Non-invasive Colorectal Cancer Screening Tests Research Articles

A blood-based screening test for colorectal cancer (CRC) using methylation sequencing.

e15089 Background: Diagnosis of CRC is biased towards later stages in India (3.8% Stage I, 16.7% Stage II, 50.7% Stage III, 28.8% Stage IV), and five-year survival at < 40% is one of the lowest in the world. A blood-based non-invasive screening test for CRC using cell-free DNA (cfDNA) methylation sequencing is developed here from the blood of 212 controls and 67 treatment naive CRC patients from 21 sites across India and processed in Strand’s reference lab in Bangalore. Methods: Steps involved cfDNA extraction, NEB Enzymatic Methyl-Seq library preparation, Twist Human Methylome hybridisation capture, 2x150bp sequencing on NovaSeq 6000/X. Methylation + fragmentomic features were calculated for each target region. Samples were split randomly into a leave-in set of 170 controls + 53 cancers (I: 8, II 16, III: 23, IV: 6) and a leave-out set of 42 controls + 14 cancers, (I: 5, II: 4, III: 2, IV: 3) with 20 rounds of 4-fold cross-validation done on the leave-in set (random splits). Feature selection per fold was performed using the KS test without access to ¼ of the leave-in set and to the entire leave-out set. Gradient boosted trees with monotonic constraints reflecting the expected association of the scores with cancer were used to build “explainable” models. Test robustness was assessed using differentially methylated regions (DMRs) from other studies, and by assessing predictability using sample metadata alone. Results: At a 91% specificity level, the ensemble model had a median sensitivity of 62.5% for Stage I (95%CI 38%-86%), 87% for Stage II (95% CI 75%-95%), 87% for Stage III (95% CI 75%-95%) and 83.4% for Stage IV (95% CI 84%-100%) in cross-validation, and 60% for Stage I (95%CI 60%-80%), 100% for Stage II (95% CI 80%-100%), 100% for Stage III (95% CI 100%-100%) and 100% for Stage IV (95% CI 100%-100%) on the leave-out set. At a ~98% specificity level, the model had a median sensitivity of 37.5% for Stage I (95%CI 37%-50%), 69% for Stage II (95% CI 56%-75%), 69% for Stage III (95% CI 60%-84%) and 67% for Stage IV (95% CI 50%-84%) in cross-validation, and 40% for Stage I (95%CI 20%-60%), 75% for Stage II (95% CI 75%-100%), 100% for Stage III (95% CI 100%-100%) and 100% for Stage IV (95% CI 66%-100%) with a slight decrease in specificity to 95.2% on the leave-out set. Using DMRs derived from TCGA data and other publications, yielded a comparable (to our models) cross-validation area under the curve (AUC: 0.93-0.95). Cross-validation performance using only the sample metadata in table 1 and without access to the data was significantly poorer (AUC 0.75-0.81). Conclusions: cfDNA-based methylation profiles are consistent across studies and ethnicities, leading to robust and “explainable” CRC screening predictions. [Table: see text]

Real-world multi-target stool DNA longitudinal adherence for colorectal cancer re-screening in a large, national population.

e15633 Background: Colorectal cancer (CRC) is the fourth most diagnosed cancer, as well as the second leading cause of cancer death in the United States – with an estimated 152,810 diagnoses and 53,010 fatal cases in 2024. Regular screening and early detection can reduce CRC incidence and improve overall survival; however, recent national survey data (2021) demonstrate that only 59% of the US screen-eligible population (≥ age 45) is up to date. Home-based, non-invasive CRC screening test options, such as the multi-target stool DNA (mt-sDNA) test, have the potential to improve patient outcomes and overcome CRC screening adherence barriers at multiple levels. Given that the recommended interval for mt-sDNA is three years, a better understanding of use in repeat users is warranted. We evaluated the effective rescreen rate of previous mt-sDNA test users. Methods: In this retrospective cohort study, we included patients between the ages of 45 and 75 years who were shipped an mt-sDNA test kit between January 1st – December 31st, 2023, and had previously completed mt-sDNA screening with a negative result > 2.5 years prior. Our primary variable of interest was mt-sDNA completion rate on repeat testing, defined as kit receipt with a valid result within 120 days of the shipment date. Regression analysis was performed to determine baseline characteristics associated with repeat test completion rate. Results: During the analysis period, a total of 481,748 patients who met the inclusion criteria received an mt-sDNA kit. The majority of the cohort was female (61.4%) and between the ages of 65-75 years (50.9%). Overall repeat test completion rate was 83.6%, with the average time to kit return being 18.9 days. Completion rates were similar between males (83.8%) and females (83.6%), and patients receiving included navigation support via mobile phones demonstrated the shortest average time to kit return (18.7 days). Completion rates increased concordantly with patient age: 81.6%, (45-49 years), 82.2% (50-64 years), and 85% (65-75 years). For first-time rescreen participants (2nd lifetime mt-sDNA test), the completion rate was 83.1%. For second-time rescreen participants (3rd lifetime mt-sDNA test), the completion rate was even higher at 93.6%. Logistic regression analyses revealed that patients re-screening for a second-time were three times more likely to return the mt-sDNA kit for CRC screening (OR = 3.118; p < 0.001). Conclusions: Data from this large, retrospective cohort study revealed that repeat CRC screening with the mt-sDNA test is associated with high adherence to triennial follow-up among participants. suggesting a high-level of perceived patient confidence in repeat performance of the mt-sDNA test. These novel data provide relevant insights regarding strong patient willingness to continue with home-based, non-invasive mt-sDNA testing over multiple cycles of average-risk CRC screening.

Machine learning-based identification of colorectal advanced adenoma using clinical and laboratory data: a phase I exploratory study in accordance with updated World Endoscopy Organization guidelines for noninvasive colorectal cancer screening tests.

The recent World Endoscopy Organization (WEO) guidelines now recognize precursor lesions of colorectal cancer (CRC) as legitimate screening targets. However, an optimal screening method for detecting advanced adenoma (AA), a significant precursor lesion, remains elusive. We employed five machine learning methods, using clinical and laboratory data, to develop and validate a diagnostic model for identifying patients with AA (569 AAs vs. 3228 controls with normal colonoscopy). The best-performing model was selected based on sensitivity and specificity assessments. Its performance in recognizing adenoma-carcinoma sequence was evaluated in line with guidelines, and adjustable thresholds were established. For comparison, the Fecal Occult Blood Test (FOBT) was also selected. The XGBoost model demonstrated superior performance in identifying AA, with a sensitivity of 70.8% and a specificity of 83.4%. It successfully detected 42.7% of non-advanced adenoma (NAA) and 80.1% of CRC. The model-transformed risk assessment scale provided diagnostic performance at different positivity thresholds. Compared to FOBT, the XGBoost model better identified AA and NAA, however, was less effective in CRC. The XGBoost model, compared to FOBT, offers improved accuracy in identifying AA patients. While it may not meet the recommendations of some organizations, it provides value for individuals who are unable to use FOBT for various reasons.

Associations between sociodemographic factors and breast, cervical, and colorectal cancer screening in the United States.

Cancer is the second leading cause of death globally and in the U.S., but screening can reduce cancer-related deaths. We analyzed data from a nationwide survey to compare how sociodemographic factors were associated with never or not timely screening for multiple types of cancer, and the use of different colorectal cancer screening procedures. We analyzed data from the 2019 U.S. National Health Interview Survey. To understand breast, cervical, and colorectal cancer screening participation among those recommended to screen, we respectively analyzed 8,110 women 45 to 74 years of age, 9,583 women 21 to 65 years of age, and 13,497 individuals 50 to 75 years of age at survey. Weighted Poisson regression was used to estimate the unadjusted and confounding-adjusted prevalence ratio and 95% confidence intervals. In our analysis populations, 6.9% never had a mammogram, 14.6% never screened for cervical cancer, and 26.8% never screened for colorectal cancer; the prevalence respectively increased to 24.7%, 23.8%, and 32.3% for not timely screening according to national guidelines. The prevalence of never screening was 81.9% for non-invasive colorectal cancer tests, compared with 32.5% for colonoscopy or sigmoidoscopy. Individuals with lower education level, with no health insurance, or in poverty had higher prevalence of never screening for all three cancers. There was low sociodemographic disparity for the use of non-invasive colorectal cancer screening tests. Socioeconomically disadvantaged individuals have higher prevalence of never or not timely screening. The utilization of non-invasive colorectal cancer screening procedures remains low across sociodemographic groups.

The impact of multi-target stool DNA testing in clinical practice in the United States: A real-world evidence retrospective study

Widely endorsed screening modalities for colorectal cancer (CRC) include structural visualization (e.g. colonoscopy) and stool-based tests including multitarget stool DNA (mt-sDNA), fecal immunochemical tests (FIT), or high-sensitivity guaiac-based fecal occult blood tests (gFOBT). However, CRC screenings are underutilized, hence understanding the screening utilization trends is important, particularly with respect to the newest guideline-endorsed option (mt-sDNA). The objective of this study was to assess patterns in overall CRC screenings following clinical availability of the mt-sDNA test among average-risk individuals in the Ascension Wisconsin healthcare system focusing primarily on individuals aged 50–75 years old. We also reported CRC screening behaviors among individuals < 50 and > 75 years old. Electronic medical records of individuals aged ≥ 40 years from 2015 to 2018 were reviewed to identify average-risk and screen-eligible members. For those with screening data available, we determined the proportion who were up-to-date with any United States Preventive Services Task Force (USPSTF) recommended screening strategy; the number of screening tests performed in the measurement year; and the distribution of screening modalities. Temporal trends were assessed using regression analysis, including subgroup analyses across age groups and screening modalities. A total of 172,045 unique patients aged ≥ 40 years were included, of which 115,708 individuals aged 50–75 years. When considering all individuals up-to-date and screened in the measurement year, overall adherence increased significantly over the 4-year study period, from 39,105 to 49,698 patients or 47 % to 59 % (p < 0.0001). The screening incidence between 2015 and 2018 increased from 19.44 to 23.66 tests per 1,000 persons for gFOBT and FIT, a 1.2-fold increase, and from 6.54 to 29.78 tests per 1,000 persons for mt-sDNA (p < 0.05), a 4.6-fold increase. During the same time period, the screening incidence of colonoscopy decreased from 119.99 to 110.58 tests per 1,000 persons, corresponding to a decrease of 8 %. Similar patterns in screening incidence rates were observed among those aged < 50 and > 75 years old. Growing adoption, higher preference, and the broad availability of mt-sDNA testing may be associated with an increase in overall CRC screening rates in the average-risk population, in parallel with a slight increase in the use of other non-invasive CRC screening tests.

PPV and Detection Rate of mt-sDNA Testing, FIT, and CT Colonography for Advanced Neoplasia: A Hierarchic Bayesian Meta-Analysis of the Noninvasive Colorectal Screening Tests.

BACKGROUND. Noninvasive tests for colorectal cancer (CRC) screening and prevention limit the need for invasive colonoscopy to follow up positive test results. However, the relative performance characteristics of available noninvasive tests have not yet been adequately compared. OBJECTIVE. We performed a systematic review and meta-analysis to compare the diagnostic performance of the available noninvasive CRC screening tests, including multitarget stool DNA (mt-sDNA) testing, fecal immunochemical testing (FIT), and CT colonography (CTC), with an emphasis on comparison of PPV and detection rate (DR) for advanced neoplasia (AN; encompassing cases of advanced adenomas and CRC). EVIDENCE ACQUISITION. After systematic searches of MEDLINE and Google Scholar databases, 10 mt-sDNA, 27 CTC, and 88 FIT published screening studies involving 25,132, 33,493, and 2,355,958 asymptomatic adults, respectively, were included. Meta-analysis with hierarchic Bayesian modeling was conducted in accordance with Cochrane Collaboration and PRISMA guidelines to determine test positivity rates (TPRs) leading to optical colonoscopy, as well as PPVs and DRs for both AN and CRC. Different positivity thresholds were considered for FIT and CTC. EVIDENCE SYNTHESIS. Point estimates (with 95% credible intervals) from pooled Bayesian meta-analysis combining all thresholds for FIT and stratifying CTC results by a polyp size threshold of 6 mm or larger (CTC6) and 10 mm or larger (CTC10) were calculated. TPR was 13.5% (10.9-16.6%) for mt-sDNA testing, 6.4% (5.8-7.2%) for FIT, 13.4% (11.4-15.6%) for CTC6, and 6.6% (5.2-7.7%) for CTC10. AN PPV was 26.9% (95% credible interval, 21.8-33.2%) for mt-sDNA testing, 31.8% (29.3-34.5%) for FIT, 34.4% (27.2-41.0%) for CTC6, and 61.0% (54.0-70.0%) for CTC10. CRC PPV was 2.4% (1.5-3.9%) for mt-sDNA testing, 4.9% (4.3-5.3%) for FIT, 3.5% (2.5-4.8%) for CTC6, and 6.0% (4.3-8.0%) for CTC10. The DR for AN was 3.4% (95% credible interval, 2.5-4.8%) for mt-SDNA, 2.0% (1.8-2.3%) for FIT, 4.8% (4.0-6.5%) for CTC6, and 4.0% (3.0-4.6%) for CTC10. When FIT is restricted to a lower threshold (< 10 μg Hb/g feces), its performance profile is similar to that of mt-sDNA testing, although available data are limited. AN PPV odds ratios (relative to CTC10 as the reference) were 0.24 (95% credible interval, 0.17-0.33) for mt-sDNA testing, 0.30 (0.24-0.45) for FIT, and 0.33 (0.25-0.47) for CTC6. CONCLUSION. Among noninvasive CRC screening tests, CTC with a polyp size threshold of 10 mm or larger most effectively targets AN, preserving detection while also decreasing unnecessary colonoscopies compared with mt-sDNA testing and FIT. CLINICAL IMPACT. CTC performed with a polyp size threshold for colonoscopy referral set at 10 mm or larger represents the most effective and efficient noninvasive screening test for CRC prevention and detection.

Noninvasive Colorectal Cancer Screening Tests Help Close Screening Gaps During Coronavirus Disease 2019 Pandemic

The coronavirus disease 2019 (COVID-19) pandemic has upended routine preventive care across the country. Health systems worldwide have seen a drastic decrease in utilization of preventive care services, including colorectal cancer (CRC) screening.1 In response to the pandemic, the US Surgeon General advised in March 2020 that all hospitals and ambulatory surgical centers delay nonurgent surgeries and medical procedures, including screening and surveillance colonoscopies. In line with these recommendations, the University of California Los Angeles (UCLA) health system temporarily ceased elective endoscopies and purposefully encouraged the use of stool-based CRC screening modalities among patients and providers through weekly system-wide e-mails to primary care and gastroenterology providers, virtual meetings with primary care leadership, and standardized educational materials for fecal immunochemical testing (FIT).

Stool DNA test targeting methylated syndecan-2 (SDC2) as a noninvasive screening method for colorectal cancer.

Despite the steadily increasing worldwide incidence of colorectal cancer (CRC), an effective noninvasive approach for early detection of CRC is still under investigation. The guaiac-based fecal occult blood test (FOBT) and fecal immunochemical test (FIT) have gained popularity as noninvasive CRC screening tests owing to their convenience and relatively low costs. However, the FOBT and FIT have limited sensitivity and specificity. To develop a noninvasive tool for the detection of CRC, we investigated the sensitivity, specificity, and accuracy of a stool DNA test targeting methylated syndecan-2 (SDC2), which is frequently methylated in patients with CRC. The present study enrolled 62 patients diagnosed as having stage 0-IV CRC and 76 healthy participants between July 2018 and June 2019 from two institutions. Approximately 4.5 g of stool sample was collected from each participant for detection of human methylated SDC2 gene. In total, 48 of 62 (77.4%) patients with CRC showed positive results, whereas 67 out of 76 (88.2%) healthy participants showed negative results. The area under the curve of the receiver operating characteristic curve constructed was 0.872 for discrimination between patients with CRC and healthy individuals. The present study highlights the potential of the fecal methylated SDC2 test as a noninvasive detection method for CRC screening with a relatively favorable sensitivity of 77.4%, a specificity of 88.2% and a positive predictive value of 84.2% compared with other available fecal tests. Further multicenter clinical trials comprising subjects of varied ethnicities are required to validate this test for the mass screening of patients with CRC.

Progress in research of biomarkers for colorectal cancer screening and early detection

Disease burden caused by colorectal cancer is growing, which has become a major concern in public health. Population-based screening has been proved effective in reducing the morbidity and mortality of colorectal cancer. To date, more evidences regarding the changes in genetics, epigenetics and microbiome of colorectal cancer have been recognized. Emerging technologies for gene sequencing and molecular detection shed lights on the development of informative colorectal cancer related biomarkers. In this article, we summarize the latest findings in research of biomarkers for colorectal cancer screening and early detection to provide references for the development of novel effective and non-invasive colorectal cancer screening tests in the future.

New fecal bacterial signature for colorectal cancer screening reduces the fecal immunochemical test false-positive rate in a screening population.

Guidelines recommend routine screening for colorectal cancer (CRC) in asymptomatic adults starting at age 50. The most extensively used noninvasive test for CRC screening is the fecal immunochemical test (FIT), which has an overall sensitivity for CRC of approximately 61.0%-91.0%, which drops to 27.0%-67.0% for advanced adenomas. These figures contain a high false-positive rate and a low positive predictive value. This work aimed to develop a new, noninvasive CRC screening tool based on fecal bacterial markers capable of decreasing FIT false-positive rates in a FIT-positive population. We defined a fecal bacterial signature (RAID-CRC Screen) in a proof-of-concept with 172 FIT-positive individuals and validated the obtained results on an external cohort of 327 FIT-positive subjects. All study participants had joined the national CRC screening program. In the clinical validation of RAID-CRC Screen, a sensitivity of 83.9% and a specificity of 16.3% were obtained for the detection of advanced neoplasm lesions (advanced adenomas and/or CRC). FIT 20 μg/g produced 184 false-positive results. Using RAID-CRC Screen, this value was reduced to 154, thus reducing the false-positive rate by 16.3%. The RAID-CRC Screen test could be implemented in CRC screening programs to allow a significant reduction in the number of colonoscopies performed unnecessarily for FIT-positive participants of CRC screening programs.

Biomarkers for detecting colorectal cancer non-invasively: DNA, RNA or proteins?

Colorectal cancer (CRC) is a global problem affecting millions of people worldwide. This disease is unique because of its slow progress that makes it preventable and often curable. CRC symptoms usually emerge only at advanced stages of the disease, consequently its early detection can be achieved only through active population screening, which markedly reduces mortality due to this cancer. CRC screening tests that employ non-invasively detectable biomarkers are currently being actively developed and, in most cases, samples of either stool or blood are used. However, alternative biological substances that can be collected non-invasively (colorectal mucus, urine, saliva, exhaled air) have now emerged as new sources of diagnostic biomarkers. The main categories of currently explored CRC biomarkers are: (1) Proteins (comprising widely used haemoglobin); (2) DNA (including mutations and methylation markers); (3) RNA (in particular microRNAs); (4) Low molecular weight metabolites (comprising volatile organic compounds) detectable by metabolomic techniques; and (5) Shifts in gut microbiome composition. Numerous tests for early CRC detection employing such non-invasive biomarkers have been proposed and clinically studied. While some of these studies generated promising early results, very few of the proposed tests have been transformed into clinically validated diagnostic/screening techniques. Such DNA-based tests as Food and Drug Administration-approved multitarget stool test (marketed as Cologuard®) or blood test for methylated septin 9 (marketed as Epi proColon® 2.0 CE) show good diagnostic performance but remain too expensive and technically complex to become effective CRC screening tools. It can be concluded that, despite its deficiencies, the protein (haemoglobin) detection-based faecal immunochemical test (FIT) today presents the most cost-effective option for non-invasive CRC screening. The combination of non-invasive FIT and confirmatory invasive colonoscopy is the current strategy of choice for CRC screening. However, continuing intense research in the area promises the emergence of new superior non-invasive CRC screening tests that will allow the development of improved disease prevention strategies.

Rethinking the Re-Prep: Attitudes Toward Noninvasive Colorectal Cancer Screening Tests After Inadequate Bowel Preparation.

To assess patient preferences for colorectal cancer screening with stool-based tests after initial colonoscopy with suboptimal bowel preparation. An online scenario-based survey of adults aged 45 to 75 years at average risk for colorectal cancer was performed. When presented with a hypothetical scenario of screening colonoscopy with suboptimal bowel preparation, 59% of respondents chose stool-based testing as a next step, 29% preferred a repeat colonoscopy within a year, and 12% preferred a repeat colonoscopy in 10 years (N = 1,080). Clinicians should consider offering stool-based screening tests as an alternative to repeat colonoscopy after suboptimal bowel preparation.

Combined Plasma MicroRNA and Fecal Occult Blood Tests in Early Detection of Colorectal Cancer.

Colorectal cancer (CRC) is one of the most common malignancies and a major cause of cancer-related death worldwide. Fecal occult blood tests (FOBT) are non-invasive colorectal cancer screening tests. In recent years plasma microRNAs (miRNAs) have shown great potential in early non-invasive cancer detection. FOBT (immunochemical) and a panel of 12 plasma miRNAs were tested in two independent groups: 57 CRC patients and 125 neoplasm free controls, in addition to 58 advanced adenoma patients and 67 neoplasm free controls. miRNA levels were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Plasma levels of 7 miRNAs (miR-18a, miR-20a, miR-21, miR-92a, miR-133a, miR-143, miR-145) differed significantly between CRC patients and neoplasm free controls. miRNA plasma levels did not differ between advanced adenoma patients and controls. For 7 dysregulated miRNAs in CRC patients, AUCs ranged from 0.585 to 0.632 for CRC detection, in comparison to an AUC of 0.857 for iFOBT. The combination of miR-133a and iFOBT achieved a higher AUC (0.894) than iFOBT alone. At 97.8% specificity, miRNAs showed much lower sensitivities than iFOBT, but the miRNA panel and iFOBT in combination detected CRC with a higher sensitivity than iFOBT alone. The diagnostic performance of miRNAs was poorer than iFOBT. Nevertheless, plasma miRNA profiles offer an innovative non-invasive approach for early CRC detection. The potential advantage of combining plasma miRNA profiles with iFOBT needs to be further studied in a larger cohort of patients.

Mo1608 - Re-Thinking the Re-Prep: Attitudes Towards Non-Invasive Colorectal Cancer Screening Tests in the Setting of Inadequate Bowel Preparation

Mo1608 - Re-Thinking the Re-Prep: Attitudes Towards Non-Invasive Colorectal Cancer Screening Tests in the Setting of Inadequate Bowel Preparation

Deregulation of methylation of transcribed-ultra conserved regions in colorectal cancer and their value for detection of adenomas and adenocarcinomas.

Expression of Transcribed Ultraconserved Regions (T-UCRs) is often deregulated in cancer. The present study assesses the expression and methylation of three T-UCRs (Uc160, Uc283 and Uc346) in colorectal cancer (CRC) and explores the potential of T-UCR methylation in circulating DNA for the detection of adenomas and adenocarcinomas.Expression levels of Uc160, Uc283 and Uc346 were lower in neoplastic tissues from 64 CRC patients (statistically significant for Uc160, p<0.001), compared to non-malignant tissues, while methylation levels displayed the inverse pattern (p<0.001, p=0.001 and p=0.004 respectively). In colon cancer cell lines, overexpression of Uc160 and Uc346 led to increased proliferation and migration rates. Methylation levels of Uc160 in plasma of 50 CRC, 59 adenoma patients, 40 healthy subjects and 12 patients with colon inflammation or diverticulosis predicted the presence of CRC with 35% sensitivity and 89% specificity (p=0.016), while methylation levels of the combination of all three T-UCRs resulted in 45% sensitivity and 74.3% specificity (p=0.013). In conclusion, studied T-UCRs’ expression and methylation status are deregulated in CRC while Uc160 and Uc346 appear to have a complicated role in CRC progression. Moreover their methylation status appears a promising non-invasive screening test for CRC, provided that the sensitivity of the assay is improved.

Abstract 1559: Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression

Abstract Background Early diagnosis of colorectal cancer (CRC) and identification of its precursor lesions (adenomas) is crucial in reducing CRC mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects human protein hemoglobin. Although FIT is beneficial in its current form with a sensitivity of ~65% for detection of CRC and ~27% for adenomas, its performance is still suboptimal and needs to be further improved. Adenoma-to-carcinoma progression is accompanied by alternative splicing, which results in expression of tumor-specific protein variants. These may yield novel biomarkers suitable for improving detection of progressive adenomas and CRCs. Aim We aim to identify novel biomarkers to improve early detection of CRC. Materials and methods RNA was isolated from 3D organoid cultures derived from 5 adenomas and 4 CRC tissues. RNA and proteins were isolated from 18 healthy human colon tissues, 30 adenomas and 30 CRCs. Samples were analyzed by RNA sequencing (Illumina) and in-depth tandem mass spectrometry proteomics (QExactive). For both organoid- and tissue-datasets differential splicing analysis was performed on RNA level to enrich the sequence database, against which mass spectra were searched, with predicted protein isoforms. Results Comparative splicing analysis between CRC and adenoma organoids revealed ~90 differentially spliced genes, yielding candidate biomarkers from epithelial origin. In the tissues, differential splicing analysis between CRCs and controls and between CRCs and adenomas identified over 1000 of splice variants. These include known alternatively spliced genes involved in cancer such as CD44 and VEGFA and a number of candidates overlapping with the isoforms derived from the organoids. Proteomics analysis revealed that approximately 150 of the splice variants were expressed on protein level. Conclusion and Discussion We have confirmed that adenoma-to-carcinoma progression is accompanied by aberrant splicing. Analysis of the organoid cultures allowed us to identify gene isoforms from (neoplastic) epithelial origin. Tissue analysis yielded tumor-specific splice variants that represent novel protein candidate biomarkers for early detection of CRC. The diagnostic performance of these splice variant proteins will be validated in series of stool and FIT samples. Citation Format: Malgorzata A. Komor, Thang V. Pham, Sander R. Piersma, Anne S. Bolijn, Tim Schelfhorst, Pien M. Delis-van Diemen, Marianne Tijssen, Annemieke C. Hiemstra, Meike de Wit, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond J. Fijneman. Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1559. doi:10.1158/1538-7445.AM2017-1559

Deregulation of methylation of transcribed-ultra conserved regions in colorectal cancer and their diagnostic and prognostic value.

e15130 Background: Expression of Transcribed Ultra Conserved Regions (T-UCRs) is often deregulated in cancer. We investigated the role of three T-UCRs (Uc160, Uc283 and Uc346) in colorectal adenocarcinomas and their prognostic and diagnostic value. Methods: Expression and methylation levels of the T-UCRs were assessed in neoplastic and paired non-malignant fresh frozen (FF) tissue specimens from 64 colorectal cancer (CRC) patients, as well as in 6 FF adenoma tissue specimens. In addition, T-UCR methylation levels were assessed in FFPE tumor tissues from 80 CRC patients and in plasma from 161 patients (50 CRC, 59 adenoma patients, 40 healthy subjects and 12 patients with colon inflammation or diverticulosis). Results: Expression levels of all three T-UCRs were lower in neoplastic, compared to non-malignant tissues, although at a statistically significant level only for Uc160 ( p&lt; 0.001). Also, methylation levels of Uc160, Uc283 and Uc346 were higher in tumors compared to non-malignant tissues ( p&lt; 0.001, p= 0.001 and p= 0.004 respectively). Tissue methylation levels of Uc160 were associated with TTP ( p= 0.017). The combination of Uc283 and Uc346 methylation levels was related to OS, however without reaching statistical significance ( p= 0.066). Methylation status of Uc160 and Uc346 in plasma differed significantly among the four patient groups with CRC patients exhibiting the higher levels. Moreover, a strong correlation was found between Uc160 plasma methylation levels and adenoma or adenocarcinoma size and lymph node infiltration ( p&lt; 0.001 and p= 0.024 respectively). When methylation status was used to predict if a subject has CRC, sensitivity and specificity were 35% and 89% respectively, while the values changed to 45% and 74.3% respectively when we combined the sum of the three T-UCR plasma methylation levels. For adenomas, the combination of Uc160 and Uc346 plasma methylation displayed 30.2% (sensitivity) and 80.7% (specificity). Conclusions: T-UCR expression and methylation is deregulated in CRC while their methylation has prognostic value and appears a promising non-invasive screening test for CRC and adenomas, provided that the sensitivity of the assay is improved.

Abstract C80: Colonoscopy follow up after abnormal colorectal cancer screening tests at a large Federally Qualified Community Health Center

Abstract Background. Screening for colorectal cancer (CRC) can reduce cancer incidence and mortality, but participation rates are low among underserved populations. Federally Qualified Health Centers (FQHCs) in many states have an opportunity to be at the vanguard of improving screening rates among underserved populations, due to new acquisition of Medicaid insurance by patients. Many FQHCs are employing non-invasive strategies, such as the fecal immunochemical test (FIT), to increase screening rates. Non-invasive tests such as the FIT are generally inexpensive, convenient, and often acceptable for patients. However, effectiveness of non-invasive screening in prevention or early detection of CRC depends heavily on ability to ensure diagnostic colonoscopy after abnormal screening tests. Specifically, prevention and early detection benefits of identifying patients through non-invasive screening at increased risk for CRC and polyps can only be realized if rates of diagnostic colonoscopy after positive tests are high. Indeed, up to 1 in 33 patients with an abnormal FIT have CRC. As part of a community-academic partnership between Family Health Centers of San Diego (FHCSD), San Diego State University, and UC San Diego Moores Cancer Center, we aimed to characterize CRC screening processes, including rates of complete diagnostic follow up after abnormal FIT testing. Methods. FHCSD is a large FQHC serving 134,788 patients annually through 19 community clinics. The patient population is largely Latino (55%); 97% live at or below 200% of poverty, with most patients having less than a high school education. Following the Quality of Cancer Care Continuum principles adapted by Tiro et al.1 for CRC screening, we mapped the CRC screening process at FHCSD, and characterized drop-offs at various steps in the screening process by querying the electronic health record to identify all individuals with FIT orders over a six-month period (10/01/15 - 03/31/16). Outcomes of interest included rates of FIT completion, abnormal test results, and colonoscopy orders and completion among patients with an abnormal FIT, characterized via descriptive statistics. Results. Over a six-month period, across 19 clinics within FHCSD, 9,378 FITs were ordered. Patients returned 25% of FITs ordered (2327/9378). Among returned FITs, 7% were abnormal (156/2327). Among patients with an abnormal FIT 85% (132/156) had orders for referral colonoscopy, and 21% had documented evidence of colonoscopy completion (33/156). FIT return was statistically significantly higher for patients without (33%; 368/1119) vs. with insurance (24%; 1959/8259; p comparison = &amp;lt;0.001). However, diagnostic colonoscopy completion after abnormal FIT was higher for patients with (24%; 31/132) vs. without insurance (8%; 2/24), though the difference was not statically significant. Conclusions.Low rates of diagnostic colonoscopy after abnormal non-invasive CRC screening tests may adversely impact effectiveness of CRC screening programs. Research should focus on understanding reasons for fall offs in the screening process, and developing multilevel interventions to optimize follow up, particularly given the expanding array of non-invasive CRC screening tests being made available in usual practice. Conducting these studies in FQHC settings is critical, since increases in screening in these settings may largely occur as a result of implementation and promotion of non-invasive tests.

Abstract 4920: Evaluation of a diagnostic blood test for colorectal cancer screening and as a triage tool to stratify patients for colonoscopy

Abstract Worldwide, colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer death, with an annual incidence in 2012 of 1.4 million CRC cases and an annual mortality around 700,000 [1]. Fortunately the majority of colorectal cancer (CRC) cases are preventable by early detection and removal by colonoscopy or surgery. Currently in Australia, the only widely used non-invasive screening test for CRC is the immunological faecal occult blood test (iFOBT), which has been shown to reduce CRC incidence and mortality by 15-25% [2]. There are however significant issues that limit its effectiveness as a diagnostic screening tool, such as a poor positive predictive value of 5.3% for suspected cancer and low participation rate of approximately 33.5% in 2013, as seen in the Australian National Bowel Cancer Screening Program (NBCSP)[2]. Evidence indicates a robust, blood-based, diagnostic assay would increase screening participation and compliance. In our systematic analysis of 68 individual biomarkers using logistic regression strategies, we have identified a unique 3 protein biomarker panel blood test consisting of Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2)[3]. This panel not only differentiates between CRC and normal patient sera with 95% specificity and 73% sensitivity in a single measurement (c.f. FOBT: 35-50 sensitivity [4]) but early stage disease. Currently, we are prospectively collecting a new cohort of over 1,000 blood samples from volunteers that have undergone colonoscopy, that include CRC patients, controls and other pathologies (IBD, other cancers) to specifically determine the performance of this blood test in asymptomatic and surveillance screening populations. We will also evaluate directly the accuracy and performance of our biomarker panel, as a diagnostic test suitable for CRC screening versus the iFOBT used in the NBCSP, as an intermediary test in the triage of individuals with positive iFOBT result for need and urgency to have a colonoscopy. 1. Ferlay J, Soerjomataram I, Ervik M, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray, F. GLOBOCAN 2012 v1.1, Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 11 2. National Bowel Cancer Screening Program: monitoring report 2012-2013. AIHW &amp; Australian Government Department of Health and Ageing, 2014. 3. Fung KYC et al 2015. Blood-based protein biomarker panel for the detection of colorectal cancer. PloS one. 2015;10(3):e0120425. 4. Morikawa, T et al., A comparison of the immunochemical fecal occult blood test and total colonoscopy in the asymptomatic population. Gastroenterology, 2005. 129(2): p. 422-8. Citation Format: Leah J. Cosgrove, Kathy Surinya, Kim YC Fung, Ilka Priebe, Mike Buckley, Tim Adams, Bruce Tabor, Leanne Purins, Trevor Lockett, Hugo Leroux, Peter Gibbs, Jiangqin Wei, Ed Nice, Tony Burgess, Michelle Thomas, James Moore, Raj Singh, Andrew Ruszkiewicz. Evaluation of a diagnostic blood test for colorectal cancer screening and as a triage tool to stratify patients for colonoscopy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4920.

Abstract 848: Proteogenomic analysis of alternative splicing: the search for novel biomarkers for colorectal cancer

Abstract Introduction Early detection of colorectal cancer (CRC) and its precursor lesions (adenomas) is crucial to reduce mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test detecting blood-derived protein hemoglobin. However, FIT sensitivity is suboptimal especially in detection of CRC precursor lesions. As adenoma-to-carcinoma progression is accompanied by alternative splicing, tumor-specific proteins derived from alternatively spliced RNA transcripts might serve as candidate biomarkers for CRC detection. Materials and methods RNA and proteins were isolated from CRC cell line SW480 before and after siRNA-mediated down-modulation of the splicing machinery: SF3B1, U2AF1, and SRSF1. To identify splice variants, mRNA was sequenced (Illumina HiSeq) and analyzed. RNA-seq analysis included quality checks (FASTQ, RSeQC), reads mapping (STAR), differential gene expression (DESeq2) and differential expression of splicing isoforms between conditions (MATS). Results from the in silico analysis were validated by qRT-PCR. Proteins were analyzed by in-depth tandem mass spectrometry (QExactive). A proteogenomic data analysis pipeline was established to enrich the sequence database, against which the mass spectra are searched, with the predicted protein splice variants and identify protein isoforms. To further extend the splice-variant database, PacBio sequencing of full-length transcripts is being performed for the SW480 siSF3B1- and control-samples. Results Differential expression analysis on RNA and protein level proved that the knock-down experiments were performed successfully. The RNA-seq analysis revealed hundreds of mRNA splice variants, including positive controls described in literature. For example, down-modulation of SF3B1 resulted in quantitative mRNA changes of spliced isoforms of ADD3 both in RNA-seq and RT-PCR data. The proteomics experiment yielded over 6000 proteins per sample, among which a number of protein isoforms resulting from alternative splicing. Conclusions and discussion We established a proteogenomic pipeline for the analysis of alternative splicing and provided experimental proof of concept. We expect, however, that the true complexity of RNA variant information remains highly underestimated. We therefore are performing PacBio long-read RNA-seq to validate our approach and to identify additional (novel) splicing events. In future studies we will apply the mRNA-seq based proteogenomic pipeline for detection of protein alterations to a series of adenomas at low- and high-risk of progression, and CRCs to validate the isoforms in a clinically relevant setting. Novel findings will be evaluated for their performance as screening markers for CRC. This work was financially supported by KWF project nr: VU 2013-6025. Citation Format: Malgorzata A. Komor, Annemieke C. Hiemstra, Thang V. Pham, Sander R. Piersma, Robert P. Sebra, Bo W. Han, Meredith Ashby, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond JA Fijneman. Proteogenomic analysis of alternative splicing: the search for novel biomarkers for colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 848.