Pub Date : 2021-07-01DOI: 10.1158/1538-7445.am2021-2610
Linhao Xu, Jun Wang, Weifeng Ma, Xin Liu, Ting Yang, Sihui Li, Qian Hu, Jinsheng Tao, Z. Ye, Zhiwei Chen, Jian-Bing Fan
Introduction: Early detection is critical to improving cancer patient survival and quality of life. Cell-free DNA (cfDNA) methylation profiling is a promising diagnostic approach for early detection of cancer, even before symptoms appear. We previously reported a non-invasive and cost-effective methylation test, Aurora, which is able to detect three major cancer types with high specificity and sensitivity especially at early stages (I/II), including lung cancer (LC), breast cancer (BC), colorectal cancer (CRC). We have improved this test to include two additional major cancer types, gastric cancer (GC) and esophageal cancer (EC). Taking together, these five cancer types represent 56% of new cancer cases and 60% of cancer-related deaths in China. Methods: We developed a novel high-throughput targeted methylation profiling platform, Aurora 2.0 (an improved version of Aurora 1.0, as presented in AACR 2020), to efficiently enrich and capture cancer-specific DNA methylation markers in plasma, prior to analysis via next-generation sequencing on a MiSeqDx system. About 100 cases each for GC and EC patients (mostly at Stage I/II), together with ~200 healthy controls, have been analyzed by using Aurora 2.0 and used for model development and validation. Results and Discussion: cfDNA methylation profiles have been obtained from 409 plasma samples, comprising 206 healthy controls, 98 GC and 105 EC patients. Logistic regression model has been developed with the Area Under Curve (AUC) of 94.0% and 93.5% for GC and EC, respectively. Overall, the performance (AUC) of Aurora 2.0 for LC/BC/CRC/GC/EC are 97.3%, 96.2%, 92%, 94% and 93.5%, respectively. An independent cohort (~2,000 plasma samples, five cancer types including lung, breast, colorectal, gastric and esophageal cancers with healthy controls) study is undergoing to further validate this test prospectively. The superior performance and cost-effectiveness (~$100) of the test could make early cancer screening of multiple major cancers in symptom-free and average-risk populations more achievable. Citation Format: Linhao Xu, Jun Wang, Weifeng Ma, Xin Liu, Ting Yang, Sihui Li, Qian Hu, Jinsheng Tao, Zhujia Ye, Zhiwei Chen, Jian-Bing Fan. A high performance blood test for multiple cancer early screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2610.
{"title":"Abstract 2610: A high performance blood test for multiple cancer early screening","authors":"Linhao Xu, Jun Wang, Weifeng Ma, Xin Liu, Ting Yang, Sihui Li, Qian Hu, Jinsheng Tao, Z. Ye, Zhiwei Chen, Jian-Bing Fan","doi":"10.1158/1538-7445.am2021-2610","DOIUrl":"https://doi.org/10.1158/1538-7445.am2021-2610","url":null,"abstract":"Introduction: Early detection is critical to improving cancer patient survival and quality of life. Cell-free DNA (cfDNA) methylation profiling is a promising diagnostic approach for early detection of cancer, even before symptoms appear. We previously reported a non-invasive and cost-effective methylation test, Aurora, which is able to detect three major cancer types with high specificity and sensitivity especially at early stages (I/II), including lung cancer (LC), breast cancer (BC), colorectal cancer (CRC). We have improved this test to include two additional major cancer types, gastric cancer (GC) and esophageal cancer (EC). Taking together, these five cancer types represent 56% of new cancer cases and 60% of cancer-related deaths in China. Methods: We developed a novel high-throughput targeted methylation profiling platform, Aurora 2.0 (an improved version of Aurora 1.0, as presented in AACR 2020), to efficiently enrich and capture cancer-specific DNA methylation markers in plasma, prior to analysis via next-generation sequencing on a MiSeqDx system. About 100 cases each for GC and EC patients (mostly at Stage I/II), together with ~200 healthy controls, have been analyzed by using Aurora 2.0 and used for model development and validation. Results and Discussion: cfDNA methylation profiles have been obtained from 409 plasma samples, comprising 206 healthy controls, 98 GC and 105 EC patients. Logistic regression model has been developed with the Area Under Curve (AUC) of 94.0% and 93.5% for GC and EC, respectively. Overall, the performance (AUC) of Aurora 2.0 for LC/BC/CRC/GC/EC are 97.3%, 96.2%, 92%, 94% and 93.5%, respectively. An independent cohort (~2,000 plasma samples, five cancer types including lung, breast, colorectal, gastric and esophageal cancers with healthy controls) study is undergoing to further validate this test prospectively. The superior performance and cost-effectiveness (~$100) of the test could make early cancer screening of multiple major cancers in symptom-free and average-risk populations more achievable. Citation Format: Linhao Xu, Jun Wang, Weifeng Ma, Xin Liu, Ting Yang, Sihui Li, Qian Hu, Jinsheng Tao, Zhujia Ye, Zhiwei Chen, Jian-Bing Fan. A high performance blood test for multiple cancer early screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2610.","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82237755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2578
C. Dampier, M. Devall, J. Bryant, S. Eaton, J. Huyghe, Andre E Kim, Virginia Díez-Obrero, F. V. Duijnhoven, Duncan C. Thomas, S. Powell, W. Gauderman, U. Peters, G. Casey
Background: Observational studies indicate that calcium, a micronutrient involved in numerous cell-signaling cascades, may protect against colon cancer. Stratified analyses suggest the protective effect of calcium may depend on sex and anatomic subsite, but these hypotheses have been difficult to test experimentally. Here, we employ human-derived normal colon 3D organoids as a model of the healthy colon crypt to interrogate the effect of calcium exposure on gene expression and the effect of donor sex and biopsy anatomic subsite on the response to calcium. Methods: A total of 39 3D colon organoid lines derived from colon biopsies (22 proximal, 17 distal) obtained from unrelated subjects (21 female, 18 male) during screening colonoscopy were grown under low (1.7 mM) calcium conditions, and a matching set of the same lines were grown under high (5.0 mM) calcium conditions. After 72 hours, total RNA was extracted from organoid lines, libraries were prepared with poly-A selection, and bulk RNA-sequencing was used to measure gene expression. DNA was extracted from the same lines and genotyped using the OncoArray 500K beadchip. Missing genotypes were imputed to the TOPMed reference panel using the TOPMed Imputation Server. Polygenic risk scores for colorectal cancer were calculated for each organoid line using Plink and 135 of 141 genome-wide significant SNPs associated with colorectal cancer in recent genome-wide association studies. Relative expression between low and high calcium conditions was tested using generalized linear models as implemented in DESeq2. Functional enrichment of gene ontologies among differentially expressed genes was performed with ToppFun. The effects of donor sex, biopsy subsite, and organoid polygenic risk score on response to calcium were tested using single and multiple linear regression as implemented in the base R lm function. Results: Exposure to calcium induced differential expression of 767 genes with a false discovery rate of 5%. Differentially expressed genes were enriched for biological processes including extracellular structure organization (Bonferroni p=1.6E-3) and positive regulation of apoptosis (Bonferroni p=2.2E-2). Although stratified analyses demonstrated more differentially expressed genes in 3D colon organoids derived from male subjects, no statistically significant effect of sex, subsite, or polygenic risk score on response to calcium was observed. Conclusion: We tested the effect of calcium exposure on gene expression in human-derived normal colon 3D organoids and found that calcium modulated processes related to differentiation and apoptosis, but the response to calcium was not affected by sex, anatomic subsite, or polygenic risk score. Citation Format: Christopher H. Dampier, Matthew Devall, Jennifer Bryant, Stephen D. Eaton, Jeroen R. Huyghe, Andre E. Kim, Virginia Diez-Obrero, Franzel J. van Duijnhoven, Duncan C. Thomas, Steven M. Powell, W James Gauderman, Ulrike Peters, Graham Casey. Calcium modul
背景:观察性研究表明,钙,一种参与许多细胞信号级联反应的微量营养素,可能预防结肠癌。分层分析表明,钙的保护作用可能取决于性别和解剖亚位,但这些假设很难通过实验来验证。在这里,我们采用人类来源的正常结肠3D类器官作为健康结肠隐窝的模型,来探究钙暴露对基因表达的影响,以及供体性别和活检解剖亚位点对钙反应的影响。方法:在结肠镜筛查过程中,从无亲缘关系的受试者(21名女性,18名男性)获得结肠活检标本(22名近端,17名远端),在低钙(1.7 mM)条件下培养39个3D结肠类器官细胞系,在高钙(5.0 mM)条件下培养一组相同的细胞系。72h后,提取类器官细胞系的总RNA,采用poly-A选择建立文库,采用大体积RNA测序法测定基因表达。从相同的细胞系中提取DNA,使用OncoArray 500K头芯片进行基因分型。使用TOPMed Imputation Server将缺失的基因型输入到TOPMed参考面板。在最近的全基因组关联研究中,使用Plink和141个与结直肠癌相关的全基因组显著snp中的135个计算了每个类器官系的结直肠癌多基因风险评分。采用DESeq2中实现的广义线性模型检验低钙和高钙条件之间的相对表达。利用ToppFun对差异表达基因的基因本体进行功能富集。供体性别、活检亚部位和类器官多基因风险评分对钙反应的影响采用基础R - lm函数中实施的单线性和多元线性回归进行测试。结果:钙暴露诱导767个基因差异表达,错误发现率为5%。差异表达基因富集于细胞外结构组织(Bonferroni p=1.6E-3)和细胞凋亡的正向调控(Bonferroni p= 2.22 e -2)等生物过程。虽然分层分析显示,来自男性受试者的三维结肠类器官中有更多的差异表达基因,但没有观察到性别、亚位点或多基因风险评分对钙反应的统计学显著影响。结论:我们测试了钙暴露对人源性正常结肠3D类器官基因表达的影响,发现钙调节了与分化和凋亡相关的过程,但对钙的反应不受性别、解剖亚位点或多基因风险评分的影响。引用格式:Christopher H. Dampier, Matthew Devall, Jennifer Bryant, Stephen D. Eaton, Jeroen R. Huyghe, Andre E. Kim, Virginia Diez-Obrero, Franzel J. van Duijnhoven, Duncan C. Thomas, Steven M. Powell, W James Gauderman, Ulrike Peters, Graham Casey。钙调节人类正常结肠3D类器官的凋亡和分化,而不受供体性别和活检部位的影响[摘要]。见:美国癌症研究协会2021年年会论文集;2021年4月10日至15日和5月17日至21日。费城(PA): AACR;癌症杂志,2021;81(13 -增刊):2578。
{"title":"Abstract 2578: Calcium modulates apoptosis and differentiation in human normal colon 3D organoids irrespective of donor sex and biopsy site","authors":"C. Dampier, M. Devall, J. Bryant, S. Eaton, J. Huyghe, Andre E Kim, Virginia Díez-Obrero, F. V. Duijnhoven, Duncan C. Thomas, S. Powell, W. Gauderman, U. Peters, G. Casey","doi":"10.1158/1538-7445.AM2021-2578","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2578","url":null,"abstract":"Background: Observational studies indicate that calcium, a micronutrient involved in numerous cell-signaling cascades, may protect against colon cancer. Stratified analyses suggest the protective effect of calcium may depend on sex and anatomic subsite, but these hypotheses have been difficult to test experimentally. Here, we employ human-derived normal colon 3D organoids as a model of the healthy colon crypt to interrogate the effect of calcium exposure on gene expression and the effect of donor sex and biopsy anatomic subsite on the response to calcium. Methods: A total of 39 3D colon organoid lines derived from colon biopsies (22 proximal, 17 distal) obtained from unrelated subjects (21 female, 18 male) during screening colonoscopy were grown under low (1.7 mM) calcium conditions, and a matching set of the same lines were grown under high (5.0 mM) calcium conditions. After 72 hours, total RNA was extracted from organoid lines, libraries were prepared with poly-A selection, and bulk RNA-sequencing was used to measure gene expression. DNA was extracted from the same lines and genotyped using the OncoArray 500K beadchip. Missing genotypes were imputed to the TOPMed reference panel using the TOPMed Imputation Server. Polygenic risk scores for colorectal cancer were calculated for each organoid line using Plink and 135 of 141 genome-wide significant SNPs associated with colorectal cancer in recent genome-wide association studies. Relative expression between low and high calcium conditions was tested using generalized linear models as implemented in DESeq2. Functional enrichment of gene ontologies among differentially expressed genes was performed with ToppFun. The effects of donor sex, biopsy subsite, and organoid polygenic risk score on response to calcium were tested using single and multiple linear regression as implemented in the base R lm function. Results: Exposure to calcium induced differential expression of 767 genes with a false discovery rate of 5%. Differentially expressed genes were enriched for biological processes including extracellular structure organization (Bonferroni p=1.6E-3) and positive regulation of apoptosis (Bonferroni p=2.2E-2). Although stratified analyses demonstrated more differentially expressed genes in 3D colon organoids derived from male subjects, no statistically significant effect of sex, subsite, or polygenic risk score on response to calcium was observed. Conclusion: We tested the effect of calcium exposure on gene expression in human-derived normal colon 3D organoids and found that calcium modulated processes related to differentiation and apoptosis, but the response to calcium was not affected by sex, anatomic subsite, or polygenic risk score. Citation Format: Christopher H. Dampier, Matthew Devall, Jennifer Bryant, Stephen D. Eaton, Jeroen R. Huyghe, Andre E. Kim, Virginia Diez-Obrero, Franzel J. van Duijnhoven, Duncan C. Thomas, Steven M. Powell, W James Gauderman, Ulrike Peters, Graham Casey. Calcium modul","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85803613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2521
A. Mazumder, A. Jimenez, R. Ellsworth, S. Freedland, S. George, M. Bainbridge, S. Haricharan
{"title":"Abstract 2521: Race specific differences in DNA damage repair dysregulation in breast cancer and association with outcome","authors":"A. Mazumder, A. Jimenez, R. Ellsworth, S. Freedland, S. George, M. Bainbridge, S. Haricharan","doi":"10.1158/1538-7445.AM2021-2521","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2521","url":null,"abstract":"","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"86 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76811698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2568
W. N. Jungbauer, Mustafa M. Ali, B. Wuertz, F. Ondrey
Successful Fanconi anemia (FA) treatment allows greater longevity for these patients. However, there is a greatly increased risk of squamous malignancies of the head and neck which are quite deadly in these young patients. There is an unmet need for non DNA damaging therapies for this malignancy which could augment surgery. Our approach has been to examine potential treatments based on known pathophysiology of the disease which would be acceptable for this population so we examined the effects of metformin and pioglitazone, as well as two cell cycle kinase inhibitors, in FA and leukoplakia cell lines. We examined dose-dependent and combination effects on cell proliferation, as judged by MTT assay. We examined metformin, pioglitazone, the polo-like kinase 1 inhibitor, GSK461364, and Wee1 kinase inhibitor, AZD1775.In single agent studies, we observed dose-dependent decreases in cell proliferation with all 4 single agents. We observed decreased cell proliferation in all cell lines at 72 hours at clinically achievable serum levels of 85% to 55% of control levels (P Citation Format: Walter N. Jungbauer, Mustafa M. Ali, Beverly R. Wuertz, Frank G. Ondrey. Use of kinase inhibitors in Fanconi anemia oral cancercell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2568.
成功的范可尼贫血(FA)治疗可以延长这些患者的寿命。然而,头颈部鳞状恶性肿瘤的风险大大增加,这在这些年轻患者中是相当致命的。对这种恶性肿瘤的非DNA损伤治疗的需求尚未得到满足,这可能会增加手术。我们的方法是根据已知的疾病病理生理学来检查潜在的治疗方法,这对这个人群来说是可以接受的,所以我们检查了二甲双胍和吡格列酮,以及两种细胞周期激酶抑制剂对FA和白斑细胞系的影响。通过MTT试验,我们检测了剂量依赖性和联合作用对细胞增殖的影响。我们检测了二甲双胍、吡格列酮、polo样激酶1抑制剂GSK461364和Wee1激酶抑制剂AZD1775。在单药研究中,我们观察到所有4种单药对细胞增殖的剂量依赖性降低。我们观察到,在临床可达到的血清水平为对照水平的85%至55%的情况下,所有细胞系在72小时内的细胞增殖均下降(P引用格式:Walter N. Jungbauer, Mustafa M. Ali, Beverly R. Wuertz, Frank G. Ondrey)。激酶抑制剂在范可尼贫血口腔癌细胞系中的应用[摘要]。见:美国癌症研究协会2021年年会论文集;2021年4月10日至15日和5月17日至21日。费城(PA): AACR;癌症杂志,2021;81(13 -增刊):摘要第2568期。
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Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2548
Badriprasad Ananthanarayanan, Regina Nieu, Evan Bishop, Shireen S. Rudina, A. Harwig, Bijee George, D. Suhy
{"title":"Abstract 2548: Preclinical development of EARLI-001, a genetic platform producing cancer-activated synthetic biomarkers for the early detection of malignancies","authors":"Badriprasad Ananthanarayanan, Regina Nieu, Evan Bishop, Shireen S. Rudina, A. Harwig, Bijee George, D. Suhy","doi":"10.1158/1538-7445.AM2021-2548","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2548","url":null,"abstract":"","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77390556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2531
Dongyu Zhang, L. Abraham, J. Demb, D. Miglioretti, S. Advani, B. Sprague, L. Henderson, Tracy Onega, K. Wernli, L. Walter, K. Kerlikowske, J. Schousboe, E. O'Meara, D. Braithwaite
{"title":"Abstract 2531: Function-related indicator and outcomes of screening mammography in older women from the BCSC-Medicare Cohort","authors":"Dongyu Zhang, L. Abraham, J. Demb, D. Miglioretti, S. Advani, B. Sprague, L. Henderson, Tracy Onega, K. Wernli, L. Walter, K. Kerlikowske, J. Schousboe, E. O'Meara, D. Braithwaite","doi":"10.1158/1538-7445.AM2021-2531","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2531","url":null,"abstract":"","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76871049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2603
F. Ambrosi, C. Ricci, Federico Chiarucci, Stefano Chilotti, Doriana Donatella Di Nanni, A. G. Corradini, Maria Antonietta Cumiento, D. Biase, M. Fiorentino
Introduction: Serrated lesions are a heterogeneous group of lesions routinely evaluated with different morphologic subtypes, and colorectal carcinogenesis has been related to the understanding of the serrated pathway in these lesions. In this setting, BRAF V600E mutation has been demonstrated as a marker for the serrated carcinogenic evolution, while the mismatch repair protein (MMR) was recognized in a small subset of hyperplastic polyps. Design: This study aimed to evaluate the interobserver agreement among 6 pathologists in the morphological diagnosis of the serrated lesion according to WHO Classification; furthermore, the additional MMR (MLH1, PMS2, MSH2, MSH6) and BRAF V600E (VE1) mutation status were studied by immunohistochemistry and NGS analysis. Results: We evaluated 52 serrated lesions of the colon retrieved from our pathology archives in 2019. The cohort included 48 patients: 21 males and 27 females, with a mean age of 67 years (range 50-89), of which 77.1% were identified according to regional screening protocol. All hematoxylin and eosin slides were independently reviewed by each pathologist, who classified all samples according to the WHO Classification of Digestive System Tumor (Fleiss Kappa: 0.75). The immunohistochemical expression of MMR and BRAF was evaluated in 42 samples. Loss of MLH1 and PMS2 was recorded in one serrated sessile lesion (LSS) with dysplasia, but NGS analysis resulted negative. In contrast, BRAF V600E IHC resulted positive in 22 samples (52.4%), specifically in 5 hyperplastic polyps (71.4%), 10 LSS (66.6%), 5 LSS with dysplasia (45.5%) and 2 adenomatous polyps (100%), 1 TSA negative. All BRAF V600E IHC positive cases were confirmed by NGS analysis. Conclusion: To conclude, the interobserver agreement for morphological classification of serrated lesions resulted substantial; however, behind the morphological appearance, BRAF V600E resulted in predominant mutation in LSS and hyperplastic polyps, these observations confirmed the possibility to improve the classification with IHC BRAF V600E; especially for hyperplastic polyps, it may be crucial to identify precancerous lesions and different clinical management. Citation Format: Francesca Ambrosi, Costantino Ricci, Federico Chiarucci, Stefano Chilotti, Doriana Donatella Di Nanni, Angelo Gianluca Corradini, Maria Antonietta Cumiento, Dario De Biase, Michelangelo Fiorentino. What9s more in serrated lesions: interobserver agreement and molecular features [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2603.
{"title":"Abstract 2603: What's more in serrated lesions: interobserver agreement and molecular features","authors":"F. Ambrosi, C. Ricci, Federico Chiarucci, Stefano Chilotti, Doriana Donatella Di Nanni, A. G. Corradini, Maria Antonietta Cumiento, D. Biase, M. Fiorentino","doi":"10.1158/1538-7445.AM2021-2603","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2603","url":null,"abstract":"Introduction: Serrated lesions are a heterogeneous group of lesions routinely evaluated with different morphologic subtypes, and colorectal carcinogenesis has been related to the understanding of the serrated pathway in these lesions. In this setting, BRAF V600E mutation has been demonstrated as a marker for the serrated carcinogenic evolution, while the mismatch repair protein (MMR) was recognized in a small subset of hyperplastic polyps. Design: This study aimed to evaluate the interobserver agreement among 6 pathologists in the morphological diagnosis of the serrated lesion according to WHO Classification; furthermore, the additional MMR (MLH1, PMS2, MSH2, MSH6) and BRAF V600E (VE1) mutation status were studied by immunohistochemistry and NGS analysis. Results: We evaluated 52 serrated lesions of the colon retrieved from our pathology archives in 2019. The cohort included 48 patients: 21 males and 27 females, with a mean age of 67 years (range 50-89), of which 77.1% were identified according to regional screening protocol. All hematoxylin and eosin slides were independently reviewed by each pathologist, who classified all samples according to the WHO Classification of Digestive System Tumor (Fleiss Kappa: 0.75). The immunohistochemical expression of MMR and BRAF was evaluated in 42 samples. Loss of MLH1 and PMS2 was recorded in one serrated sessile lesion (LSS) with dysplasia, but NGS analysis resulted negative. In contrast, BRAF V600E IHC resulted positive in 22 samples (52.4%), specifically in 5 hyperplastic polyps (71.4%), 10 LSS (66.6%), 5 LSS with dysplasia (45.5%) and 2 adenomatous polyps (100%), 1 TSA negative. All BRAF V600E IHC positive cases were confirmed by NGS analysis. Conclusion: To conclude, the interobserver agreement for morphological classification of serrated lesions resulted substantial; however, behind the morphological appearance, BRAF V600E resulted in predominant mutation in LSS and hyperplastic polyps, these observations confirmed the possibility to improve the classification with IHC BRAF V600E; especially for hyperplastic polyps, it may be crucial to identify precancerous lesions and different clinical management. Citation Format: Francesca Ambrosi, Costantino Ricci, Federico Chiarucci, Stefano Chilotti, Doriana Donatella Di Nanni, Angelo Gianluca Corradini, Maria Antonietta Cumiento, Dario De Biase, Michelangelo Fiorentino. What9s more in serrated lesions: interobserver agreement and molecular features [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2603.","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81015548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2611
Satyanarayan Rao, A. Han, Alexis Zukowski, E. Kopin, P. Kabos, S. Ramachandran
{"title":"Abstract 2611: Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype","authors":"Satyanarayan Rao, A. Han, Alexis Zukowski, E. Kopin, P. Kabos, S. Ramachandran","doi":"10.1158/1538-7445.AM2021-2611","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2611","url":null,"abstract":"","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83030996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2586
Margaret Hoyt, Jianjun Zhang
Pancreatic cancer is one of the deadliest malignancies in the US. Most cases are diagnosed in the late, non-resectable stages largely due to lack of effective screening tests. There is an urgent need to identify modifiable risk factors for primary prevention of this malignancy. To date, only a few risk factors (family history, smoking, and type-2 diabetes) have been identified for pancreatic cancer. Although several lines of evidence suggest that nutrition plays a role in pancreatic cancer, few nutrients have been consistently associated with its risk in epidemiologic studies. Therefore, the present study sought to investigate the association between the 2015 Healthy Eating Index (HEI-2015) score and pancreatic cancer risk among participants in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO). The HEI-2015 is a measure of overall diet quality used to assess how well a diet conforms to key recommendations of the 2015-2020 Dietary Guidelines for Americans. The HEI score is made up of 13 food components, with higher scores (ranged 0-100 points) indicating better dietary quality. In the present study, the HEI-2015 scores were calculated from participant responses to two food frequency questionnaires, dietary questionnaire (DQX) and dietary history questionnaire (DHQ) administered at baseline and the three-year anniversary of enrollment, respectively. During a median follow-up of 12.2 years, 279 cases of pancreatic cancer were identified among 58,477 participants who completed the DQX, while 101,721 participants who responded to the DHQ gave rise to 380 cases of pancreatic cancer over a median follow-up of 8.9 years. Hazard ratios (HR) and 95% confidence internals (CI) were estimated using Cox proportional hazards regression for total HEI score and individual score components, classified into adequacy components (total fruit, whole fruits, total vegetables, greens and beans, whole grains, dairy, total protein foods, seafood and plant proteins, and fatty acids) and moderation components (refined grains, sodium, added sugars, and saturated fats). After adjustment for confounders, no significant association between total HEI score and pancreatic cancer was identified [HR (95% CI) for quartile (Q) 4 vs. Q1: 0.86 (0.60, 1.09) for DQX and 1.03 (0.77, 1.39) for DHQ]. The individual component scores for total vegetables and added sugar in the DHQ analysis and whole grain score in the DQX analysis were inversely associated with pancreatic cancer risk [HR (95% CI) for one-point score increase: 0.89 (0.81, 0.98), 0.95 (0.91, 0.99), and 0.94 (0.89, 0.99), respectively]. In summary, our study did not find a significant association between overall diet quality and pancreatic cancer risk but revealed significant associations with total vegetables, added sugar, and whole grains in the PLCO trial. Citation Format: Margaret L. Hoyt, Jianjun Zhang. Association between healthy eating index score and risk of pancreatic cancer in the prostate, lung,
{"title":"Abstract 2586: Association between healthy eating index score and risk of pancreatic cancer in the prostate, lung, colorectal, and ovarian cancer screening trial (PLCO)","authors":"Margaret Hoyt, Jianjun Zhang","doi":"10.1158/1538-7445.AM2021-2586","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2586","url":null,"abstract":"Pancreatic cancer is one of the deadliest malignancies in the US. Most cases are diagnosed in the late, non-resectable stages largely due to lack of effective screening tests. There is an urgent need to identify modifiable risk factors for primary prevention of this malignancy. To date, only a few risk factors (family history, smoking, and type-2 diabetes) have been identified for pancreatic cancer. Although several lines of evidence suggest that nutrition plays a role in pancreatic cancer, few nutrients have been consistently associated with its risk in epidemiologic studies. Therefore, the present study sought to investigate the association between the 2015 Healthy Eating Index (HEI-2015) score and pancreatic cancer risk among participants in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO). The HEI-2015 is a measure of overall diet quality used to assess how well a diet conforms to key recommendations of the 2015-2020 Dietary Guidelines for Americans. The HEI score is made up of 13 food components, with higher scores (ranged 0-100 points) indicating better dietary quality. In the present study, the HEI-2015 scores were calculated from participant responses to two food frequency questionnaires, dietary questionnaire (DQX) and dietary history questionnaire (DHQ) administered at baseline and the three-year anniversary of enrollment, respectively. During a median follow-up of 12.2 years, 279 cases of pancreatic cancer were identified among 58,477 participants who completed the DQX, while 101,721 participants who responded to the DHQ gave rise to 380 cases of pancreatic cancer over a median follow-up of 8.9 years. Hazard ratios (HR) and 95% confidence internals (CI) were estimated using Cox proportional hazards regression for total HEI score and individual score components, classified into adequacy components (total fruit, whole fruits, total vegetables, greens and beans, whole grains, dairy, total protein foods, seafood and plant proteins, and fatty acids) and moderation components (refined grains, sodium, added sugars, and saturated fats). After adjustment for confounders, no significant association between total HEI score and pancreatic cancer was identified [HR (95% CI) for quartile (Q) 4 vs. Q1: 0.86 (0.60, 1.09) for DQX and 1.03 (0.77, 1.39) for DHQ]. The individual component scores for total vegetables and added sugar in the DHQ analysis and whole grain score in the DQX analysis were inversely associated with pancreatic cancer risk [HR (95% CI) for one-point score increase: 0.89 (0.81, 0.98), 0.95 (0.91, 0.99), and 0.94 (0.89, 0.99), respectively]. In summary, our study did not find a significant association between overall diet quality and pancreatic cancer risk but revealed significant associations with total vegetables, added sugar, and whole grains in the PLCO trial. Citation Format: Margaret L. Hoyt, Jianjun Zhang. Association between healthy eating index score and risk of pancreatic cancer in the prostate, lung,","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88796070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-LB013
E. Klein, D. Richards, A. Cohn, M. Tummala, R. Lapham, D. Cosgrove, G. Chung, J. Clement, Jingjing Gao, N. Hunkapiller, A. Jamshidi, K. Kurtzman, M. Seiden, C. Swanton, Minetta C. Liu
Introduction: A multi-cancer early detection (MCED) test as a complement to existing screening tests could increase the number of cancer cases detected in a population, potentially improving patient outcomes and survival as well as decreasing harmful and aggressive treatments. The Circulating Cell-free Genome Atlas study (CCGA; NCT02889978) was designed to develop and validate a blood-based MCED test analyzing plasma cell-free DNA (cfDNA) to detect cancer signals across multiple cancer types and simultaneously predict their signal origin. Here, the results of the third and final pre-specified CCGA validation sub-study for a refined MCED test in a large cohort in preparation for clinical use are reported. Methods: CCGA is a prospective, multicenter, case-control, observational study with longitudinal follow-up (overall population N=15,254). In this sub-study (n=5309), key primary objectives were to evaluate test performance for cancer signal detection (specificity, overall sensitivity, sensitivity by clinical stage) and signal origin prediction (accuracy). cfDNA from evaluable samples was analyzed using a targeted methylation bisulfite sequencing assay and a machine learning algorithm. The classifier was trained to target a specificity of 99.4% and locked before analysis of the independent validation set. Overall, 4077 participants comprised the independent validation set with confirmed status (cancer: n=2823; non-cancer: n=1254 with non-cancer status confirmed at year-one follow-up). MCED test results are reported for this confirmed status set. Results: Mean (SD) age in the cancer and non-cancer groups was 62.6 (11.76) and 56.2 (12.63) years, respectively. Specificity for cancer signal detection was 99.5% (1248/1254; 95% confidence interval: 99.0-99.8%). Overall sensitivity for cancer signal detection was 51.5% (1453/2823; 49.6-53.3%); sensitivity increased with stage (Stage I: 16.8% [14.5-19.5%], Stage II: 40.4% [36.8-44.1%], Stage III: 77.0% [73.4-80.3%], Stage IV: 90.1% [87.5-92.2%]). Stage I-III sensitivity was 67.6% (593/877; 64.4-70.6%) in a pre-specified set of 12 high-signal cancers accounting for ~63% of annual US cancer deaths [1] and was 40.7% (863/2118; 38.7-42.9%) in all cancers. Cancer signals were detected across >50 cancer types [2]. Overall accuracy of signal origin prediction in true positives was 88.7% (87.0-90.2%). Conclusions: In this pre-specified, large-scale, clinical validation sub-study of CCGA, the MCED test detected cancer signals across >50 cancer types, which is critical to maximize the number of cancer cases detected in a population. This MCED test performed with high specificity and high accuracy of signal origin prediction. These data lay the foundation for population-scale clinical implementation of this test. 1.US Mortality Data 1969-2016 (www.seer.cancer.gov); based on 2015-2016. 2.Amin et al. CA Cancer J Clin. 2017;67:93e99. Citation Format: Eric A. Klein, Donald Richards, Allen Cohn, Mohan Tummala, Rosanna La
多种癌症早期检测(MCED)测试作为现有筛查测试的补充,可以增加人群中检测到的癌症病例数量,潜在地改善患者的预后和生存率,并减少有害和积极的治疗。循环无细胞基因组图谱研究(CCGA);NCT02889978)旨在开发和验证基于血液的MCED测试,分析血浆游离DNA (cfDNA),以检测多种癌症类型的癌症信号并同时预测其信号来源。本文报告了第三个也是最后一个预先指定的CCGA验证子研究的结果,该子研究是在一个大型队列中为临床应用做准备的一项改进的MCED试验。方法:CCGA是一项前瞻性、多中心、病例对照、观察性的纵向随访研究(总人群N=15,254)。在这个子研究中(n=5309),主要目的是评估癌症信号检测的测试性能(特异性、总体敏感性、临床分期敏感性)和信号起源预测(准确性)。使用靶向甲基化亚硫酸酯测序法和机器学习算法分析可评估样品中的cfDNA。经过训练,分类器的特异性为99.4%,并在独立验证集分析之前锁定。总体而言,4077名参与者组成了确认状态的独立验证集(癌症:n=2823;非癌症:n=1254,在一年随访中确认非癌症状态)。MCED测试结果将报告此确认状态集。结果:肿瘤组和非肿瘤组的平均(SD)年龄分别为62.6(11.76)岁和56.2(12.63)岁。肿瘤信号检测特异性为99.5% (1248/1254;95%置信区间:99.0-99.8%)。肿瘤信号检测的总灵敏度为51.5% (1453/2823;49.6 - -53.3%);敏感性随分期升高(ⅰ期:16.8%[14.5-19.5%],ⅱ期:40.4%[36.8-44.1%],ⅲ期:77.0%[73.4-80.3%],ⅳ期:90.1%[87.5-92.2%])。I-III期敏感性为67.6% (593/877;64.4-70.6%),在一组预先指定的12种高信号癌症中占美国每年癌症死亡人数的约63%[1],为40.7% (863/2118;38.7-42.9%)。在超过50种癌症类型中检测到癌症信号[2]。真阳性患者信号源预测的总体准确率为88.7%(87.0-90.2%)。结论:在这个预先指定的、大规模的、临床验证的CCGA子研究中,MCED检测检测了超过50种癌症类型的癌症信号,这对于最大限度地提高人群中癌症病例的检测数量至关重要。该MCED测试具有高特异性和高准确度的信号起源预测。这些数据为该测试在人群规模的临床实施奠定了基础。1.1969-2016年美国死亡率数据(www.seer.cancer.gov);基于2015-2016年。2.阿明等人。中华肿瘤杂志,2017;37(3):391 - 391。引文格式:Eric A. Klein, Donald Richards, Allen Cohn, Mohan Tummala, Rosanna Lapham, David Cosgrove, Gina Chung, Jessica Clement, jing Gao, Nathan Hunkapiller, Arash Jamshidi, Kathryn Kurtzman, Michael V. Seiden, Charles Swanton, Minetta C. Liu靶向甲基化多癌早期检测试验的临床验证[摘要]。见:美国癌症研究协会2021年年会论文集;2021年4月10日至15日和5月17日至21日。费城(PA): AACR;癌症杂志,2021;81(13 -增刊):摘要nr LB013。
{"title":"Abstract LB013: Clinical validation of a targeted methylation-based multi-cancer early detection test","authors":"E. Klein, D. Richards, A. Cohn, M. Tummala, R. Lapham, D. Cosgrove, G. Chung, J. Clement, Jingjing Gao, N. Hunkapiller, A. Jamshidi, K. Kurtzman, M. Seiden, C. Swanton, Minetta C. Liu","doi":"10.1158/1538-7445.AM2021-LB013","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-LB013","url":null,"abstract":"Introduction: A multi-cancer early detection (MCED) test as a complement to existing screening tests could increase the number of cancer cases detected in a population, potentially improving patient outcomes and survival as well as decreasing harmful and aggressive treatments. The Circulating Cell-free Genome Atlas study (CCGA; NCT02889978) was designed to develop and validate a blood-based MCED test analyzing plasma cell-free DNA (cfDNA) to detect cancer signals across multiple cancer types and simultaneously predict their signal origin. Here, the results of the third and final pre-specified CCGA validation sub-study for a refined MCED test in a large cohort in preparation for clinical use are reported. Methods: CCGA is a prospective, multicenter, case-control, observational study with longitudinal follow-up (overall population N=15,254). In this sub-study (n=5309), key primary objectives were to evaluate test performance for cancer signal detection (specificity, overall sensitivity, sensitivity by clinical stage) and signal origin prediction (accuracy). cfDNA from evaluable samples was analyzed using a targeted methylation bisulfite sequencing assay and a machine learning algorithm. The classifier was trained to target a specificity of 99.4% and locked before analysis of the independent validation set. Overall, 4077 participants comprised the independent validation set with confirmed status (cancer: n=2823; non-cancer: n=1254 with non-cancer status confirmed at year-one follow-up). MCED test results are reported for this confirmed status set. Results: Mean (SD) age in the cancer and non-cancer groups was 62.6 (11.76) and 56.2 (12.63) years, respectively. Specificity for cancer signal detection was 99.5% (1248/1254; 95% confidence interval: 99.0-99.8%). Overall sensitivity for cancer signal detection was 51.5% (1453/2823; 49.6-53.3%); sensitivity increased with stage (Stage I: 16.8% [14.5-19.5%], Stage II: 40.4% [36.8-44.1%], Stage III: 77.0% [73.4-80.3%], Stage IV: 90.1% [87.5-92.2%]). Stage I-III sensitivity was 67.6% (593/877; 64.4-70.6%) in a pre-specified set of 12 high-signal cancers accounting for ~63% of annual US cancer deaths [1] and was 40.7% (863/2118; 38.7-42.9%) in all cancers. Cancer signals were detected across >50 cancer types [2]. Overall accuracy of signal origin prediction in true positives was 88.7% (87.0-90.2%). Conclusions: In this pre-specified, large-scale, clinical validation sub-study of CCGA, the MCED test detected cancer signals across >50 cancer types, which is critical to maximize the number of cancer cases detected in a population. This MCED test performed with high specificity and high accuracy of signal origin prediction. These data lay the foundation for population-scale clinical implementation of this test. 1.US Mortality Data 1969-2016 (www.seer.cancer.gov); based on 2015-2016. 2.Amin et al. CA Cancer J Clin. 2017;67:93e99. Citation Format: Eric A. Klein, Donald Richards, Allen Cohn, Mohan Tummala, Rosanna La","PeriodicalId":20290,"journal":{"name":"Prevention Research","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89789915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}