Simultaneous fingerprint and high‐wavenumber fiber‐optic Raman spectroscopy enhances real‐time in vivo diagnosis of adenomatous polyps during colonoscopy

Colorectal cancer can be prevented if detected early (e.g., precancerous polyps‐adenoma). Endoscopic differential diagnosis of hyperplastic polyps (that have little or no risk of malignant transformation) and adenomas (that have prominent malignant latency) remains an unambiguous clinical challenge. Raman spectroscopy is an optical vibrational technique capable of probing biomolecular changes of tissue associated with neoplastic transformation. This work aims to apply a fiber‐optic simultaneous fingerprint (FP) and high wavenumber (HW) Raman spectroscopy technique for real‐time in vivo assessment of adenomatous polyps during clinical colonoscopy. We have developed a fiber‐optic Raman endoscopic technique capable of simultaneously acquiring both the FP (i.e., 800–1800 cm^–1) and HW (i.e., 2800–3600 cm^–1) Raman spectra from colorectal tissue subsurface (<200 µm) for real‐time assessment of colorectal carcinogenesis. In vivo FP/HW Raman spectra were acquired from 50 patients with 17 colorectal polyps during clinical colonoscopy. Prominent Raman spectral differences (p < 0.001) were found between hyperplastic (n = 118 spectra), adenoma (n = 184 spectra) that could be attributed to changes in inter‐ and intra‐cellular proteins, lipids, DNA and water structures and conformations. Simultaneous FP/HW Raman endoscopy provides a diagnostic sensitivity of 90.9% and specificity of 83.3% for differentiating adenoma from hyperplastic polyps, which is superior to either the FP or HW Raman technique alone. This study shows that simultaneous FP/HW Raman spectroscopy technique has the potential to be a clinically powerful tool for improving early diagnosis of adenomatous polyps in vivo during colonoscopic examination.

     

Association between BMI and metabolic syndrome and adenomatous colonic polyps in Korean men

Obesity and insulin resistance are associated with the risk of colon cancer. Adenomatous colonic polyps are precancerous lesions of colon cancer. We investigated whether BMI and the metabolic syndrome are associated with the presence of adenomatous colonic polyps in Korean men. Anthropometric measurements, metabolic risk factors, and colonoscopic pathologic findings were assessed in 1,898 men who underwent routine colonoscopy at the Health Promotion Center of Asan Medical Center in 2005. The modified National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATP III) and International Diabetes Federation (IDF) criteria were used for the definition of the metabolic syndrome. Multiple logistic regression analysis was used to evaluate the association between BMI and the metabolic syndrome and adenomatous polyps. Compared with men in the 1st quintile of the BMI, the adjusted odds ratio (OR) and 95% confidence interval (CI) for adenomatous polyps in men in the 2nd, 3rd, 4th, and 5th quintiles of the BMI were 1.55 (1.10-2.19), 1.57 (1.10-2.24), 1.94 (1.34-2.81), and 1.99 (1.31-3.01), respectively (P for trend <0.0001). Men with triglycerides (TGs) > or = 150 mg/dl were significantly more likely to have adenomatous polyps than were men with TG <150 mg/dl (OR 1.29; 95% CI 1.03-1.62). As a function of the number of metabolic risk factors, the ORs for adenomatous polyps were 1.41 (1.03-1.93), 1.52 (1.08-2.12), 1.46 (1.01-2.12), and 1.77 (1.08-2.90) for 1, 2, 3, and > or = 4 risk factors, respectively (P for trend <0.05). Adenomatous colonic polyps were significantly associated with increased BMI levels. Subjects with even one component of the metabolic syndrome had a significantly higher risk for developing adenomatous polyps compared to those subjects without any component in Korean men.     

Combining near-infrared-excited autofluorescence and Raman spectroscopy improves in vivo diagnosis of gastric cancer

This study aims to evaluate the diagnostic utility of the combined near-infrared (NIR) autofluorescence (AF) and Raman spectroscopy for improving in vivo detection of gastric cancer at clinical gastroscopy. A rapid Raman endoscopic technique was employed for in vivo spectroscopic measurements of normal (n=1098) and cancer (n=140) gastric tissues from 81 gastric patients. The composite NIR AF and Raman spectra in the range of 800-1800 cm(-1) were analyzed using principal component analysis (PCA) and linear discriminant (LDA) to extract diagnostic information associated with distinctive spectroscopic processes of gastric malignancies. High quality in vivo composite NIR AF and Raman spectra can routinely be acquired from the gastric within 0.5s. The integrated intensity over the range of 800-1800 cm(-1) established the diagnostic implications (p=1.6E-14) of the change of NIR AF intensity associated with neoplastic transformation. PCA-LDA diagnostic modeling on the in vivo tissue NIR AF and Raman spectra acquired yielded a diagnostic accuracy of 92.2% (sensitivity of 97.9% and specificity of 91.5%) for identifying gastric cancer from normal tissue. The integration area under the receiver operating characteristic (ROC) curve using the combined NIR AF and Raman spectroscopy was 0.985, which is superior to either the Raman spectroscopy or NIR AF spectroscopy alone. This work demonstrates that the complementary Raman and NIR AF spectroscopy techniques can be integrated together for improving the in vivo diagnosis and detection of gastric cancer at endoscopy.     

Age-related increase in colorectal cancer stem cells in macroscopically normal mucosa of patients with adenomas: A risk factor for colon cancer

It is becoming increasingly evident that cancer stem cells play a vital role in development and progression of cancers and relapse following chemotherapy. The present study examines the presence of cancer stem-like cells (CSC) in adenomatous polyps and in normal appearing colonic mucosa in humans during aging. The number of polyps was found to increase linearly with advancing age (r² = 0.92, p < 0.02). Immunohistochemical analysis revealed co-localization of CSC markers CD44 and CD166 in colonic polyps. Real-time RT-PCR analysis of normal appearing mucosa from subjects with adenomatous polyps showed an age-related rise in CSC as evidenced by the increased expression of CD44, CD166 and ESA. A similar phenomenon was also observed for EGFR. In addition, the expression each CSC marker was found to be about 2-fold higher in subjects with 3–4 polyps than those with 1–2 polyps. In conclusion, our results show that colon cancer stem-like cells are present in the premalignant adenomatous polyps as well in normal appearing colonic mucosa. Moreover, our observation of the age-related rise in CSC in macroscopically normal colonic mucosa suggests a predisposition of the organ to developing colorectal cancer.     

甘油二酯激酶α在结直肠癌中的表达及其与PKC、TNFα的相关性

目的探讨甘油二酯激酶α(DGKα)在结直肠癌中的表达及其与蛋白激酶C(PKC)、肿瘤坏死因子α(TNFα)表达的相关性。方法应用免疫组化方法检测DGKα、PKC和TNFα在48例结直肠癌、癌旁正常组织和9例腺瘤性息肉中的表达。结果 DGKα在结直肠癌组织和癌旁正常组织有表达,结直肠癌组织中DGKα阳性表达率(79.2%)显著高于腺瘤性息肉(阴性)和癌旁正常组织(33.3%,P0.05);PKC主要分布在结直肠癌和癌旁正常组织中,结直肠癌组织中PKC阳性表达率(35.4%)显著高于腺瘤性息肉(阴性),与癌旁正常组织(20.8%)相比无显著性差异(P0.05);TNFα在三种组织中均表达阳性,结直肠癌组织中TNFα阳性表达率(95.8%)显著高于腺瘤性息肉(55.6%,P0.05),与癌旁正常组织(87.5%)相比无显著性差异(P0.05);结直肠癌组织中,DGKα与PKC的表达呈负相关(r=-0.437,P0.05),与TNFα的表达没有相关性(r=0.185,P0.05)。结论DGKα在结直肠癌组织中的表达高于腺瘤性息肉,DGKα可能抑制了PKC的活性,但对TNFα没有明显的抑制作用,在临床病理鉴别诊断中有辅助价值。     

In vivo fluorescence-based endoscopic detection of colon dysplasia in the mouse using a novel peptide probe

Colorectal cancer (CRC) is a major cause of cancer-related deaths in much of the world. Most CRCs arise from pre-malignant (dysplastic) lesions, such as adenomatous polyps, and current endoscopic screening approaches with white light do not detect all dysplastic lesions. Thus, new strategies to identify such lesions, including non-polypoid lesions, are needed. We aim to identify and validate novel peptides that specifically target dysplastic colonic epithelium in vivo. We used phage display to identify a novel peptide that binds to dysplastic colonic mucosa in vivo in a genetically engineered mouse model of colo-rectal tumorigenesis, based on somatic Apc (adenomatous polyposis coli) gene inactivation. Binding was confirmed using confocal microscopy on biopsied adenomas and excised adenomas incubated with peptide ex vivo. Studies of mice where a mutant Kras allele was somatically activated in the colon to generate hyperplastic epithelium were also performed for comparison. Several rounds of in vivo T7 library biopanning isolated a peptide, QPIHPNNM. The fluorescent-labeled peptide bound to dysplastic lesions on endoscopic analysis. Quantitative assessment revealed the fluorescent-labeled peptide (target/background: 2.17±0.61) binds ～2-fold greater to the colonic adenomas when compared to the control peptide (target/background: 1.14±0.15), p<0.01. The peptide did not bind to the non-dysplastic (hyperplastic) epithelium of the Kras mice. This work is first to image fluorescence-labeled peptide binding in vivo that is specific towards colonic dysplasia on wide-area surveillance. This finding highlights an innovative strategy for targeted detection to localize pre-malignant lesions that can be generalized to the epithelium of hollow organs.     

Colonic adenoma-associated Escherichia coli express specific phenotypes

Specific Escherichia coli strains have been associated to colorectal cancer, while no data are available on genotypic and phenotypic features of E. coli colonizing premalignant adenomatous polyps and their pathogenic potential. This study was aimed at characterizing isolates collected from polyps and adjacent tissue in comparison with those from normal mucosa.From colonoscopy biopsies, 1500 E. coli isolates were retrieved and genotyped; 272 were characterized for phylogroup and major phenotypic traits (i.e., biofilm formation, motility, hemolysins, and proteases). Selected isolates were analyzed for extraintestinal pathogenic E. coli (ExPEC)-associated virulence genes and in vivo pathogenicity using Galleria mellonella.The majority of isolates collected from polyps were strong biofilm and poor protease producers, whereas those isolates from normal mucosa were highly motile, proteolytic and weak biofilm formers. Isolates from adjacent tissues shared features with those from both polyps and normal mucosa. Among selected E. coli isolates, ExPEC gene content/profile was variable and uncorrelated with the tissue of collection and larval mortality.Despite the heterogeneous virulence-gene carriage of the E. coli intestinal population, E. coli colonizing colonic adenomatous polyps express specific phenotypic traits that could represent an initial pathoadaptation to local environmental changes characterizing these lesions.     

Identification of lymphatics within the colonic lamina propria in inflammation and neoplasia using the monoclonal antibody D2-40

CONTEXT: Lymphatic vessels are believed to be absent in the colon above the level of the mucularis mucosae. However, in our experience, lymphatic vessels are sometimes identifiable within the lamina propria in the setting of inflammation and neoplasia.OBJECTIVE: We sought to assess the presence of lymphatics within the colonic lamina propria in neoplastic and inflammatory conditions using the lymphatic endothelium-specific immunohistochemical marker D2-40.DESIGN: Representative sections of normal colon, inflamed colon, hyperplastic polyps, inflammatory polyps, adenomatous polyps, adenomatous polyps containing intramucosal carcinoma, and invasive colonic adenocarcinomas were subjected to immunohistochemical staining with D2-40. The presence of immunopositive lymphatic vessels was assessed. Lymphatic density within the lamina propria was calculated quantitatively, and the presence of inflammation was graded subjectively on a four-tiered scale (0-3).RESULTS: Lymphatics were not identified within the lamina propria of normal colon. However, lymphatics were identified within the lamina propria in the majority of cases with neoplasia and/or inflammation. Additionally, there was a non-significant trend toward higher lymphatic vessel density in cases with increasing inflammation.CONCLUSIONS: Lymphatic vessels are present within the lamina propria of colon in pathologic states, including cases of intramucosal carcinoma. This “aberrant” lymphangiogenesis is likely to be driven by inflammation and/or neoplasia.     

Interphasic nucleolar organizer region distribution as a diagnostic parameter to differentiate benign from malignant epithelial tumors of human intestine

The distribution of the interphasic nucleolar organizer regions (NORs) has been investigated in five hyperplastic polyps, five adenomatous polyps and fifteen colonic adenocarcinomas. The study was performed using electron microscopy and paraffin-embedded sections stained for Ag-NOR proteins. Malignant tumor cells were characterized by a large number of NORs which were small in size and showed a scattered distribution. Nuclei of both types of polyp had only a small number of large-sized NORs in a clustered distribution. In two adenomatous polyps, cells were also observed with an NOR distribution pattern intermediate between that of frankly benign and malignant lesions.     

Is Surveillance Colonoscopy Necessary for Patients with Sporadic Gastric Hyperplastic Polyps?

Background

Gastric polyps, such as adenomas and hyperplastic polyps, can be found in various colonic polyposis syndromes. Unlike in sporadic gastric adenomas, in which the increased risk of colorectal neoplasia has been well characterized, information in sporadic gastric hyperplastic polyps was limited.

Aim

To evaluate the association of sporadic gastric hyperplastic polyps with synchronous colorectal neoplasia in a large cohort.

Methods

Patients with sporadic gastric hyperplastic polyps who underwent colonoscopy simultaneously or within six months were consecutively enrolled. Each patient was compared with two randomly selected age and sex matched controls without gastric polyps who also underwent colonoscopy in the same period. Data of patients’ demographics and characteristics of the gastrointestinal polyps were documented.

Results

A total of 261 cases in 118,576 patients who underwent esophagogastroduodenoscopy were diagnosed as sporadic gastric hyperplastic polyps, and 192 of 261 (73.6%) patients underwent colonoscopy. Colorectal neoplasias were identified in 46 (24.0%) of 192 cases and in 40 (10.4%) of 384 controls (P＜0.001). The mean size and distribution of colorectal neoplasias were not significantly different between the two groups. There was a significantly higher rate of colorectal adenoma (odds ratio [OR] 3.2, 95% confidence interval [CI] 1.9–5.3) in the gastric hyperplastic polyps group than in the control group, while the prevalence of colorectal cancer was similar in the two groups. Logistic regression analysis also suggested that the presence of gastric hyperplastic polyps (OR 2.5, 95% CI 1.5–4.0) was an independent risk factor for colorectal neoplasias.

Conclusion

The risk of colorectal adenoma increases in patients with sporadic gastric hyperplastic polyps, and surveillance colonoscopy for these patients should be considered.     

Benign epithelial gastric polyps--frequency,location, and age and sex distribution

Prospective investigation has been undertaken with the aim to study the frequency, location and age and sex distribution of various histological types of benign gastric epithelial polyps. Histological type--adenomatous, hyperplastic and fundic gland polyps--was diagnosed on the basis of at least three histological samples taken from the polyp. Biopsy samples were also taken from the antrum and the body of the stomach so that gastritis could be graded and classified, and the presence of H. pylori could be determined by histology. All 6,700 patients, who had undergone upper gastrointestinal endoscopy in a one-year period, participated in this study. Among them 42 benign gastric epithelial polyp were found in 31 patients: adenomatous gastric polyps in 7 patients, hyperplastic gastric polyp in 21 and fundic gland polyp in 3 patients. All patients with hyperplastic polyps had chronic active superficial gastritis, whereas most of the patients with adenomatous polyps had a chronic atrophic gastritis with high prevalence of intestinal metaplasia. Among 21 patients with hyperplastic gastric polyps, 16 (76%) patients were positive for H. pylori infection in contrast to only 2 patients (29%) with adenomatous gastric polyps and 1 patient (33%) with fundic gland polyp. Presented data indicates that hyperplastic gastric polyps are the most common and they are associated with the presence of chronic active superficial gastritis and concomitant H. pylori infection. Adenomatous polyps are rarer and they tend to be associated with chronic atrophic gastritis and intestinal metaplasia. Fundic gland polyp is the rarest type of gastric polyps.     

Large intron 14 rearrangement in APC results in splice defect and attenuated FAP

Familial adenomatous polyposis [FAP (OMIM 175100)] is an autosomal dominant colorectal cancer predisposition syndrome characterized by hundreds to thousands of colonic polyps and, if untreated by a combination of screening and/or surgical intervention, a ~99% lifetime risk of colorectal cancer. A subset of FAP patients develop an attenuated form of the condition characterized by lower numbers of colonic polyps (highly variable, but generally less than 100) and a lower lifetime risk of colorectal cancer, on the order of 70%. We report the diagnosis of three attenuated FAP families due to a 1.4-kb deletion within intron 14 of APC, originally reported clinically as a variant of unknown significance (VUS). Sequence analysis suggests that this arose through an Alu-mediated recombination event with a locus on chromosome 6q22.1. This mutation is inherited by family members who presented with an attenuated FAP phenotype, with variable age of onset and severity. Sequence analysis of mRNA revealed an increase in the level of aberrant splicing of exon 14, resulting in the generation of an exon 13–exon 15 splice-form that is predicted to lead to a frameshift and protein truncation at codon 673. The relatively mild phenotypic presentation and the intra-familial variation are consistent with the leaky nature of exon 14 splicing in normal APC. The inferred founder of these three families may account for as yet undetected affected branches of this kindred. This and similar types of intronic mutations may account for a significant proportion of FAP cases where APC clinical analysis fails because of the current limitations of testing options.     

Inhibitory effects of anti-CXCR4 antibodies on human colon cancer cells

Background: CXCR4, the chemokine receptor for CXCL12, has recently been involved in the metastatic process of several neoplasms. Materials and methods: The expression of CXCR4 was evaluated by immunohistochemistry of colorectal tissue samples and by flow cytometry on Caco2, GEO, SW480, SW48, Lovo and SW620 human colon carcinoma cell lines. Correlations with pathological characteristics of the specimens were analysed with chi-square test. To verify the functional status of CXCR4, cell lines were tested in adhesion, migration, and proliferation assays. Results: We studied the expression of CXCR4 in 88 human colorectal tissues and we found that CXCR4 was expressed in >10% of epithelial cells in 50% of normal mucosae (7/14), in 55% of polyps (29/53), in all of carcinomas (16/16) and hepatic metastasis (5/5). Notably, CXCR4 was significantly over-expressed in cancerous lesions (carcinomas and metastasis) compared to non-cancerous lesions (normal mucosa and polyps) (P=0.003) and in adenomatous polyps versus hyperplastic polyps (P=0.009). The diameter of a polyp was also significantly associated with CXCR4 expression (P=0.031). SW480, SW48 and SW620 cell lines showed the highest levels of CXCR4 (60–80% of positive cells). Adhesion, migration, and proliferation increased in response to the CXCL12 chemokine. These effects were abrogated by the addition of anti-CXCR4 antibodies. Further, CXCL12 activated ERK1/2 in SW480 cells. Conclusions: These data suggest that CXCR4 might play a role in colon cancer cell properties and that anti-CXCR4 antibodies could have therapeutic effects against colorectal cancer.Partially presented at the 94th Annual Meeting of the American Association for Cancer Research, Washington, DC, 11–14 July 2003 (abstract LB-132).     

Expression of Abelson interactor 1 (Abi1) correlates with inflammation, KRAS mutation and adenomatous change during colonic carcinogenesis

Background

Abelson interactor 1 (Abi1) is an important regulator of actin dynamics during cytoskeletal reorganization. In this study, our aim was to investigate the expression of Abi1 in colonic mucosa with and without inflammation, colonic polyps, colorectal carcinomas (CRC) and metastases as well as in CRC cell lines with respect to BRAF/KRAS mutation status and to find out whether introduction of KRAS mutation or stimulation with TNFalpha enhances Abi1 protein expression in CRC cells.

Methodology/Principal Findings

We immunohistochemically analyzed Abi1 protein expression in 126 tissue specimens from 95 patients and in 5 colorectal carcinoma cell lines with different mutation status by western immunoblotting. We found that Abi1 expression correlated positively with KRAS, but not BRAF mutation status in the examined tissue samples. Furthermore, Abi1 is overexpressed in inflammatory mucosa, sessile serrated polyps and adenomas, tubular adenomas, invasive CRC and CRC metastasis when compared to healthy mucosa and BRAF-mutated as well as KRAS wild-type hyperplastic polyps. Abi1 expression in carcinoma was independent of microsatellite stability of the tumor. Abi1 protein expression correlated with KRAS mutation in the analyzed CRC cell lines, and upregulation of Abi1 could be induced by TNFalpha treatment as well as transfection of wild-type CRC cells with mutant KRAS. The overexpression of Abi1 could be abolished by treatment with the PI3K-inhibitor Wortmannin after KRAS transfection.

Conclusions/Significance

Our results support a role for Abi1 as a downstream target of inflammatory response and adenomatous change as well as oncogenic KRAS mutation via PI3K, but not BRAF activation. Furthermore, they highlight a possible role for Abi1 as a marker for early KRAS mutation in hyperplastic polyps. Since the protein is a key player in actin dynamics, our data encourages further studies concerning the exact role of Abi1 in actin reorganization upon enhanced KRAS/PI3K signalling during colonic tumorigenesis.     

Melanin quantification by in vitro and in vivo analysis of near‐infrared fluorescence

Objective measurements of melanin can provide important information for differentiating melanoma from benign pigmented lesions and in assessing pigmentary diseases. Herein, we evaluate near‐infrared (NIR) fluorescence as a possible tool to quantify melanin. Various concentrations of in vitro Sepia melanin in tissue phantoms were measured with NIR fluorescence and diffuse reflectance spectroscopy. Similar optic measurements were conducted in vivo on 161 normal human skin sites. Diffuse reflectance spectroscopy was used to quantify the melanin content via Stamatas–Kollias algorithm. At physiologic concentrations, increasing in vitro melanin concentrations demonstrated higher fluorescence that was linearly correlated (R² = 0.99, p < .001). At higher concentrations, the fluorescence signal plateaued. A linear relationship was also observed with melanin content in human skin (R² = 0.59, p < .001). Comparing the fluorescence and reflectance signals with in vitro and in vivo samples, the estimated melanin concentration in human skin ranged between 0 and 1.25 mg/ml, consistent with previous quantitative studies involving invasive methods.     

Germline mutations of the adenomatous polyposis coli (APC) gene in Algerian familial adenomatous polyposis cohort: first report

Background

Familial adenomatous polyposis (known also as classical or severe FAP) is a rare autosomal dominant colorectal cancer predisposition syndrome, characterized by the presence of hundreds to thousands of adenomatous polyps in the colon and rectum from an early age. In the absence of prophylactic surgery, colorectal cancer (CRC) is the inevitable consequence of FAP. The vast majority of FAP is caused by germline mutations in the adenomatous polyposis coli (APC) tumor suppressor gene (5q21). To date, most of the germline mutations in classical FAP result in truncation of the APC protein and 60% are mainly located within exon 15.

Material and methods

In this first nationwide study, we investigated the clinical and genetic features of 52 unrelated Algerian FAP families. We screened by PCR-direct sequencing the entire exon 15 of APC gene in 50 families and two families have been analyzed by NGS using a cancer panel of 30 hereditary cancer genes.

Results

Among 52 FAP index cases, 36 had 100 or more than 100 polyps, 37 had strong family history of FAP, 5 developed desmoids tumors, 15 had extra colonic manifestations and 21 had colorectal cancer. We detected 13 distinct germline mutations in 17 FAP families. Interestingly, 4 novel APC germline pathogenic variants never described before have been identified in our study.

Conclusions

The accumulating knowledge about the prevalence and nature of APC variants in Algerian population will contribute in the near future to the implementation of genetic testing and counseling for FAP patients.

     

Mutation analysis of <Emphasis Type="Italic">K-ras</Emphasis> protooncogene in colorectal adenocarcinomas and polyps in Russian patients

To estimate diagnostic value of K-ras mutations during cancer risk group formation, they were studied in the samples of sporadic carcinomas (n = 58), benign (n = 33), and malignant (n = 13) polyps of large intestine obtained during surgery or polypectomy. Using PCR analysis, restriction analysis, SSCP analysis and automated sequencing, eight various point mutations were revealed. Six of them were located in codon 12 and two, in codon 13 of the K-ras gene. Mutation frequency in carcinomas, benign and malignant polyps was 43, 49, and 69%, respectively. In the normal tissue samples of colorectum, no changes in codons 12 and 13 in the K-ras gene were observed. Mutations in the groups of Russian patients examined partially overlapped. In patients with colorectal carcinoma the mutation frequency in the K-ras gene was not associated with disease onset age, location, and the extent of tumor differentiation while it was associated with the stage of tumor process. In polyps, the maximum mutation frequency was revealed among patients over 70 years of age as well as in the adenomas of villous histology and large size (≥1cm). No correlation between the K-ras mutation frequency and the extent of polyp dysplasia was observed.     

Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon

Background

Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps can have overlapping morphological features resulting in sessile serrated polyps diagnosed as hyperplastic. While sessile serrated polyps can progress into colon cancer, hyperplastic polyps have virtually no risk for colon cancer. Objective measures, differentiating these types of polyps would improve cancer prevention and treatment outcome.

Methods

RNA-seq training data set and Affimetrix, Illumina testing data sets were obtained from Gene Expression Omnibus (GEO). RNA-seq single-end reads were filtered with FastX toolkit. Read mapping to the human genome, gene abundance estimation, and differential expression analysis were performed with Tophat-Cufflinks pipeline. Background correction, normalization, and probe summarization steps for Affimetrix arrays were performed using the robust multi-array method (RMA). For Illumina arrays, log₂-scale expression data was obtained from GEO. Pathway analysis was implemented using Bioconductor package GSAR. To build a platform-independent molecular classifier that accurately differentiates sessile serrated and hyperplastic polyps we developed a new feature selection step. We also developed a simple procedure to classify new samples as either sessile serrated or hyperplastic with a class probability assigned to the decision, estimated using Cantelli’s inequality.

Results

The classifier trained on RNA-seq data and tested on two independent microarray data sets resulted in zero and three errors. The classifier was further tested using quantitative real-time PCR expression levels of 45 blinded independent formalin-fixed paraffin-embedded specimens and was highly accurate. Pathway analyses have shown that sessile serrated polyps are distinguished from hyperplastic polyps and normal controls by: up-regulation of pathways implicated in proliferation, inflammation, cell-cell adhesion and down-regulation of serine threonine kinase signaling pathway; differential co-expression of pathways regulating cell division, protein trafficking and kinase activities.

Conclusions

Most of the differentially expressed pathways are known as hallmarks of cancer and likely to explain why sessile serrated polyps are more prone to neoplastic transformation than hyperplastic. The new molecular classifier includes 13 genes and may facilitate objective differentiation between two polyps.

     

Analyse de la taille et de la répartition des glandes coliques en endomicroscopie confocale de fluorescence : une voie prometteuse pour différencier in vivo les grades de néoplasie intra-épithéliale ?

Staining techniques currently used during endomicroscopic procedures do not allow in vivo differentiation between grades of intraepithelial neoplasia. This information is essential because it informs the degree of malignancy of the lesion and determines the most appropriate therapeutic treatment. The use of the Cellvizio^®GI system (Mauna Kea Technologies, Paris, France) allowed us to report here a series of observations relating to the size of colonic glands, and their layout on epithelial surface. These quantitative data were determined thanks to the analysis of several images mosaics from normal mucosa, hyperplastic polyps, and tubular adenoma. Our results showed that the glandular diameter and spacing had different features according to the histology and the grade of intraepithelial neoplasia.     

Decomposition and Mineralization of Organic Residues Predicted Using Near Infrared Spectroscopy

Characterization of decomposition characteristics is important for sound management of organic residues for both soils and livestock, but routine residue quality analysis is hindered by slow and costly laboratory methods. This study tested the accuracy and repeatability of near-infrared spectroscopy (NIR) for direct prediction of in vitro dry matter digestibility (IVDMD) and C and N mineralization for a diverse range of organic materials (mostly crop and tree residues) of varying quality (n = 32). The residue samples were aerobically incubated in a sandy soil and amounts of C and N mineralized determined after 28 days. IVDMD and quality attributes were determined using wet chemistry methods. Repeatability was higher with NIR than the original wet chemistry methods: on average NIR halved the measurement standard deviation. NIR predicted IVDMD and C and N mineralization more accurately than models based on wet chemical analysis of residue quality attributes: reduction in root mean square error of prediction with NIR, compared with using quality attributes, was IVDMD, 6%; C mineralization after 28 days, 8%; and N mineralization after 28 days, 8%. Cross-validated r ² values for measured wet chemistry vs. NIR-predicted values were: IVDMD, 0.88; C mineralization, 0.82; and N mineralization, 0.87. Direct prediction of decomposition and mineralization from NIR is faster, more accurate and more repeatable than prediction from residue quality attributes determined using wet chemistry. Further research should be directed towards establishment of diverse NIR calibration libraries under controlled conditions and direct calibration of soil quality, crop and livestock responses in the field to NIR characteristics of residues.