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Summary Spiral grain refers to the helical patterns formed by the wood grain in the trunks of many tree species. In most gymnosperms, grain near the pith is vertical but wood formed after several years of growth has a slight to pronounced left-handed twist. Grain changes presumably involve the slow rotation of cells within the vascular cambium, but the mechanisms that allow this reorientation to occur remain unclear. Understanding this process is, however, important as the presence of strong spiral grain within the corewood of gymnosperms is a major wood quality issue devaluing cut timber. In this study, we measured wood grain in stems of Pinus radiata (radiata pine) saplings through reconstructions of resin canals that follow the grain, visualised by serial sectioning and scanning with circularly polarised light, and through X-ray computed microtomography (μCT) and image analysis in ImageJ. Vertical trees retained a symmetrical grain pattern that was weakly right-handed near the pith, but which became progressively more left-handed during the first eight months of growth. In tilted trees, however, the development of left-handed grain was inhibited by the formation of compression wood on the lower side of the tree whereas the wood on the upper side of the tree developed increasingly more left-handed grain as in the vertical controls. These results demonstrate that a previously unidentified link exists between compression wood formation and the inhibition of grain development.

SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of the evolution and spread of pathogens and to inform policy decisions. Most efforts have focused on international or country-wide transmission, which are unable to highlight state-wide trends. We sequenced virus genomes from over 22,000 patients tested at Mayo Clinic Laboratories between 2020-2022 and leveraged detailed patient metadata to describe county-to-county spread in Minnesota. Our findings indicate that spread in the state was mostly dominated by viruses from Hennepin County, which contains the largest metropolis. For many counties, we found that state government restrictions eventually led to a decrease in the diversity of circulating viruses from other counties and that their complete removal in May of 2021 saw a drastic revert to levels at or greater than those observed during the months before. We also linked over 14,000 genomes with patient risk characteristics and infection-related phenotypes from the Mayo Clinic electronic health record. We found that the genetic relationship of Omicron viruses was structured by clinical outcomes when stratifying by patient risk factor and variant of concern. However, we were unable to identify nucleotide variants that drove this association.

SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020-2022 and use Bayesian phylodynamics to describe county and regional spread in Minnesota.The earliest introduction into Minnesota was to Hennepin County from a domestic source around January 22, 2020; six weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota, and eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International (MSP) airport) totaling 45 (out of 107) over the two-year period. Southern Minnesota counties were most common for domestic introductions with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n=772) over the two-year period.We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases or major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have impact on virus diversity across each individual county.ImportanceWe analyzed over 22,000 SARS-CoV-2 genomes of patient samples tested at Mayo Clinic Laboratories during a two-year period in the COVID-19 pandemic that included Alpha, Delta, and Omicron VoCs to examine the roles and relationships of Minnesota virus transmission.We found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after its initial introduction with the virus in early 2020 from an international source, while other counties acted as transmission “sinks”. In addition, major policies such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties.

Background: COVID-19 causes significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. It remains unclear which host factors determine disease severity and survival. Given the propensity of clonal hematopoiesis (CH) to promote inflammation in healthy individuals, we investigated its effect on COVID-19 outcomes. Methods: We performed a multi-omics interrogation of the genome, epigenome, transcriptome, and proteome of peripheral blood mononuclear cells from COVID-19 patients (n=227). We obtained clinical data, laboratory studies, and survival outcomes. We determined CH status and TET2-related DNA methylation. We performed single-cell proteogenomics to understand clonal composition in relation to cell phenotype. We interrogated single-cell gene expression in isolation and in conjunction with DNA accessibility. We integrated these multi-omics data to understand the effect of CH on clonal composition, gene expression, methylation of cis-regulatory elements, and lineage commitment in COVID-19 patients. We performed shRNA knockdowns to validate the effect of one candidate transcription factor in myeloid cell lines. Results: The presence of CH was strongly associated with COVID-19 severity and all-cause mortality, independent of age (HR 3.48, 95% CI 1.45-8.36, p=0.005). Differential methylation of promoters and enhancers was prevalent in TET2-mutant, but not DNMT3A-mutant CH. TET2-mutant CH was associated with enhanced classical/intermediate monocytosis and single-cell proteogenomics confirmed an enrichment of TET2 mutations in these cell types. We identified cell-type specific gene expression changes associated with TET2 mutations in 102,072 single cells (n=34). Single-cell RNA-seq confirmed the skewing of hematopoiesis towards classical and intermediate monocytes and demonstrated the downregulation of EGR1 (a transcription factor important for monocyte differentiation) along with up-regulation of the lncRNA MALAT1 in monocytes. Combined scRNA-/scATAC-seq in 43,160 single cells (n=18) confirmed the skewing of hematopoiesis and up-regulation of MALAT1 in monocytes along with decreased accessibility of EGR1 motifs in known cis-regulatory elements. Using myeloid cell lines for functional validation, shRNA knockdowns of EGR1 confirmed the up-regulation of MALAT1 (in comparison to wildtype controls). Conclusions: CH is an independent prognostic factor in COVID-19 and skews hematopoiesis towards monocytosis. TET2-mutant CH is characterized by differential methylation and accessibility of enhancers binding myeloid transcriptions factors including EGR1. The ensuing loss of EGR1 expression in monocytes causes MALAT1 overexpression, a factor known to promote monocyte differentiation and inflammation. These data provide a mechanistic insight to the adverse prognostic impact of CH in COVID-19. Citation Format: Moritz Binder, Terra L. Lasho, Wazim Mohammed Ismail, Nana A. Ben-Crentsil, Jenna A. Fernandez, Minsuk Kim, Susan M. Geyer, Amelia Mazzone, Christy M. Finke, Abhishek A. Mangaonkar, Jeong-Heon Lee, Kwan Hyun Kim, Vernadette A. Simon, Fariborz Rakhshan Rohakthar, Amik Munankarmy, Susan M. Schwager, Jonathan J. Harrington, Melissa R. Snyder, Nathalie M. Droin, Eric Solary, Keith D. Robertson, Eric D. Wieben, Eric Padron, Nicholas Chia, Alexandre Gaspar-Maia, Mrinal M. Patnaik. Enhancer deregulation inTET2-mutant clonal hematopoiesis is associated with increased COVID-19 severity and mortality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 806.

For investigating the potential for personalized treatment of pancreatic cancer, two- and three-photon autofluorescence and second and third harmonic generation images were simultaneously generated from in vivo pancreatic tumor patient-derived xenograft (PDX) mice. Two different treatment regimens were administered to PDX mice for 5 weeks and compared. Control mice were treated only with saline. Mice were classified into three groups according to their response to the treatment: responsive, resistant, and control. Optical redox ratios were calculated from tumor regions which showed differences between the responsive group compared to the resistant and control groups.

Mature age Pinus radiata D. Don trees were sampled across nine sites in northern New South Wales, Australia, that were expected, based on site quality and inventory metrics, to exhibit significant variation in productivity and wood quality. Twenty trees per site were harvested and 13 mm diameter, pith-to-bark increment cores were extracted from three trees per site from eight of the nine sites for SilviScan analysis. Outerwood increment cores were collected from all trees for basic density measurement. The same trees were also sampled using an IML PD400 (Resi) instrument. Radial mean properties of wood basic density derived from Resi traces were found to correlate strongly with the mean density data derived from SilviScan analyses and from increment cores. The Resi-derived basic density of 10 mm radial segments was strongly correlated with SilviScan measures of basic density averaged at similar intervals.

Simultaneous label-free autofluorescence multi-harmonic (SLAM) microscopy images of treated and non-treated mice with xenografts derived from human pancreatic tumors were acquired and analyzed for evaluation of chemotherapeutic drug response.

BACKGROUND Aberrantly methylated genes represent important markers for cancer diagnosis. We describe a multiplex detection approach to efficiently quantify these markers for clinical applications such as colorectal cancer screening. METHODS Quantitative allele-specific real-time target and signal amplification (QuARTS) combines a polymerase-based target amplification with an invasive cleavage-based signal amplification. The fluorescence signal is detected in a fashion similar to real-time PCR. We measured the dynamic range and analytical sensitivity of multiplex QuARTS reactions with titrated plasmid DNA. We used the QuARTS technology to quantify methylated BMP3, NDRG4, VIM, and TFPI2 genes on 91 DNA samples extracted from colorectal tissues, including 37 cancers, 25 adenomas, and 29 healthy epithelia. The assays were designed in triplex format that incorporated ACTB as a reference gene. Percent methylation was calculated by dividing methylated strands over ACTB strands and multiplying by 100. RESULTS The QuARTS method linearly detected methylated or unmethylated VIM gene down to 10 copies. No cross-reactivity was observed when methylated assays were used to amplify 105 copies of unmethylated gene and vice versa. The multiplex assay detected methylated genes spiked in unmethylated genes at a 0.01% ratio and vice versa. At a diagnostic specificity cutoff of 95%, methylated BMP3, NDRG4, VIM, and TFPI2 detected 84%, 92%, 86%, and 92% of colorectal cancers and 68%, 76%, 76%, and 88% of adenomas, respectively. CONCLUSIONS The QuARTS technology provides a promising approach for quantifying methylated markers. The markers assayed highly discriminated colorectal neoplasia from healthy epithelia.

Current stool DNA tests identify about half of individuals with colorectal cancers and miss most individuals with advanced adenomas. We developed a digital melt curve (DMC) assay to quantify low-abundance mutations in stool samples for detection of colorectal neoplasms and compared this test with other approaches.We combined a melt curve assay with digital polymerase chain reaction and validated the quantitative range. We then evaluated its ability to detect neoplasms in 2 clinical studies. In study I, stool samples from patients with colorectal tumors with known mutations (KRAS, APC, BRAF, TP53) were assayed. In study II, archived stool samples from patients with advanced adenomas containing known KRAS mutations were assayed, along with controls. Results were compared with those from the stool DNA test PreGenPlus (Exact Sciences, Marlborough, MA), Hemoccult, and HemoccultSensa (both Beckman-Coulter, Fullerton, CA).The DMC assay detected samples in which only 0.1% of target genes were mutated. In study I, the DMC assay detected known mutations in 28 (90%) of 31 tumor samples and 6 (75%) of 8 advanced adenoma samples. In study II, the DMC assay detected 16 (59%) of 27 advanced adenoma samples that contained KRAS mutations, compared with 7% with the Hemoccult, 15% with the HemoccultSensa, and 26% with the PreGenPlus assays (P.05 for each, compared with the DMC assay); specificities did not differ significantly.The DMC assay has a high level of sensitivity in detecting individuals with colon neoplasms and is better than current stool screening methods in detecting those with advanced adenomas. Further studies are indicated.

Human long DNA in stool may reflect nonapoptotic exfoliation and has been used as a colorectal cancer (CRC) marker. Targeting human-specific Alu repeats represents a logical but untested approach. A real-time Alu PCR assay was developed for quantifying long human DNA in stool and evaluated in this study. The accuracy and reproducibility of this assay and the stability of long DNA during room temperature fecal storage were assessed using selected patient stools and stools added to human DNA. Thereafter, long DNA levels were determined in blinded fashion from 18 CRC patients and 20 colonoscopically normal controls. Reproducibility of real-time Alu PCR for quantifying fecal long DNA was high (r2 = 0.99; P < 0.01). Long DNA levels in nonbuffered stools stored at room temperature fell a median of 75% by 1 day and 81% by 3 days. An EDTA buffer preserved DNA integrity during such storage. Human long DNA was quantifiable in all stools but was significantly higher in stools from CRC patients than from normal controls (P < 0.05). At a specificity of 100%, the sensitivity of long DNA for CRC was 44%. Results indicate that real-time Alu PCR is a simple method to sensitively quantify long human DNA in stool. This study shows that not all CRCs are associated with increased fecal levels of long DNA. Long DNA degrades with fecal storage, and measures to stabilize this analyte must be considered for optimal use of this marker. (Cancer Epidemiol Biomarkers Prev 2006;15(6):1115–9)

Colorectal tumor-associated antigens are attractive targets for novel stool-screening assays. MUC1, a glycoprotein antigen, is aberrantly expressed in transformed colorectal mucosa and represents a candidate fecal biomarker. In this study, tissue staining and stool testing were performed to further clarify the discriminant potential of MUC1 in markedly different biologic media. One anti-MUC1 monoclonal antibody (MA5) was used for immunohistochemistry and two commercially available MUC1 assay kits (ELSA-CA 15-3 and Truquant BR) were used for stool detection. On tissue staining, MUC1 expression was strong in 40/40 (100%) adenocarcinomas, moderate in 42/55 (76%) adenomas, faint in 8/28 (29%) juxtatumoral mucosa specimens, and absent in 15/15 (0%) nonadjacent mucosa specimens. Conversely MUC1 levels in stool testing did not differ between colorectal cancer cases (N = 14) and controls (N = 14). Based on these results, MUC1 appears to be a functional tumor biomarker in colorectal tissue but not in stool. Bacterial metabolism within stool may unmask the core antigen of MUC1 and account for this discordance in immunoreactivity.

Background & Aims It is not clear what proportion of synchronous or metachronous colorectal cancers (CRCs) are associated with DNA mismatch repair (MMR) alterations or unsuspected Lynch syndrome. On the basis of tissue analyses, the aims were to evaluate DNA MMR expression in metachronous, synchronous, and isolated sporadic CRCs and to assess within-patient concordance of MMR expression in metachronous and synchronous CRCs. Methods Tissue was evaluated from 34 patients with metachronous CRC, 34 matched solitary CRC patients, and 40 patients with synchronous CRCs. Subjects with known hereditary CRC were excluded. Immunohistochemical staining for MLH1 and MSH2 was performed on all tissues. Results Absent MLH1 or MSH2 staining of the initial metachronous tumor was observed in 27% compared with 21% of control CRCs, P = .58. The odds of metachronicity with absent immunostaining were 1.33 (95% confidence interval, 0.46–3.84). Loss of MMR expression was observed in at least one cancer in 30% of patients with synchronous CRC. MMR expression loss was discordant in 70% of metachronous CRCs and 50% of synchronous CRCs. Lynch syndrome was subsequently diagnosed in 2 patients with synchronous CRCs, both with concordant tumor MMR loss but in no patient with metachronous CRC. Conclusions Among those without known Lynch syndrome, development of multiple primary CRCs appears to be due largely to somatic events and often occurs via different molecular pathways within the same patient. Altered MMR expression in sporadic CRC has low predictive value for metachronicity. MMR expression analysis in cases of multiple primary CRC might identify a small number of patients with unsuspected Lynch syndrome.

Discriminant markers are required for accurate cancer screening. We evaluated genes frequently methylated in colorectal neoplasia to identify the most discriminant ones. Four genes specifically methylated in colorectal cancer [bone morphogenetic protein 3 (BMP3), EYA2, aristaless-like homeobox-4 (ALX4), and vimentin] were selected from 41 candidate genes and evaluated on 74 cancers, 62 adenomas, and 70 normal epithelia. Methylation status was analyzed qualitatively and quantitatively and confirmed by bisulfite genomic sequencing. Effect of methylation on gene expression was evaluated in five colon cancer cell lines. K-ras and BRAF mutations were detected by sequencing. Methylation of BMP3, EYA2, ALX4, or vimentin was detected respectively in 66%, 66%, 68%, and 72% of cancers; 74%, 48%, 89%, and 84% of adenomas; and 7%, 5%, 11%, and 11% of normal epithelia (P < 0.01, cancer or adenoma versus normal). Based on area under the curve analyses, discrimination was not significantly improved by combining markers. Comethylation was frequent (two genes or more in 72% of cancers and 84% of adenomas), associated with proximal neoplasm site (P < 0.001), and linked with both BRAF and K-ras mutations (P < 0.01). Cell line experiments supported silencing of expression by methylation in all four study genes. This study shows BMP3, EYA2, ALX4, and vimentin genes are methylated in most colorectal neoplasms but rarely in normal epithelia. Comethylation of these genes is common, and pursuit of complementary markers for methylation-negative neoplasms is a rational strategy to optimize screening sensitivity. (Cancer Epidemiol Biomarkers Prev 2007;16(12):2686–96)

Background: Assay of methylated DNA markers in stool is a promising approach for colorectal cancer (CRC) screening. A method to capture hypermethylated CpG islands from stool would enrich target analyte and allow optimal assay sensitivity.Methods: Methyl-binding domain (MBD) protein was produced using a pET6HMBD plasmid with MBD DNA sequence cloned from rat MeCP2 gene and bound to a column of nickel-agarose resin. We first established the feasibility of using the MBD column to extract methylated human DNA in a high background of fecal bacterial DNA. To explore the impact of MBD enrichment on detection sensitivity, the tumor-associated methylated vimentin gene was assayed with methylation-specific PCR from stools to which low amounts of cancer cell DNA (0–50 ng) were added and from stools from CRC patients and healthy individuals. Stools from cancer patients were selected with low amounts of human DNA (median 7 ng, range 0.5–832 ng).Results: With MBD enrichment, methylated vimentin was detected in stools enriched with ≥10 ng of cancer cell DNA and in CRC stool with a range of native human DNA amounts from 4 to 832 ng. Without MBD enrichment, methylated vimentin was not detected in the enriched stools and was detected in only 1 cancer stool with high human DNA (832 ng). In stools from healthy individuals methylated vimentin was not detected, with or without MBD enrichment.Conclusions: MBD capture increases assay sensitivity for detecting methylated DNA markers in stool. Applied clinical studies for stool cancer screening are indicated.

Alpha-defensins 1-3 (human neutrophil peptides [HNP]1-3), reported to be elevated in tumor tissue and serum of patients with colorectal cancer (CRC), have not been studied in stool. We evaluated the neoplasm specificity of HPN1-3 and their discriminant value as stool markers for CRC.Protein and mRNA expression of HPN1-3 were assayed in CRC cell lines, microdissected CRC and normal epithelium, and white blood cells. HNP1-3 proteins in stools were quantified in blinded fashion from 30 normal subjects, 20 patients with CRC, 10 with a large colorectal adenoma, 10 with upper gastrointestinal cancer, and 10 with IBD. Stool lactoferrin was also quantified.HPN1-3 proteins were not detected in CRC cell lines but were high (4000 ng/mL) in white blood cells. mRNA levels of HPN1-3 were comparably low in CRC cell lines, microdissected CRC, and normal colon epithelium, but they were1000-fold and30,000-fold higher in white blood cells and neutrophils, respectively. Mean stool HPN1-3 levels were 17 ng/mL with normals, 125 ng/mL with CRC, 62 ng/mL with adenoma, 63 ng/mL with upper gastrointestinal cancer, and 231 ng/mL with IBD (P.01 for each patient group vs normals). HPN1-3 levels in IBD were higher than in CRC (P = .04). At 90% specificity, sensitivity of stool defensins was 35% for CRC, 40% for adenoma, 40% for upper gastrointestinal cancers, and 80% for IBD. Stool defensins and lactoferrin levels correlated (R2 = 0.70, P.001).Alpha-defensins 1-3 levels are nonspecifically elevated in stools from patients with colorectal neoplasia and likely originate from white blood cells. Alpha-defensins 1-3 in stool might serve as markers of inflammatory bowel conditions.

This study explored the eyes absent 4 (EYA4) gene promoter methylation in noncolitic colorectal tissues and assessed its discrimination for neoplasia in chronic ulcerative colitis (CUC).The methylation status of noncolitic specimens was confirmed by direct bisulfite sequencing. Methylation-specific polymerase chain reaction (MSP) primers were designed to evaluate colorectal tissues, including 50 noncolitic patients comprising 24 normal epithelia, 14 polyps, and 12 cancers. The assay was tested on tissues from 67 CUC patients including 31 surveillance neoplasia-positive patients and nonneoplastic controls including 22 CUC surveillance-negative and 14 CUC short-disease duration. Remote colonic tissue was included from each of 27 of the 31 CUC neoplasia cases. The expression of EYA4 was quantified in cell lines by use of reverse-transcription polymerase chain reaction.Within noncolitic tissues, bisulfite sequencing showed EYA4 promoter hypermethylation in 80% (8 of 10) of colorectal cancers but in none (0 of 9) of the normal tissues. MSP was positive in 81% (21 of 26) of cancers and polyps and in only 4% (1 of 14) of normal mucosa. In CUC, MSP was positive in 81% (25 of 31) of neoplastic cases but in none (0 of 36) of the nonneoplastic controls. RNA expression was decreased in methylated compared with unmethylated cell lines (P.001). Treatment with 5-Aza-2'-deoxycytidine (DAC)/Trichostatin (TSA) increased the overall messenger RNA expression (P = .005).The EYA4 gene promoter is hypermethylated commonly in sporadic and colitic neoplasia and may be associated with gene silencing. EYA4 methylation represents a candidate marker for CUC surveillance.

Most esophageal adenocarcinomas arise within Barrett's esophagus but the cause of this increasingly prevalent condition remains unknown. Early detection improves survival and discriminant screening markers for Barrett's esophagus and cancer are needed. This study was designed to explore the natural history of eyes absent 4 (EYA4) gene methylation in the neoplastic progression of Barrett's esophagus and to evaluate methylated EYA4 as a candidate marker. Aberrant promoter methylation of EYA4 was studied by methylation-specific PCR using bisulfite-treated DNA from esophageal adenocarcinomas, Barrett's esophagus, and normal epithelia, and then confirmed by sequencing. Eight cancer cell lines were treated with the demethylation agent 5-aza-2′-deoxycytidine, and EYA4 mRNA expression with and without treatment was quantified by real-time reverse-transcription PCR. EYA4 hypermethylation was detected in 83% (33 of 40) of esophageal adenocarcinomas and 77% (27 of 35) of Barrett's tissues, but only in 3% (2 of 58) of normal esophageal and gastric mucosa samples (P < 0.001). The unmethylated cancer cell lines had much higher EYA4 mRNA expression than the methylated cancer cell lines. Demethylation caused by 5-aza-2′-deoxycytidine increased the mRNA expression level by a median of 3.2-fold in methylated cells, but its effect on unmethylated cells was negligible. Results indicate that aberrant promoter methylation of EYA4 is very common during tumorigenesis in Barrett's esophagus, occurs in early metaplasia, seems to be an important mechanism of down-regulating EYA4 expression, and represents an intriguing candidate marker for Barrett's metaplasia and esophageal cancer.

Hypermethylation of secreted frizzled-related proteins (SFRP) genes frequently occurs with several cancers but has not been studied in esophageal adenocarcinoma or its precursor-Barrett's esophagus. To explore the role of SFRP methylation in the neoplastic progression of Barrett's esophagus and to evaluate methylated SFRP genes as biomarkers for Barrett's esophagus and cancer, methylation of SFRP genes was determined in esophageal adenocarcinomas, Barrett's esophagus and normal epithelia using methylation-specific PCR. Protein expression of SFRP genes was then assessed in these tissues by immunohistochemistry. The mRNA expression of SFRP genes was quantified by real-time reverse-transcription PCR in esophageal adenocarcinoma cell lines with and without demethylation by 5-aza-2'deoxycytidine and inhibition of deacetylation by trichostatin A treatment. Hypermethylation of SFRP1, 2, 4 and 5 was detected in 93%, 83%, 73% and 85% of 40 cancers; 81%, 89%, 78% and 73% of 37 Barrett's epithelia; 25%, 64%, 32% and 21% of 28 adjacent normal epithelia from Barrett's patients; and 10%, 67%, 0% and 13% of 30 normal esophagogastric epithelia from healthy individuals, respectively (p < 0.001 for SFRP1, 4 and 5; p < 0.05 for SFRP2). Protein expression of SFRP1, 2 and 4 was downregulated in 87%, 67% and 90% of cancers, and expression correlated inversely with grade and stage of cancers and with grade of dysplasia. Expression of SFRP2 and SFRP4 proteins was lower in cancers with corresponding gene methylation (p < 0.05). Demethylation treatment effectively re-expressed SFRP mRNA in cancer cell lines. Thus, hypermethylation of SFRP genes is a common early event in the evolution of esophageal adenocarcinoma, and methylation of SFRP1, 4 and 5 might serve as biomarkers for Barrett's neoplasia. Aberrant promoter methylation appears to functionally silence SFRP gene expression in esophageal adenocarcinoma.

Objectives Stool testing is a well established method of screening for colorectal neoplasia. Emerging data suggest that novel biomarkers may offer performance advantages over fecal occult blood. In this large, prospective study, we assessed fecal calprotectin (a leukocyte-derived protein) as a screening biomarker for colorectal neoplasia. Fecal calprotectin was directly compared to fecal hemoglobin (Hb) and colonoscopy as the existing criterion standards for stool screening and structural evaluation, respectively. Methods Subjects included colonoscopy patients with a personal history of colorectal neoplasia, family history of colorectal cancer, or iron deficiency anemia. Stool specimens were collected before purgation, processed appropriately, and quantitatively analyzed for calprotectin (Nycomed Pharma, Oslo, Norway) and for Hb (Mayo Medical Laboratories, Rochester, MN) by masked technicians. Colonoscopies were performed by experienced endoscopists without prior knowledge of the fecal assay results. Results Among 412 subjects, 97 (24%) subjects had one or more colorectal neoplasms (including three with adenocarcinomas). Fecal calprotectin levels did not differ significantly between subjects with versus subjects without colorectal neoplasms (p = 0.33). Neither tumor number (p = 0.85) nor tumor size (p = 0.86) significantly influenced the observed fecal calprotectin concentrations. Estimates of the sensitivity, specificity, and positive and negative predictive values of fecal calprotectin for any colorectal neoplasms were 37%, 63%, 23%, and 76%, respectively. Comparable performance estimates for fecal Hb were 3%, 97%, 27%, and 77%, respectively. Conclusions In this cohort of colonoscopy patients at above average risk, fecal calprotectin was a poor screening biomarker for colorectal neoplasia. Further investigation of tumor-derived, rather than blood-based, biomarkers may be a more rewarding approach to stool screening for colorectal neoplasia.

To compare rates of detection of occult upper gastrointestinal (GI) tract bleeding by guaiac (Hemoccult II [HO]), immunochemical (HemeSelect [HS]), and heme-porphyrin (HemoQuant [HQT]) fecal occult blood tests. PATIENTS, SUBJECTS, AND METHODS: In a cross-sectional study to detect native occult upper GI tract bleeding, single stools were collected from 56 patients with iron deficiency and a proven hemorrhagic GI tract lesion. In a longitudinal study to detect simulated occult upper GI tract bleeding, 3 stool samples were serially collected from 10 clinically normal subjects after ingestion of 5 and 15 mL of autologous blood. All stool samples were subjected to blinded fecal occult blood determinations with use of the 3 tests.In the cross-sectional study, the HQT test detected 88% (37/42) of hemorrhagic upper GI tract lesions compared with 26% (11/42) detected by the HO test (P.001) and 2% (1/42) by the HS test (P.001). In the longitudinal study, all preingestion fecal occult blood test results were negative. After ingestion of 5 mL of blood, the HQT result became positive in 60% (6/10), and the HO and HS results remained negative (P=.03). After ingestion of 15 mL of blood, the HQT result became positive in all 10 cases, the HO result was positive in 6 (P=.12 vs HQT), and the HS result was positive in none (P=.002 vs HQT); all 3 stool samples collected after the 15-mL ingestion were positive in each of the 10 subjects by the HQT test but in only 1 subject by the HO test (P=.003).The HQT test detects occult upper GI tract blood loss significantly more frequently than the HO or HS test.

Background & Aims: Assay of altered DNA exfoliated into stool represents an intriguing approach to screen for colorectal neoplasia, but multiple markers must be targeted because of genetic heterogeneity. We explored the feasibility of a stool assay panel of selected DNA alterations in discriminating subjects with colorectal neoplasia from those without. Methods: Freezer-archived stools were analyzed in blinded fashion from 22 patients with colorectal cancer, 11 with adenomas ≥1 cm, and 28 with endoscopically normal colons. After isolation of human DNA from stool by sequence-specific hybrid capture, assay targets included point mutations at any of 15 sites on K- ras , p53 , and APC genes; Bat-26, a microsatellite instability marker; and highly amplifiable DNA. Results: Analyzable human DNA was recovered from all stools. Sensitivity was 91% (95% confidence interval, 71%–99%) for cancer and 82% (48%–98%) for adenomas ≥1 cm with a specificity of 93% (76%–99%). Excluding K- ras from the panel, sensitivities for cancer were unchanged but decreased slightly for adenomas to 73% (39%–94%), while specificity increased to 100% (88%–100%). Conclusions: Assay of altered DNA holds promise as a stool screening approach for colorectal neoplasia. Larger clinical investigations are indicated. GASTROENTEROLOGY 2000;119:1219-1227

Chronic diarrhea is a relatively common condition with multiple diverse etiologies. Stool testing may serve as a diagnostic aid to discriminate the presence or absence of organic pathology, such as colorectal inflammation. Calprotectin (a leukocyte-derived protein) and hemoglobin can be measured quantitatively from stool and represent candidate inflammation biomarkers. The aim of this study was to assess and compare the screening performance of fecal calprotectin and fecal hemoglobin among colonoscopy referral patients with chronic diarrhea of unknown origin or chronic colitis of unknown activity.All subjects were identified prospectively and each submitted a single stool sample before purgation. Fecal calprotectin (PhiCal; Nycomed Pharma, Oslo, Norway) and fecal hemoglobin (HemoQuant; Mayo Medical Laboratories, Rochester, MN) assays were performed in separate laboratories by masked technicians. Colonoscopic and histological findings served as criterion standards for establishing the presence or absence of colorectal inflammation.Among 110 subjects who provided complete fecal assay data, 29 (26%) had and 81 (74%) did not have colorectal inflammation. Increased fecal calprotectin levels were significantly (p = 0.0001) associated with the presence of colorectal inflammation, whereas fecal hemoglobin levels were not (p = 0.61). Direct comparison of the fecal assays revealed that calprotectin was a more sensitive biomarker for colorectal inflammation at all specificity levels (p = 0.0001).In this study of colonoscopy referral patients, colorectal inflammation was reflected by fecal calprotectin but not by fecal hemoglobin levels. Assay of fecal calprotectin holds promise as a triage tool to identify inflammatory causes of chronic diarrhea.

Characterization of shed cell elements entrapped within the colorectal surface mucus would be valuable to the study of exfoliation and candidate stool screening markers. Yet, surprisingly little is known about the cellular composition of this "mucocellular layer" (MCL). Our aim was to describe and compare the histomorphometry of the MCL that overlies colorectal cancer (CRC) and normal mucosa. From tissue archives, 20 resected CRC specimens yielding perpendicular cuts of both tumor surface and adjacent normal mucosa were consecutively selected. MCL thickness and cell number were determined in triplicate using an ocular micrometer. Cellular elements within the MCL were characterized on paraffin sections by immunohistochemistry. Mean cell density was much greater in the MCL over CRC (2,639 +/- 2,178 per mm2) than over normal mucosa (184 +/- 395 per mm2), p.001. Robust-appearing colonocytes and inflammatory cells predominated in the hypercellular MCL of CRC; the former retained expression of tumor-associated antigens. In contrast, the sparsely scattered cells within the normal MCL were typically apoptotic and of indeterminate lineage. Based on direct observations from this first descriptive study of the colorectal MCL, luminal shedding appears to be much greater from CRC than from normal mucosa.

Background: Serrated polyps are the critical precursors for 20-30% of colorectal cancers (CRCs) but have been largely excluded as screening outcomes to date. Serrated polyps, particularly the subset of sessile serrated adenomas (SSAs), are typically proximal, visually inconspicuous, rapid in growth, and characterized bymutant BRAF and aberrantlymethylated genes. Our preliminary data suggest that stool assay of mutant BRAF can detect SSAs (2010 Gastrointestinal Cancers Symposium, Orlando, FL). Aims: To assess detection of SSAs by stool assay of methylated vimentin (mVimentin) alone and in combination with mutant BRAF, and to compare detection accuracy with that of conventional fecal blood tests. Methods: In pre-study tissue analyses, mVimentin proved to discriminate SSAs from normal colonic mucosa and was selected for stool testing. Using our biospecimen archive from a multicenter screening study (Ann Intern Med 2008;149:441), unbuffered stools were identified from 14 cases with SSAs ≥1cm and blindly studied along with 19 matched controls without SSAs. Standard methods were used to extract stool DNA, and target genes were enriched by sequence capture. Following bisulfite treatment, mVimentin was quantified by methylation-specific PCR. Mutant BRAF was quantified by digital melt curve assay (Gastroenterology 2009;1136:459). Prospective Hemoccult and HemoccultSensa data (3 stools/patient) were available for comparison. Results: Median age was 68 (range 58-77) for SSA cases and 68 (55-74) for controls; respectively, 71% and 68% were female. Median SSA size was 1.5 cm (range 1-2) and 86% were proximal. Synchronous advanced adenomas were present in 36% of cases but in no controls. At 95% specificity cut-offs, stool assays of mVimentin and mutant BRAF respectively detected 57% and 50% of SSAs. In comparison, Hemoccult and HemoccultSensa each detected 7% (p

Noninvasive Detection of Colorectal Neoplasia (CRN) in Inflammatory Bowel Disease (IBD) by Stool DNA Testing: A Pilot Study John B. Kisiel, Tracy C. Yab, Fareeda Taher Nazer Hussain, William R. Taylor, Jonathan J. Harrington, Mary E. Devens, Julie A. Simonson, Megan Garrity-Park, William J. Sandborn, Edward V. Loftus, Bruce G. Wolff, David T. Rubin, Steven H. Itzkowitz, Hongzhi Zou, David A. Ahlquist

Non-apoptotic human DNA (long DNA) in stool is a discriminant marker for colorectal cancer (Gastroenterology 2000; 119:1219). Fecal long DNA may originate from either the exfoliation of dysplastic cells or from the luminal hemorrhage or exudation of leukocytes. The contribution of these potential sources long DNA in stool has not been examined. If leukocytes are the major source, then fecal human DNA and occult blood levels should correlate. If exfoliation is the major source, then fecal human DNA and occult blood should be complementary markers for colorectal cancer. AIM: To quantify and correlate human DNA and hemoglobin in stools from patients with colorectal neoplasia, and to consider a simple stool assay for cancer screening. METHODS: Subjects comprised 74 patients with colorectal cancer, 27 with adenomas >1cm, and 100 with normal colonoscopy. One stool per subject was collected in stabilization buffer before or > 1 week after colonoscopy. Fecal long DNA and occult blood were quantified in blinded fashion by real-time Alu PCR (CEBP 2006 15:1115) and the HemoQuant assay (Mayo Medical Laboratories), respectively. HemoQuant assay results are not affected by fecal storage (Ann Intern Med 1984;101:297) and could be reliably applied to archival specimens for this study. RESULTS: Fecal long DNA and occult blood showed no correlation (R2=0). At 90% specificities, long DNA testing detected 70% of colorectal cancers and 46% of adenomas while occult blood testing detected 50% and 12%, respectively. Combining these tests detected 80% colorectal cancers and 46% of adenomas at 90% specificity. For detection of colorectal cancer, AUC values were 0.82, 0.78, and 0.90 for fecal long DNA, occult blood, and combination testing, respectively (p

Background and aims: In this prospective study, we determined the long term clinical course of patients with symptomatic schatzki rings, who were treated by single dilatation. Besides we analyzed the frequency of associated esophageal disorders and their influence on the outcome. Methods: Since 1984 all patients with newly diagnosed symptomatic Schatzki rings were prospectively collected. They underwent structured interviews as well as endoscopic and/or radiographic examinations. 167 patients (124 male, 43 female) with a mean age of 57 +/14.6 (mean +/-1SD) years were studied. 133 (56,3%) patients were treated by single dilatationwith the use of malloney or savary gillard bougies (46-58F). No complications occurred. Follow up information was available in 94 of 133 patients and the average duration of follow up was 65months (range 12-254). All patients were symptom-free at the first followup examination, but late symptomatic recurrences were frequent. Duration of remission was evaluated by Kaplan-meier estimates of time to recurrence. Results: According to the KaplanMeier estimate, after 2 years of follow-up 71% (SE 4%), after 5 years 56% (SE 4%), and after 10 years 52% (SE 4%) had not yet received any repeated treatment. 40(42,2%)of the 94 patients showed further esophageal lesions like refluxesophagitis (24 patients), esophageal membranes (14 patients) and eosinophilic esophagitis (2 patients), but there were no significant influence on the time of recurrence. Conclusion: : The Schatzki Ring is frequently associated with other esophageal lesions. The most frequent of these are reflux esophagitis and esophageal membranes. However there is no influence on the likelihood of symptomatic recurrences, which is common in patients with Schatzki Ring after a successful dilatation.

Non-apoptotic human DNA (long DNA) in stool is a discriminant marker for colorectal cancer (Gastroenterology 2000; 119:1219). Fecal long DNA may originate from either the exfoliation of dysplastic cells or from the luminal hemorrhage or exudation of leukocytes. The contribution of these potential sources long DNA in stool has not been examined. If leukocytes are the major source, then fecal human DNA and occult blood levels should correlate. If exfoliation is the major source, then fecal human DNA and occult blood should be complementary markers for colorectal cancer. AIM: To quantify and correlate human DNA and hemoglobin in stools from patients with colorectal neoplasia, and to consider a simple stool assay for cancer screening. METHODS: Subjects comprised 74 patients with colorectal cancer, 27 with adenomas >1cm, and 100 with normal colonoscopy. One stool per subject was collected in stabilization buffer before or > 1 week after colonoscopy. Fecal long DNA and occult blood were quantified in blinded fashion by real-time Alu PCR (CEBP 2006 15:1115) and the HemoQuant assay (Mayo Medical Laboratories), respectively. HemoQuant assay results are not affected by fecal storage (Ann Intern Med 1984;101:297) and could be reliably applied to archival specimens for this study. RESULTS: Fecal long DNA and occult blood showed no correlation (R2=0). At 90% specificities, long DNA testing detected 70% of colorectal cancers and 46% of adenomas while occult blood testing detected 50% and 12%, respectively. Combining these tests detected 80% colorectal cancers and 46% of adenomas at 90% specificity. For detection of colorectal cancer, AUC values were 0.82, 0.78, and 0.90 for fecal long DNA, occult blood, and combination testing, respectively (p

Background and Aim: Altered expression of multidrug resistance 1 (MDR1) contributes to various cancers and its disease progression. DNA methylation is reported to present in various non-cancerous tissue as age-related phenomenon, suggesting that it occurs early in the process of tumorgenesis. We investigated the effect of MDR 1 gene promoter methylation on carcinogenesis in the stomach. Methods: In study A, we estimated the methylation ratio (MR) of the MDR1 gene promoter in both antral noncancerous mucosa and cancer lesions in 83 patients with gastric cancer (GC). In study B, we also estimated the MR in noncancerous gastric mucosa in 127 patients with GC and 82 cancer free (non-GC) subjects. Degree of histological chronic gastritis was scored according to updated Sydney systems in 200 subjects. We employed methylation-specific PCR method. Results: In the study A, MR of cancer lesions (31.3±20.5) was significantly higher than that of non noncancerous mucosa (20.9±31.3, p= 0.0004). MR was especially higher in Lauren's intestinal cancer (p

Non-apoptotic human DNA (long DNA) in stool is a discriminant marker for colorectal cancer (Gastroenterology 2000; 119:1219). Fecal long DNA may originate from either the exfoliation of dysplastic cells or from the luminal hemorrhage or exudation of leukocytes. The contribution of these potential sources long DNA in stool has not been examined. If leukocytes are the major source, then fecal human DNA and occult blood levels should correlate. If exfoliation is the major source, then fecal human DNA and occult blood should be complementary markers for colorectal cancer. AIM: To quantify and correlate human DNA and hemoglobin in stools from patients with colorectal neoplasia, and to consider a simple stool assay for cancer screening. METHODS: Subjects comprised 74 patients with colorectal cancer, 27 with adenomas >1cm, and 100 with normal colonoscopy. One stool per subject was collected in stabilization buffer before or > 1 week after colonoscopy. Fecal long DNA and occult blood were quantified in blinded fashion by real-time Alu PCR (CEBP 2006 15:1115) and the HemoQuant assay (Mayo Medical Laboratories), respectively. HemoQuant assay results are not affected by fecal storage (Ann Intern Med 1984;101:297) and could be reliably applied to archival specimens for this study. RESULTS: Fecal long DNA and occult blood showed no correlation (R2=0). At 90% specificities, long DNA testing detected 70% of colorectal cancers and 46% of adenomas while occult blood testing detected 50% and 12%, respectively. Combining these tests detected 80% colorectal cancers and 46% of adenomas at 90% specificity. For detection of colorectal cancer, AUC values were 0.82, 0.78, and 0.90 for fecal long DNA, occult blood, and combination testing, respectively (p

Stool DNA testing is a new approach to colorectal cancer detection. Few data are available from the screening setting.To compare stool DNA and fecal blood testing for detection of screen-relevant neoplasia (curable-stage cancer, high-grade dysplasia, or adenomas1 cm).Blinded, multicenter, cross-sectional study.Communities surrounding 22 participating academic and regional health care systems in the United States.4482 average-risk adults.Fecal blood and DNA markers. Participants collected 3 stools, smeared fecal blood test cards and used same-day shipment to a central facility. Fecal blood cards (Hemoccult and HemoccultSensa, Beckman Coulter, Fullerton, California) were tested on 3 stools and DNA assays on 1 stool per patient. Stool DNA test 1 (SDT-1) was a precommercial 23-marker assay, and a novel test (SDT-2) targeted 3 broadly informative markers. The criterion standard was colonoscopy.Sensitivity for screen-relevant neoplasms was 20% by SDT-1, 11% by Hemoccult (P = 0.020), 21% by HemoccultSensa (P = 0.80); sensitivity for cancer plus high-grade dysplasia did not differ among tests. Specificity was 96% by SDT-1, compared with 98% by Hemoccult (P0.001) and 97% by HemoccultSensa (P = 0.20). Stool DNA test 2 detected 46% of screen-relevant neoplasms, compared with 16% by Hemoccult (P0.001) and 24% by HemoccultSensa (P0.001). Stool DNA test 2 detected 46% of adenomas 1 cm or larger, compared with 10% by Hemoccult (P0.001) and 17% by HemoccultSensa (P0.001). Among colonoscopically normal patients, the positivity rate was 16% with SDT-2, compared with 4% with Hemoccult (P = 0.010) and 5% with HemoccultSensa (P = 0.030).Stool DNA test 2 was not performed on all subsets of patients without screen-relevant neoplasms. Stools were collected without preservative, which reduced detection of some DNA markers.Stool DNA test 1 provides no improvement over HemoccultSensa for detection of screen-relevant neoplasms. Stool DNA test 2 detects significantly more neoplasms than does Hemoccult or HemoccultSensa, but with more positive results in colonoscopically normal patients. Higher sensitivity of SDT-2 was particularly apparent for adenomas.