospective review was performed on initial average risk screening colonoscopies on patients (age 45 - 75 years) during 2012 at three institutions. Descriptive statistics and multivariable logistic regression models were used to examine the relationship between potential risk factors and the detection of adenomas. Results: Of the 2225 initial screening colonoscopies 1495 (67.2%) were performed on Black/African-Americans and 566 (25.4%) on Caucasians. Multivariable logistic regression revealed that older age, male sex, current smoking and teaching gastroenterologists were associated with higher detection of adenomas and these were less prevalent among Black/African-Americas except for age. Neither race, ethnicity, BMI, diabetes mellitus, HIV nor insurance was associated with adenoma detection. Conclusion: In this sample, there was no association between race and adenoma detection. While this may be due to a lower prevalence of risk factors for adenomas in this sample, our findings were confounded by a lower detection rate by consultant gastroenterologists at one institution. The study allowed us to rectify the problem and characterize patients for future trials.

We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn's colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR < 0.05) in microbiota were observed between macroscopically disease unaffected and affected regions of resected ileum in ileal CD patients. Accordingly, analysis of the effects of genetic and clinical factors were restricted to disease unaffected regions of the ileum. Beta-diversity differed across the three disease categories by PERMANOVA (p < 0.001), whereas no significant differences in alpha diversity were noted. Using negative binomial models, we confirmed significant effects of IBD phenotype, C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6-12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.

Oncogenic KRAS plays a vital role in controlling tumor metabolism by enhancing aerobic glycolysis. Obesity driven by chronic consumption of high-fat diet (HFD) is a major risk factor for oncogenic KRAS-mediated pancreatic ductal adenocarcinoma (PDAC). However, the role of HFD in KRAS-mediated metabolic reprogramming has been obscure. Here, by using genetically engineered mouse models expressing an endogenous level of KRASG12D in pancreatic acinar cells, we demonstrate that hyperactivation of KRASG12D by obesogenic HFD, as compared to carbohydrate-rich diet, is responsible for enhanced aerobic glycolysis that associates with critical pathogenic responses in the path towards PDAC. Ablation of Cox-2 attenuates KRAS hyperactivation leading to the reversal of both aggravated aerobic glycolysis and high-grade dysplasia under HFD challenge. Our data highlight a pivotal role of the cooperative interaction between obesity-ensuing HFD and oncogenic KRAS in driving the heightened aerobic glycolysis during pancreatic tumorigenesis and suggest that in addition to directly targeting KRAS and aerobic glycolysis pathway, strategies to target the upstream of KRAS hyperactivation may bear important therapeutic value.

Pancreatic cancer is a deadly disease with only 8% of the patients surviving 5 years (1). Recent data published for African Americans (AA) showed that this population has the highest death rate and shortest survival of any racial/ethnic group in the US for most cancers (2). The causes of this disparity are unknown; some of them may be socioeconomic as well as barriers to high-quality cancer prevention, early detection, and treatment information and services. It is clear that there is a gap between AA and Caucasian Americans (CA) concerning the development and death from pancreatic cancer. We hypothesize that there also are molecular differences in the tumors from AA and CA patients that contribute to this disparity. Importantly, The Cancer Genome Atlas (TCGA) numbers for pancreatic cancer reveals that only 7 out of 185 cases of pancreatic cancer are from African American patients. This clearly shows a prominent under-representation of tumor-related genetic information for the AA population. MicroRNAs (miRNAs) are able to regulate dozens of targets, especially those involved in cancer, making them a potential tool to study differences between populations. It is known that patients develop drug resistance against gemcitabine and one factor could be due to differential expression of miRNAs (3). The analysis of potential miRNA differences in AA and CA tumors would be a starting point to study the function(s) and mechanisms to understand the gap between these populations. We analyzed the tumor miRNAs expression of the TCGA 7 AA patients and compared the expression with 10 CA patients from TCGA to understand the main differences in expression between the two sets of samples. Using R studio, we found 26 miRNAs significantly different between CA and AA tumors. Some of them are involved in pathways related with tumor progression, cell invasion and tumor growth. We are interested in miRNAs involved in upregulating drug resistance against gemcitabine such as miR21, miR 155, or miR 196 as well as those miRNAs that dowregulate resistance to treatment like miR148, miR200 or miR34. Importantly, these miRNAs have been defined only in CA pancreatic tumor samples. We are collecting retrospective pancreatic cancer cases at SUNY Downstate Medical Center and Kings County Hospital Center to study the expression of miRNAs using Illumina technology in our AA population in Brooklyn, NY. These tissues will be matched for age, gender, body mass index, and for stage and site of disease to the best of our ability. Adjacent normal tissues will serve as standard controls. We will use CA PDAC cases from TCGA for comparison. This work is in progress. In conclusion, we found in our analysis 26 miRNAs differentially expressed between AA and CA using TCGA data. We expect to see a difference in expression of miRNAs using samples from our patient population. In addition, we are interested to see if our patients have a different expression pattern of miRNAs related to drug resistance and if this could explain the poor response often seen in AA PDAC patients. Citation Format: Maria Munoz-Sagastibelza, Mohamed Alshal, Sayed Imtiaz, Jenny E. Paredes Sanchez, Mubarak Akadri, Raavi Gupta, Maksim Agaronov, Ellen Li, Jovanny Zabaleta, Laura Martello-Rooney. African American pancreatic cancer microRNAs profile to identify links to drug resistance and tumor progression [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B059.

Background: The incidence of colorectal cancer is persistently higher in Black/African Americans than other races in the United States. It is less clear whether Black/African Americans are at higher risk for colonic precancerous polyps, which represent an earlier stage in colorectal adenoma-carcinoma progression. Methods: A retrospective chart review was performed on initial average-risk screening colonoscopies on patients (age 45-75 years) during 2012 at 3 institutions. Multivariable logistic regression models were used to examine the relationship between potential risk factors and the detection of precancerous polyps. Results: Of the 2,225 initial screening colonoscopies, 1,495 (67.2%) were performed on Black/African Americans and 566 (25.4%) on Caucasian non-Hispanic patients. The mean age of initial colonoscopies was 57.1 y and 56.0 y for Black and Caucasian patients, respectively. Male patients represented 32.0% and 42.8% of the Black and Caucasian patients, respectively. Obese patients represented 41.4% and 31% of Black and Caucasian patients. A higher percentage (30%) of the Black patients were diagnosed with diabetes mellitus compared to Caucasians (11%). Multivariable logistic regression revealed that performance of the colonoscopy by academic gastroenterologists was associated with higher precancerous polyp detection compared to contractual nonacademic gastroenterologists (OR 1.69 95% CI 1.32-2.17, p Conclusions: It is imperative that metrics of polyp detection rates be routinely monitored to ensure that all patients have access to high-quality screening colonoscopies. A prospective observational cohort study will help further identify factors associated with precancerous polyp detection, now that variations in operator detection rates have been addressed. Citation Format: Yakira David, Lorenzo Ottaviano, Jihye Park, Sadat Iqbal, Michelle Likhtshteyn, Samir Kumar, Helen Lyo, Ayanna Lewis, Brandon Lung, Jesse Frye, Li Huang, Ellen Li, Jie Yang, Laura Martello, Shivakumar Vignesh, Joshua Miller, Evan Grossman. Factors contributing to precancerous polyp detection in initial screening colonoscopies [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B102.

Colorectal cancer (CRC) is the third most common cancer among African Americans (AAs) in the US. When compared to Caucasian Americans (CAs), AAs present with higher incidence and death rates as well as worse prognosis after treatment with 5-Fluorouacil (5-FU). Previous studies have shown a correlation between microsatellite instability (MSI) and response to 5-FU and our recent findings suggest that differences in the tumor immunology and MSI status of AA and CA CRC patients are associated with the observed disparities between these populations. Therefore, we examined if cytokines secretion, protein production and cellular response to 5-FU treatment, differs between colon cancer cell lines from AAs generated in Dr. Williams’ laboratory (SB521, SB501 and CHTN06) and colon cancer cell lines from CA patients (HT29 and HCT116). Methods: We performed whole transcriptome sequencing of colon cancer cell lines (RNAseq), utilizing the NextSeq 500/550 High Output Kit v2.5 (Illumina) and Partek Flow data analysis to correlate gene expression to immune-oncology pathways. ELISA assays (RayBiotech) were used to examine the secretion of cytokines in supernatants from cells treated with interleukin 1β and tumor necrosis factor alpha. We used western blotting for protein detection of the phosphorylated form of c-Jun N-terminal kinases (JNK) as well as cell viability assays for establishing the IC50 of the cell lines to 5-FU. Results: The gene expression results indicated that the immune profiles of AA cell lines differ from CA in genes and cytokines related to cellular anti-tumor activity, including CD8B, IL-1R, IL-1R2, Granzyme B and NFKB. ELISAs of supernatants from CA and AA CRC cell lines revealed a differential cytokines secretion between the two races, namely IL-8. Lastly, the MSI AA cell line showed sensitivity to 5-FU (tenfold less) when compared to the CA cell lines and a distinct protein production pattern. Conclusions: Our gene expression findings demonstrated the differential expression of immunological pathways involved in immune-surveillance and cancer progression in the CRC cell lines between the two races. These results were in accordance with the cytokines’ and protein’s expression patterns observed in the two cohorts of cell lines. Importantly, our data indicates that 5-FU is more efficient in reducing cell viability in the MSI AA cell line than in the two CA cell lines regardless of their MSI status. Altogether, our results illustrate the value of these in vitro models to study 5-FU treatment in AA patients with MSI and MMR mutations and to elucidate the differences in chemotherapy treatment responses between AAs and CAs. In conclusion, we demonstrated distinct immunological profiles and 5-FU sensitivity of AA and CA CRC cell lines. As such, these differences observed could be used to guide new therapeutic strategies. Citation Format: Marzia Spagnardi, Jenny Paredes, Jone Garai, Ping Ji, Ellen Li, Jovanny Zabaleta, Laura Martello-Rooney, Jennie Williams. Tumor biology and cancer health disparity: Gene expression, cytokine secretion, and protein production in African American colon cancer cell lines [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr B134.

Introduction: Colorectal cancer (CRC) is the third most common cancer among African Americans (AA) and when compared to Caucasian Americans (CA), they present more advanced CRC disease and lower survival rates. Our previous findings suggest that this may be related to the differential expression in genes linked to cell recruitment and immune response. Therefore, we aimed to investigate the cellular antitumor activity and mutational profile of colon tumors from AAs. We also examined the secretion of cytokines characteristic of immune responses by different effector T helper cells (Th) subsets in AA and CA patients, as well as cell lines, to see if these differences play a role in the health disparities observed between these populations. Lastly, we observed the expression of the Program Death Ligand 1 (PD-L1) in response to the cytokines IL-17A and TNF-α in a microsatellite-unstable (MSI) AA and a microsatellite-stable (MSS) CA colon cancer cell line. Methods: Using IHC, we evaluated the cell recruitment and activation of T and natural killer cells in AA tumors. For mutational analysis, we utilized the TruSight Tumor 170 RUO kit (Illumina). ELISA assays (RayBiotech) were used to examine the secretion of cytokines linked to Th subsets (Th1, Th2, Th17) and inflammation in plasma from the AA and CA CRC patients, as well as in supernatants from the AA and CA colon cancer cell lines. Western blots were used to observe the expression of PD-L1 in the in vitro models. Results: ELISAs of plasma of CA and AA patients revealed a differential Th cytokines production patterns between early-stages (I, II) and late-stage (III) disease. The MSI AA cell line showed an increase on PD-L1 protein expression in response to IL-17A and TNF-α with an additive effect when combined in equal concentrations. Lastly, the mutational sequencing allowed us to further investigate the potential alterations that are responsible for the differences that we observed in gene expression between AAs and CAs in our RNA and cytokine expression profiling. Conclusions: Our results indicate that the immune profiles of AA patients differ from CA in terms of cytokines' production; AAs expressed elevated IL-17A, whereas CA expressed elevated IFN-γ, the latter indicative of Th1 immunity that has a more favorable prognosis. As such, these differences could be used as biomarkers and to guide therapeutic strategy for these populations. The mutational sequencing will help us to elucidate the impaired tumor immune response in AAs with colon cancer when compared to CAs that we observed in terms of cell recruitment and cytokine secretion in our previous findings. Importantly, our data indicate that IL-17A and TNF-α promote the protein production of PD-L1 in an MSI AA cell line, which may result in the impairment of T cells' antitumor activity. Taken together, the differences in the immunologic profiles in AA when compared to CA suggest a deficiency of the appropriate immune defense mechanisms in this population that may contribute to the cancer health disparities among CRC patients. Citation Format: Jenny E. Paredes, Ping Ji, Jone Garai, Marzia Spagnardi, Maria Munoz-Sagastibelza, Sayed Imtiaz, Gayle Mendez, Mubarak Akadri, Raavi Gupta, Mohamed Alshal, Maksim Agaronov, Henry Talus, Ellen Li, Jovanny Zabaleta, Laura Martello-Rooney, Jennie Williams. Tumor immune response in colon cancer African American patients and its role in cancer disparities [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C118.

Upregulation of matrix metalloproteinase MMP-14 (MT1-MMP) is associated with poor prognosis in cancer patients, but it is unclear how MMP-14 becomes elevated in tumors. Here, we show that miR-181a-5p is downregulated in aggressive human breast and colon cancers where its levels correlate inversely with MMP-14 expression. In clinical specimens, enhanced expression of MMP-14 was observed in cancer cells located at the invasive front of tumors where miR-181a-5p was downregulated relative to adjacent normal cells. Bioinformatics analyses defined a potential miR-181a-5p response element within the 3′-untranslated region of MMP-14 that was validated in reporter gene experiments. Ectopic miR-181a-5p reduced MMP-14 expression, whereas miR-181a-5p attenuation elevated MMP-14 expression. In support of a critical relationship between these two genes, miR-181a-5p–mediated reduction of MMP-14 levels was sufficient to decrease cancer cell migration, invasion, and activation of pro-MMP-2. Furthermore, this reduction in MMP-14 levels was sufficient to reduce in vivo invasion and angiogenesis in chick chorioallantoic membrane assays. Taken together, our results establish the regulation of MMP-14 in cancers by miR-181a-5p through a posttranscriptional mechanism, and they further suggest strategies to elevate miR-181a-5p to prevent cancer metastasis. Cancer Res; 75(13); 2674–85. ©2015 AACR.

// Nikki A. Evensen 1, 9, * , Yiyi Li 1, 8, * , Cem Kuscu 1, 10 , Jingxuan Liu 2 , Jillian Cathcart 1 , Anna Banach 1 , Qian Zhang 1 , Ellen Li 3 , Sonia Joshi 1 , Jie Yang 4 , Paula I Denoya 5 , Silvia Pastorekova 6 , Stanley Zucker 7 , Kenneth R. Shroyer 2 , Jian Cao 1, 2 1 Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA 2 Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA 3 Department of Medicine/Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, USA 4 Department of Preventative Medicine, Stony Brook University, Stony Brook, NY 11794, USA 5 Department of Surgery, Stony Brook University, Stony Brook, NY 11794, USA 6 Department of Molecular Medicine, Institute of Virology, Slovak Academy of Sciences, Bratislava 84505, Slovak Republic 7 Veterans Affairs Medical Center, Northport, NY 11768, USA 8 Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China 9 Department of Pediatrics, NYU Medical School, New York, NY 10016, USA 10 Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA * These authors have contributed equally to this work Correspondence to: Jian Cao, e-mail: Jian.Cao@stonybrookmedicine.edu Keywords: KIAA1199/CEMIP, migration, invasion, HIF-2α Received: February 26, 2015 Accepted: April 30, 2015 Published: May 13, 2015 ABSTRACT Hypoxic stress drives cancer progression by causing a transcriptional reprogramming. Recently, KIAA1199 was discovered to be a ce ll- m igration i nducing p rotein (renamed CEMIP) that is upregulated in human cancers. However, the mechanism of induction of CEMIP in cancer was hitherto unknown. Here we demonstrate that hypoxia induces CEMIP expression leading to enhanced cell migration. Immunohistochemistry of human colon cancer tissues revealed that CEMIP is upregulated in cancer cells located at the invasive front or in the submucosa. CEMIP localization inversely correlated with E-cadherin expression, which is characteristic of the epithelial-to-mesenchymal transition. Mechanistically, hypoxia-inducible-factor-2α (HIF-2α), but not HIF-1α binds directly to the hypoxia response element within the CEMIP promoter region resulting in increased CEMIP expression. Functional characterization reveals that CEMIP is a downstream effector of HIF-2α-mediated cell migration. Expression of CEMIP was demonstrated to negatively correlate with the expression of Jarid1A, a histone demethylase that removes methyl groups from H3K4me3 (an activation marker for transcription), resulting in altered gene repression. Low oxygen tension inhibits the function of Jarid1A, leading to increased presence of H3K4me3 within the CEMIP promoter. These results provide insight into the upregulation of CEMIP within cancer and can lead to novel treatment strategies targeting this cancer cell migration-promoting gene.

AIM To examine the relationship between elevated granulocyte-macrophage colony-stimulating factor (GM-CSF) auto-antibodies (Ab) level and time to surgical recurrence after initial surgery for Crohn’s disease (CD). METHODS We reviewed 412 charts from a clinical database at tertiary academic hospital. Patients included in the study had ileal or ileocolonic CD and surgical resection of small bowel or ileocecal region for management of disease. Serum samples were analyzed for serological assays including GM-CSF cytokine, GM-CSF Ab, ASCA IgG and IgA, and genetic markers including SNPs rs2066843, rs2066844, rs2066845, rs2076756 and rs2066847 in NOD2, rs2241880 in ATG16L1, and rs13361189 in IRGM. Cox proportional-hazards models were used to assess the predictors of surgical recurrence. RESULTS Ninety six percent of patients underwent initial ileocecal resection (ICR) or ileal resection (IR) and subsequently 40% of patients required a second ICR/IR for CD. GM-CSF Ab level was elevated at a median of 3.81 mcg/mL. Factors predicting faster time to a second surgery included elevated GM-CSF Ab [hazard ratio (HR) 3.52, 95%CI: 1.45-8.53, P = 0.005] and elevated GM-CSF cytokine (HR = 2.48, 95%CI: 1.31-4.70, P = 0.005). Factors predicting longer duration between first and second surgery included use of Immunomodulators (HR = 0.49, 95%CI: 0.31-0.77, P = 0.002), the interaction effect of low GM-CSF Ab levels and smoking (HR = 0.60, 95%CI: 0.45-0.81, P = 0.001) and the interaction effect of low GM-CSF cytokine levels and ATG16L1 (HR = 0.65, 95%CI: 0.49-0.88, P = 0.006). CONCLUSION GM-CSF bioavailability plays a critical role in maintaining intestinal homeostasis. Decreased bioavailability coupled with the genetic risk markers and/or smoking results in aggressive CD behavior.

A federally funded demonstration project (Project SCOPE) was conducted to develop a model for delivering screening colonoscopy to underinsured patients in Suffolk County, NY. The recruitment model featured collaboration between Stony Brook University Medical Center and the Suffolk County Department of Health Services’ network of community health centers; bilingual patient navigators, and reimbursement of physicians and the hospital at Medicare rates. We conducted a retrospective analysis of all (11,752) colonoscopies performed at Stony Brook Medicine, during the pre-SCOPE time period (2003–2004), during SCOPE period (2007–2008), and post-SCOPE (2010–2011), to measure the impact of SCOPE on reducing racial and ethnic disparities. Multiple logistic regression models were used to compare the likelihood of a patient being Hispanic or African American after adjusting for potential covariates. The numbers of Hispanics undergoing colonoscopies were 146 (4.3 %), 506 (12.3 %), and 262 (6 %) during the pre-SCOPE, SCOPE, and post-SCOPE time periods. The numbers of African Americans were 166 (5.1 %), 298 (7.2 %), and 255 (5.8 %). The odds ratio (OR = 1.4, 95 % CI = 1.06–1.83, p = 0.014) of a screening colonoscopy patient being Hispanic during the Project SCOPE period compared to the post-SCOPE period remained significant after taking into consideration the other covariates, such as diabetes, smoking, and insurance status. Project SCOPE had a significant impact on increasing the proportion of Hispanics undergoing screening colonoscopies. Factors such as bilingual patient navigators, in addition to removing financial barriers, may have contributed to the increase.

Background & Aims The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. Methods We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P −8 in meta-analysis with a nominal evidence ( P Results We detected SNPs at HLA-DRB1 , and African-specific SNPs at ZNF649 and LSAMP , with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication ( P −6 ): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B, PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2 ) for CD; and KCNQ2 (near TNFRSF6B ) for UC. Several of these genes, such as TNC (near TNFSF15 ), CXCR6 , and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. Conclusions We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.

Culture-independent microbiological technologies that interrogate complex microbial populations without prior axenic culture, coupled with high-throughput DNA sequencing, have revolutionized the scale, speed, and economics of microbial ecological studies. Their application to the medical realm has lead to a highly productive merger of clinical, experimental, and environmental microbiology. The functional roles played by members of the human microbiota are being actively explored through experimental manipulation of animal model systems and studies of human populations. In concert, these studies have appreciably expanded our understanding of the composition and dynamics of human-associated microbial communities (microbiota). Of note, several human diseases have been linked to alterations in the composition of resident microbial communities, so-called dysbiosis [1]. However, how changes in microbial communities contribute to disease etiology remains poorly defined. Correlation of microbial composition represents integration of only two datasets (phenotype and microbial composition). This article explores strategies for merging the human microbiome data with multiple additional datasets (e.g. host single nucleotide polymorphisms [SNP] and host gene expression) and for integrating patient-based data with results from experimental animal models to gain deeper understanding of how host-microbe interactions impact disease.

Background: NOD2 single nucleotide polymorphisms have been associated with increased risk of ileal Crohn's disease (CD). This exploratory study was conducted to compare ileal mucosal gene expression in CD patients with and without NOD2 risk alleles. Methods: Ileal samples were prospectively collected from 18 nonsmoking CD patients not treated with anti-TNF-α biologics and 9 nonsmoking control patients without inflammatory bowel disease undergoing initial resection and genotyped for the 3 major NOD2 risk alleles (Arg702Trp, Gly908Arg, Leu1007fs). Microarray analysis was performed in samples from 4 NOD2R (at least 1 risk allele) CD patients, 4 NOD2NR (no risk alleles) CD patients, and 4 NOD2NR controls. Candidate genes selected by significance analysis of microarrays (SAM) were confirmed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays of all the samples. Results: SAM detected upregulation of 18 genes in affected ileum in NOD2R compared to NOD2NR CD patients, including genes related to lymphocyte activation. SAM also detected altered ileal gene expression in unaffected NOD2NR ileal mucosal CD samples compared to NOD2NR control samples. qRT-PCR conducted on all the samples confirmed that increased CD3D expression in affected samples was associated with NOD2R status, and that increased MUC1, DUOX2, DMBT1 and decreased C4orf7 expression in unaffected samples was associated with CD, independent of NOD2 status. Conclusions: The results support the concept that NOD2 risk alleles contribute to impaired regulation of inflammation in the ileum. Furthermore, altered ileal gene expression, independent of NOD2 status, is detected in the unaffected proximal margin of resected ileum from CD patients. (Inflamm Bowel Dis 2010)

Background: Racial disparities persist in the incidence and mortality of colorectal cancer despite the availability of screening tools. Adenoma detection rates have been associated with diabetes in some studies. This study seeks to evaluate the effect of diabetes mellitus on adenoma detection rates (ADR) in initial screening colonoscopies performed at three distinct institutions. Methods: A retrospective chart review was performed on all initial average risk screening colonoscopies performed on patients between 45-75 years at an Urban Safety Net Hospital (USNH), an Urban University Hospital (UUH) and a Suburban University Hospital (SUH) from January 1st to December 30th 2012 to coordinate existing databases at the three institutions. Patients were excluded if they had a history of colon cancer, polyps, alarm symptoms, or if the current colonoscopy was incomplete or had poor bowel prep. Data points collected included sex, age, race, insurance, BMI, smoking status, diabetic status and attending provider. Univariate analysis was performed comparing ADRs between the three institutions using Graph Pad Prism. Further comparisons were made between current smoking and diabetes status with ADR. Results: There were a total of 2225 initial screening colonoscopies (SUH, n =647; UUH, n = 444; USNH, n = 1134) excluding 135 incomplete and/or poor prep colonoscopies (SUH, n = 34; UUH, n = 50; USNH, n = 51). USNH and UUH patients were more likely to be African-American (93% and 88% vs 7%, p Discussion: Diabetes and current smoking are associated with increased ADR across all three institutions despite differences in race and baseline ADR. Patients should be counseled on the increased risk associated with diabetes and smoking. Initiatives should be implemented to insure improved screening rates for adenomas among diabetics and also to screen for diabetes so that interventions can be made early to reduce the impact of diabetes on colon cancer risk. Further prospective studies are needed to validate these findings. Citation Format: Yakira David, Lorenzo Ottaviano, Sadat Iqbal, Brandon Lung, Michelle Likhtshtegyn, Samir Kumar, Ellen Li, Laura Martello-Rooney, Shivakumar Vignesh, Joshua Miller, Evan Grossman. Impact of diabetes mellitus on adenoma detection rates in three disparate institutions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4238.

Background Studies of colonoscopic fecal microbiota transplant (FMT) in patients with recurrent CDI, indicate that this is a very effective treatment for preventing further relapses. In order to provide this service at Stony Brook University Hospital, we initiated an open-label prospective study of single colonoscopic FMT among patients with ≥ 2 recurrences of CDI, with the intention of monitoring microbial composition in the recipient before and after FMT, as compared with their respective donor. We also initiated a concurrent open label prospective trial of single colonoscopic FMT of patients with ulcerative colitis (UC) not responsive to therapy, after obtaining an IND permit (IND 15642). To characterize how FMT alters the fecal microbiota in patients with recurrent Clostridia difficile infections (CDI) and/or UC, we report the results of a pilot microbiome analysis of 11 recipients with a history of 2 or more recurrences of C. difficile infections without inflammatory bowel disease (CDI-only), 3 UC recipients with recurrent C. difficile infections (CDI + UC), and 5 UC recipients without a history of C. difficile infections (UC-only). Method V3V4 Illumina 16S ribosomal RNA (rRNA) gene sequencing was performed on the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient fecal samples along with those collected from the healthy donors. Fitted linear mixed models were used to examine the effects of Group (CDI-only, CDI + UC, UC-only), timing of FMT (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on the diversity and composition of fecal microbiota. Pairwise comparisons were then carried out on the recipient vs. donor and between the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient samples within each group. Results Significant effects of FMT on overall microbiota composition (e.g., beta diversity) were observed for the CDI-only and CDI + UC groups. Marked decreases in the relative abundances of the strictly anaerobic Bacteroidetes phylum, and two Firmicutes sub-phyla associated with butyrate production (Ruminococcaceae and Lachnospiraceae) were observed between the CDI-only and CDI + UC recipient groups. There were corresponding increases in the microaerophilic Proteobacteria phylum and the Firmicutes/Bacilli group in the CDI-only and CDI + UC recipient groups. At a more granular level, significant effects of FMT were observed for 81 genus-level operational taxonomic units (OTUs) in at least one of the three recipient groups (p

The intestine and other tissues are able to synthesize retinyl esters in an acyl-CoA-dependent manner involving an acyl-CoA:retinol acyltransferase (ARAT). However, the molecular identity of this ARAT has not been established. Recent studies of lecithin:retinol acyltransferase (LRAT)-deficient mice indicate that LRAT is responsible for the preponderance of retinyl ester synthesis in the body, aside from in the intestine and adipose tissue. Our present studies, employing a number of mutant mouse models, identify diacylglycerol acyltransferase 1 (DGAT1) as an important intestinal ARAT in vivo. The contribution that DGAT1 makes to intestinal retinyl ester synthesis becomes greater when a large pharmacologic dose of retinol is administered by gavage to mice. Moreover, when large retinol doses are administered another intestinal enzyme(s) with ARAT activity becomes apparent. Surprisingly, although DGAT1 is expressed in adipose tissue, DGAT1 does not catalyze retinyl ester synthesis in adipose tissue in vivo. Our data also establish that cellular retinol-binding protein, type II (CRBPII), which is expressed solely in the adult intestine, in vivo channels retinol to LRAT for retinyl ester synthesis. Contrary to what has been proposed in the literature based on in vitro studies, CRBPII does not directly prevent retinol from being acted upon by DGAT1 or other intestinal ARATs in vivo.

Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p