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Article: The functional role of miRNAs in colorectal cancer: insights from a large population-based study.

Mullany, Lila E / Slattery, Martha L

2019 Volume 16, Issue 2, Page(s) 211–219

Abstract: Identification of causal microRNAs (miRNAs) in colorectal cancer (CRC) is elusive, due to our lack of understanding of how specific miRNAs affect biological pathways and outcomes. An miRNA can regulate many mRNAs and an mRNA can be associated with many ... ...

Abstract	Identification of causal microRNAs (miRNAs) in colorectal cancer (CRC) is elusive, due to our lack of understanding of how specific miRNAs affect biological pathways and outcomes. An miRNA can regulate many mRNAs and an mRNA can be associated with many miRNAs; appreciation of these complex networks in which miRNAs operate is necessary to transition from identifying dysregulated miRNAs to identifying individual miRNAs or groups of miRNAs that are suitable for therapeutic purposes. The aim of the paper is to compile results from a population-based study (
Language	English
Publishing date	2019-09-03
Publishing country	China
Document type	Journal Article
ZDB-ID	2676322-9
ISSN	2095-3941
ISSN	2095-3941
DOI	10.20892/j.issn.2095-3941.2018.0514
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Article: Analysis of dietary patterns in epidemiological research.

Slattery, Martha L

Applied physiology, nutrition, and metabolism = Physiologie appliquee, nutrition et metabolisme

2010 Volume 35, Issue 2, Page(s) 207–210

Abstract: Dietary patterns have been used to summarize diet consumption and to evaluate how diet is associated with diseases in epidemiological research. However, there are many issues surrounding both the use and interpretation of dietary patterns. These issues ... ...

Abstract	Dietary patterns have been used to summarize diet consumption and to evaluate how diet is associated with diseases in epidemiological research. However, there are many issues surrounding both the use and interpretation of dietary patterns. These issues include how to collect, summarize, and create dietary patterns, as well as how to interpret the results. Because labels are given arbitrarily to dietary patterns to help characterize the pattern in a meaningful way, it is often not clear from the literature as to the consistency of results among studies. Additionally, the utilization of dietary patterns as a tool for public health messages is a topic that is unresolved. These issues are discussed in this paper.
MeSH term(s)	Diet/adverse effects ; Epidemiologic Research Design ; Evidence-Based Medicine ; Feeding Behavior ; Humans ; Nutrition Surveys ; Nutritional Status ; Reproducibility of Results ; Risk Assessment ; Risk Factors ; Terminology as Topic
Language	English
Publishing date	2010-04-12
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2236708-1
ISSN	1715-5320 ; 1715-5312
ISSN (online)	1715-5320
ISSN	1715-5312
DOI	10.1139/H10-006
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Article ; Online: Accounting for Missing Data in Clinical Research.

Stevens, John R / Suyundikov, Anvar / Slattery, Martha L

JAMA

2016 Volume 315, Issue 5, Page(s) 517–518

MeSH term(s)	Albuminuria/drug therapy ; Diabetes Mellitus, Type 2/complications ; Diabetic Nephropathies/drug therapy ; Female ; Humans ; Male ; Naphthyridines/administration & dosage
Chemical Substances	Naphthyridines
Language	English
Publishing date	2016-02-02
Publishing country	United States
Document type	Comment ; Letter
ZDB-ID	2958-0
ISSN	1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
ISSN (online)	1538-3598
ISSN	0254-9077 ; 0002-9955 ; 0098-7484
DOI	10.1001/jama.2015.16461
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Article ; Online: Defining dietary consumption: is the sum greater than its parts?

Slattery, Martha L

The American journal of clinical nutrition

2007 Volume 88, Issue 1, Page(s) 14–15

MeSH term(s)	Chronic Disease/prevention & control ; Diet/standards ; Epidemiologic Studies ; Factor Analysis, Statistical ; Feeding Behavior ; Food, Organic ; Humans ; Nutritional Physiological Phenomena/physiology ; Risk Factors
Language	English
Publishing date	2007-04-18
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	280048-2
ISSN	1938-3207 ; 0002-9165
ISSN (online)	1938-3207
ISSN	0002-9165
DOI	10.1093/ajcn/88.1.14
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Article ; Online: The influence of the CHIEF pathway on colorectal cancer-specific mortality.

Slattery, Martha L / Lundgreen, Abbie

PloS one

2014 Volume 9, Issue 12, Page(s) e116169

Abstract: Many components of the CHIEF (Convergence of Hormones, Inflammation, and Energy Related Factors) pathway could influence survival given their involvement in cell growth, apoptosis, angiogenesis, and tumor invasion stimulation. We used ARTP (Adaptive Rank ...

Abstract	Many components of the CHIEF (Convergence of Hormones, Inflammation, and Energy Related Factors) pathway could influence survival given their involvement in cell growth, apoptosis, angiogenesis, and tumor invasion stimulation. We used ARTP (Adaptive Rank Truncation Product) to test if genes in the pathway were associated with colorectal cancer-specific mortality. Colon cancer (n = 1555) and rectal cancer (n = 754) cases were followed over five years. Age, center, stage at diagnosis, and tumor molecular phenotype were considered when calculating ARTP p values. A polygenic risk score was used to summarize the magnitude of risk associated with this pathway. The JAK/STAT/SOC was significant for colon cancer survival (PARTP = 0.035). Fifteen genes (DUSP2, INFGR1, IL6, IRF2, JAK2, MAP3K10, MMP1, NFkB1A, NOS2A, PIK3CA, SEPX1, SMAD3, TLR2, TYK2, and VDR) were associated with colon cancer mortality (PARTP < 0.05); JAK2 (PARTP = 0.0086), PIK3CA (PARTP = 0.0098), and SMAD3 (PARTP = 0.0059) had the strongest associations. Over 40 SNPs were significantly associated with survival within the 15 significant genes (PARTP < 0.05). SMAD3 had the strongest association with survival (HRGG 2.46 95% CI 1.44,4.21 PTtrnd = 0.0002). Seven genes (IL2RA, IL8RA, IL8RB, IRF2, RAF1, RUNX3, and SEPX1) were significantly associated with rectal cancer (PARTP < 0.05). The HR for colorectal cancer-specific mortality among colon cancer cases in the upper at-risk alleles group was 11.81 (95% CI 7.07, 19. 74) and was 10.99 (95% CI 5.30, 22.78) for rectal cancer. These results suggest that several genes in the CHIEF pathway are important for colorectal cancer survival; the risk associated with the pathway merits validation in other studies.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; Colon/metabolism ; Colon/pathology ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/metabolism ; Colorectal Neoplasms/mortality ; Colorectal Neoplasms/pathology ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Rectum/metabolism ; Rectum/pathology ; Signal Transduction
Language	English
Publishing date	2014-12-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0116169
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Article ; Online: Power in pairs: assessing the statistical value of paired samples in tests for differential expression.

Stevens, John R / Herrick, Jennifer S / Wolff, Roger K / Slattery, Martha L

BMC genomics

2018 Volume 19, Issue 1, Page(s) 953

Abstract: Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain ... ...

Abstract	Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study. Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of subject-level confounding factors. In the design scenarios considered, the statistical power in a fully-paired design is substantially (and in many cases several times) greater than in an unpaired design. Conclusions: For the many biological systems and research questions where paired samples are feasible and relevant, substantial statistical power gains can be achieved at the study design stage when genomics researchers plan on using paired samples from the largest possible proportion of subjects. Any cost savings in a study design with unpaired samples are likely accompanied by underpowered and possibly biased results.
MeSH term(s)	Biomarkers, Tumor/genetics ; Colorectal Neoplasms/genetics ; Gene Expression Regulation, Neoplastic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Models, Statistical ; Oligonucleotide Array Sequence Analysis/methods ; Research Design ; Sample Size ; Sequence Analysis, RNA/methods ; Transcriptome
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2018-12-20
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-018-5236-2
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Article: Vitamin D receptor gene (VDR) associations with cancer.

Slattery, Martha L

Nutrition reviews

2007 Volume 65, Issue 8 Pt 2, Page(s) S102–4

MeSH term(s)	Breast Neoplasms/epidemiology ; Breast Neoplasms/etiology ; Breast Neoplasms/genetics ; Female ; Genetic Variation ; Humans ; Male ; Neoplasms/epidemiology ; Neoplasms/etiology ; Neoplasms/genetics ; Prostatic Neoplasms/epidemiology ; Prostatic Neoplasms/etiology ; Prostatic Neoplasms/genetics ; Receptors, Calcitriol/genetics ; Vitamin D/metabolism
Chemical Substances	Receptors, Calcitriol ; Vitamin D (1406-16-2)
Language	English
Publishing date	2007-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	82067-2
ISSN	1753-4887 ; 0029-6643
ISSN (online)	1753-4887
ISSN	0029-6643
DOI	10.1111/j.1753-4887.2007.tb00332.x
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Zs.A 3388: Show issues

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Article ; Online: The influence of the CHIEF pathway on colorectal cancer-specific mortality.

Martha L Slattery / Abbie Lundgreen

PLoS ONE, Vol 9, Iss 12, p e

2014 Volume 116169

Abstract	Many components of the CHIEF (Convergence of Hormones, Inflammation, and Energy Related Factors) pathway could influence survival given their involvement in cell growth, apoptosis, angiogenesis, and tumor invasion stimulation. We used ARTP (Adaptive Rank Truncation Product) to test if genes in the pathway were associated with colorectal cancer-specific mortality. Colon cancer (n = 1555) and rectal cancer (n = 754) cases were followed over five years. Age, center, stage at diagnosis, and tumor molecular phenotype were considered when calculating ARTP p values. A polygenic risk score was used to summarize the magnitude of risk associated with this pathway. The JAK/STAT/SOC was significant for colon cancer survival (PARTP = 0.035). Fifteen genes (DUSP2, INFGR1, IL6, IRF2, JAK2, MAP3K10, MMP1, NFkB1A, NOS2A, PIK3CA, SEPX1, SMAD3, TLR2, TYK2, and VDR) were associated with colon cancer mortality (PARTP < 0.05); JAK2 (PARTP = 0.0086), PIK3CA (PARTP = 0.0098), and SMAD3 (PARTP = 0.0059) had the strongest associations. Over 40 SNPs were significantly associated with survival within the 15 significant genes (PARTP < 0.05). SMAD3 had the strongest association with survival (HRGG 2.46 95% CI 1.44,4.21 PTtrnd = 0.0002). Seven genes (IL2RA, IL8RA, IL8RB, IRF2, RAF1, RUNX3, and SEPX1) were significantly associated with rectal cancer (PARTP < 0.05). The HR for colorectal cancer-specific mortality among colon cancer cases in the upper at-risk alleles group was 11.81 (95% CI 7.07, 19. 74) and was 10.99 (95% CI 5.30, 22.78) for rectal cancer. These results suggest that several genes in the CHIEF pathway are important for colorectal cancer survival; the risk associated with the pathway merits validation in other studies.
Keywords	Medicine ; R ; Science ; Q
Subject code	610 ; 616
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Overall survival is the lowest among young women with postpartum breast cancer.

Shagisultanova, Elena / Gao, Dexiang / Callihan, Eryn / Parris, Hannah J / Risendal, Betsy / Hines, Lisa M / Slattery, Martha L / Baumgartner, Kathy / Schedin, Pepper / John, Esther M / Borges, Virginia F

European journal of cancer (Oxford, England : 1990)

2022 Volume 168, Page(s) 119–127

Abstract: Background: Women diagnosed with breast cancer prior to age 45 years (<45y) and within the first 5 years postpartum (postpartum breast cancer, PPBC) have the greatest risk for distal metastatic recurrence.: Methods: Pooling data from the Colorado ... ...

Abstract	Background: Women diagnosed with breast cancer prior to age 45 years (<45y) and within the first 5 years postpartum (postpartum breast cancer, PPBC) have the greatest risk for distal metastatic recurrence. Methods: Pooling data from the Colorado Young Women Breast Cancer cohort and the Breast Cancer Health Disparities Study (N = 2519 cases), we examined the association of parity, age, and clinical factors with overall survival (OS) of breast cancer over 15 years of follow-up. Results: Women with PPBC diagnosed at <45y had the lowest OS (p < 0.0001), while OS of nulliparous cases diagnosed at <45y did not differ from OS of cases diagnosed at 45-65y regardless of parity status. After adjustment for study site, race/ethnicity, clinical stage, year of diagnosis and stratification for oestrogen receptor status, PPBC remained an independent factor associated with poor OS. Among cases diagnosed at <45y, nulliparous cases had 1.6 times better OS (hazard ratio (HR) = 0.61, 95%CI 0.42-0.87) compared to those with PPBC, with a more pronounced survival difference among stage I breast cancers (HR = 0.30, 95%CI 0.11-0.79). Among very young women diagnosed at age ≤35y, nulliparous cases had 2.3 times better OS (HR = 0.44, 95%CI 0.23-0.84) compared to PPBC. Conclusion: Our results suggest that postpartum status is the main driver of poor prognosis in young women with breast cancer, with the strongest association in patients diagnosed at age ≤35y and in those with stage I disease.
MeSH term(s)	Breast Neoplasms/pathology ; Cohort Studies ; Female ; Humans ; Middle Aged ; Parity ; Postpartum Period ; Pregnancy ; Prognosis ; Proportional Hazards Models
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	82061-1
ISSN	1879-0852 ; 0277-5379 ; 0959-8049 ; 0964-1947
ISSN (online)	1879-0852
ISSN	0277-5379 ; 0959-8049 ; 0964-1947
DOI	10.1016/j.ejca.2022.03.014
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Article ; Online: Identifying factors associated with the direction and significance of microRNA tumor-normal expression differences in colorectal cancer.

Stevens, John R / Herrick, Jennifer S / Wolff, Roger K / Slattery, Martha L

BMC cancer

2017 Volume 17, Issue 1, Page(s) 707

Abstract: Background: microRNAs are small non-protein-coding RNA molecules that regulate gene expression, and have a potential epigenetic role in disease progression and survival of colorectal cancer. In terms of tumor-normal expression differences, many ... ...

Abstract	Background: microRNAs are small non-protein-coding RNA molecules that regulate gene expression, and have a potential epigenetic role in disease progression and survival of colorectal cancer. In terms of tumor-normal expression differences, many microRNAs exhibit evidence of being up-regulated in some subjects but down-regulated in others, or are dysregulated only for a subset of the population. We present and implement an approach to identify factors (lifestyle, tumor molecular phenotype, and survival-related) that are associated with the direction and/or significance of these microRNAs' tumor-normal expression differences in colorectal cancer. Methods: Using expression data for 1394 microRNAs and 1836 colorectal cancer subjects (each with both tumor and normal samples), we perform a dip test to identify microRNAs with multimodal distributions of tumor-normal expression differences. For proximal, distal, and rectal tumor sites separately, these microRNAs are tested for tumor-normal differential expression using a signed rank test, both overall and within levels of each lifestyle, tumor molecular phenotype, and survival-related factor. Appropriate adjustments are made to control the overall FDR. Results: We identify hundreds of microRNAs whose direction and/or significance of tumor-normal differential expression is associated with one or more lifestyle, tumor molecular phenotype, or survival-related factors. Conclusions: The results of this study demonstrate the benefit to colorectal cancer researchers to consider multiple subject-level factors when studying dysregulation of microRNAs, whose tumor-related changes in expression can be associated with multiple factors. Our results will serve as a publicly-available resource to provide clarifying information about various factors associated with the direction and significance of tumor-normal differential expression of microRNAs in colorectal cancer.
Language	English
Publishing date	2017-10-30
Publishing country	England
Document type	Journal Article
ISSN	1471-2407
ISSN (online)	1471-2407
DOI	10.1186/s12885-017-3690-x
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