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Correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP)

ABSTRACT: Background: We seek to understand correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP). Methodology: We evaluated clinical features, salivary RNA metrics and differential expression of candidate genes in unfractionated saliva samples from 48 individuals (31% female, 55% ever-smoking) randomly selected from two groups stratified by high versus low severe negative life events and difficulties within the last year as as measured by the Life Events and Difficulties Schedule (LEDS, Brown & Harris, 1978). We used multiple analytical platforms, multiple reference genes and 18 replicates of all gene expression assays (assays). We chose 38 candidate genes previously identified as differentially expressed in a genome-wide scan of monocyte RNA in 11 familial caregivers of glioblastoma multiforme patients and 10 control subjects matched on age (middle-aged), gender (57% female), ethnicity and marital status and free of major stressors during the previous year. Principal Findings: We observed significant differences in smoking prevalence (Pearson’s χ22d.f.=4.5, P=0.035) and RNA integrity score (t=2.12, P=0.039) between stress strata. We analyzed quantitative PCR data using both the comparative standard curve (CSC) and relative standard curve (RSC) methods because 34% of assays had efficiency estimates <90%. Assay data exhibited excellent linearity and low variability. We observed significant under expression of five assays in the high stress stratum using both methods, four of which interrogate glucocorticoid receptor regulated genes. Post-hoc analyses identified significant associations of RNA yield, integrity score, gender, ever-smoking and/or stress with results of normalized gene expression in 22/37 assays. IL8 expression remained significantly associated with chronic stress after adjustment for clinical and salivary RNA variables. Salivary IL8 expression has been previously associated with oropharyngeal squamous cell cancer. Conclusions: A gene expression signature of chronic stress previously observed in adult hematopoietic samples is observed in the unfractionated saliva of young adults. Future investigation will need to analyze associated clinical, metabolic, meta-genomic, and proteomic components of unfractionated saliva to elucidate factors influencing the salivary transcriptome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE27144 | GEO | 2012/06/15

SECONDARY ACCESSION(S): PRJNA137571

REPOSITORIES: GEO

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Project description:Background: We seek to understand correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP). Methodology: We evaluated clinical features, salivary RNA metrics and differential expression of candidate genes in unfractionated saliva samples from 48 individuals (31% female, 55% ever-smoking) randomly selected from two groups stratified by high versus low severe negative life events and difficulties within the last year as as measured by the Life Events and Difficulties Schedule (LEDS, Brown & Harris, 1978). We used multiple analytical platforms, multiple reference genes and 18 replicates of all gene expression assays (assays). We chose 38 candidate genes previously identified as differentially expressed in a genome-wide scan of monocyte RNA in 11 familial caregivers of glioblastoma multiforme patients and 10 control subjects matched on age (middle-aged), gender (57% female), ethnicity and marital status and free of major stressors during the previous year. Principal Findings: We observed significant differences in smoking prevalence (Pearson’s ?22d.f.=4.5, P=0.035) and RNA integrity score (t=2.12, P=0.039) between stress strata. We analyzed quantitative PCR data using both the comparative standard curve (CSC) and relative standard curve (RSC) methods because 34% of assays had efficiency estimates <90%. Assay data exhibited excellent linearity and low variability. We observed significant under expression of five assays in the high stress stratum using both methods, four of which interrogate glucocorticoid receptor regulated genes. Post-hoc analyses identified significant associations of RNA yield, integrity score, gender, ever-smoking and/or stress with results of normalized gene expression in 22/37 assays. IL8 expression remained significantly associated with chronic stress after adjustment for clinical and salivary RNA variables. Salivary IL8 expression has been previously associated with oropharyngeal squamous cell cancer. Conclusions: A gene expression signature of chronic stress previously observed in adult hematopoietic samples is observed in the unfractionated saliva of young adults. Future investigation will need to analyze associated clinical, metabolic, meta-genomic, and proteomic components of unfractionated saliva to elucidate factors influencing the salivary transcriptome. Gene expression was performed on a Fluidigm 48 x 48 array on 48 individuals for 38 target genes and 6 possible reference genes (represented by 9 reference assays) in triplicate. Quantitative Q-PCR datas were normalized according to relative levels of four reference genes (CDKN1B, YWHAZ, RPL13A, and UBC).

Project description:Pancreatic cancer is the fourth leading cause of cancer death. Lack of early detection technology for pancreatic cancer invariably leads to a typical clinical presentation of incurable disease at initial diagnosis. Oral fluid (saliva) meets the demand for non-invasive, accessible, and highly efficient diagnostic medium. The level of salivary analytes, such as mRNA and microflora, vary upon disease onset; thus possess valuable signatures for early detection and screening. In this study, we evaluated the performance and translational utilities of the salivary transcriptomic and microbial biomarkers for non-invasive detection of early pancreatic cancer. Two biomarker discovery technologies were used to profile transcriptome in saliva supernatant and microflora in saliva pellet. The Affymetrix Human Genome U133 Plus 2.0 Array was used to discover altered gene expression in saliva supernatant. The Human Oral Microbe Identification Microarray (HOMIM) was used to investigate microflora shift in saliva pellet. Biomarkers selected from both studies were subjected to an independent clinical validation using a cohort of 30 early pancreatic cancer, 30 chronic pancreatitis and 30 healthy matched-control saliva samples. Two panels of salivary biomarkers, including eleven mRNA biomarkers and two microbial biomarkers were discovered and validated for pancreatic cancer detection. The logistic regression model with the combination of three mRNA biomarkers (ACRV1, DMXL2 and DPM1) yielded a ROC-plot AUC value of 0.974 (95% CI, 0.896 to 0.997; P < 0.0001) with 93.3% sensitivity and 90% specificity in distinguishing pancreatic cancer patients from healthy subjects. The logistic regression model with the combination of two bacterial biomarkers (Neisseria elongata and Streptococcus mitis) yielded a ROC-plot AUC value of 0.895 (95% CI, 0.784 to 0.961; P < 0.0001) with 96.4% sensitivity and 82.1% specificity in distinguishing pancreatic cancer patients from healthy subjects. Importantly, the logistic regression model with the combination of four biomarkers (mRNA biomarkers, ACRV1, DMXL2 and DPM1; bacterial biomarker, S. mitis) could differentiate pancreatic cancer patients from all non-cancer subjects (chronic pancreatitis and healthy control), yielding a ROC-plot AUC value of 0.949 (95% CI, 0.877 to 0.985; P < 0.0001) with 92.9% sensitivity and 85.5% specificity. This study comprehensively compared the salivary transcriptome and microflora between pancreatic cancer and control subjects. We have discovered and validated eleven mRNA biomarkers and two microbial biomarkers for early detection of pancreatic cancer in saliva. The logistic regression model with four salivary biomarkers can detect pancreatic cancer specifically without the complication of chronic pancreatitis. This is the first report demonstrating the value of multiplex salivary biomarkers for the non-invasive detection of a high impact systemic cancer. Keywords: Salivary biomarker, pancreatic cancer, early detection, salivary transcriptome, salivary microflora This study, which was approved by the UCLA Institutional Review Board, started sample collection in February 2006 and ended in April 2008. It had a discovery and verification phase, followed by an independent validation phase. All patients with clinically diagnosed early or locally advanced pancreatic cancer, chronic pancreatitis and matched healthy control were recruited from the UCLA Medical Center. The controls were matched for gender, age, ethnicity and smoking history. We chose early and locally advanced pancreatic cancers because they were considered early stage diseases. All patients were recently diagnosed with primary disease, and had not received any prior treatment in the form of chemotherapy, radiotherapy, surgery, or alternative remedies. No subjects had a history of prior malignancy, immunodeficiency, autoimmune disorders, hepatitis, or HIV infection. Written informed consent was obtained from all patients who agreed to serve as saliva donors. Unstimulated saliva samples were collected and processed as previously described. The saliva bank of pancreatic disease at the UCLA Dental Research Institute has collected 283 saliva samples since 2006. Of these, 114 samples, from 42 pancreatic cancer patients, 30 chronic pancreatitis patients and 42 healthy control subjects, met the following eligibility criteria: the disease subjectsâ?? samples were obtained immediately after primary diagnosis from patients without evidence of metastasis; the saliva sample was free of blood (Table 1 in accompanying manuscript). Of the 114 samples, 12 pancreatic cancer samples and 12 healthy control samples were chosen for the discovery and verification phase. The transcriptomic approach profiled the saliva supernatant samples from 12 pancreatic cancer patients and 12 healthy control subjects using the Affymetrix Human Genome U133 Plus 2.0 Array platform.

Project description:Saliva (oral fluids) is an emerging biofluid poised for clinical diseases detection. Although the rationale for oral diseases applications (e.g. oral cancer) is clear, the rationale and relationship between systemic diseases and saliva biomarkers are unknown. In this study, we used mouse models of melanoma and non-small cell lung cancer and compared the transcriptome biomarker profiles of tumor-bearing mice to those of control mice. Microarray analysis showed that salivary transcriptomes were significantly altered in tumor-bearing mice vs. controls. Analysis of the transcriptomes in the mouse tumors, serum, salivary glands and saliva revealed that salivary biomarkers have multiple origins. Furthermore, we identified that the expression of two groups of significantly altered transcription factors Runx1, Mlxipl, Trim30 and Egr1, Tbx1, Nr1d1 in melanoma-bearing mice that can potentially be responsible for 82.6% of the up-regulated genes expression and 62.5% of the down-regulated gene expression in the mice saliva, respectively. We also confirmed that the ectopic production of nerve growth factor (NGF) in the melanoma tumor tissue as a tumor-released mediator that can induce expression of the transcription factor Egr-1 in the salivary gland. Taken together, our data support the conclusion that upon systemic disease development, a disease-specific change occurs in the salivary biomarker profile. Although the origins of the disease-specific salivary biomarkers are both systemic and local, stimulation of salivary gland by mediators released from remote tumors play an important role in regulating the salivary surrogate biomarker profiles. Experiment Overall Design: Mice (either C57BL/6 mice or DBA/2 mice) were randomly assigned to control group and tumor group (15 animals per group). Melanoma mice model was induced by subcutaneous (s.c.) injection of B16-F1 cells in 0.1 ml PBS into the lower-right flank of C57BL/6 mice. The lung cancer model was established by s.c. injection of KLN-205 cells in DBA/2 mice. Control animal were injected with PBS alone. Established tumors were observed after 2-3 weeks. Experiment Overall Design: When tumors reached 15 mm in diameter saliva was collected and the mice were sacrificed. Mild anesthesia was induced. Mice saliva was stimulated, obtained and immediately placed in pre-schilled 1.5-ml microcentrifuge tubes. Collection was completed in 20 minutes and samples were stored at -80ÂºC until analyzed.In addition, Blood was collected in BD Vacutainer tubes containing clot activator (BD Biosciences). Salivary gland and tumor tissue were removed from mice, snap-frozen in liquid nitrogen and stored at -80ÂºC. Experiment Overall Design: Experiment Overall Design: Salivary,salivary gland, serum or tumor RNA was isolated using the RNeasy Mini Kit (Qiagen) as described previously. There are 15 mice in the control group or tumor group (totally 30 C57BL/6 mice for melanoma mouse model, another 30 DBA/2 mice for lung cancer mouse model). Samples derived from 5 mice in each group were pooled and RNA extracted. The pooling is necessary to ensure sufficient salivary mRNA can be obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase (Ambion, Austin, TX). For microarray analysis, mRNA from mouse saliva, gland or tumor was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA were in vitro transcribed and biotinylated using GeneChip Expression 3â-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). The labeled RNAs was subsequently fragmented, hybridization and scanning.

Project description:A sensitive assay to identify biomarkers that can accurately diagnose the onset of breast cancer using non-invasively collected clinical specimens is ideal for early detection. In this study, we have conducted a prospective sample collection and retrospective blinded validation (PRoBE design) to evaluate the performance and translational utilities of salivary transcriptomic and proteomic biomarkers for the non-invasive detection of breast cancer. The Affymetrix HG U133 Plus 2.0 Array and 2D-DIGE were used to profile transcriptomes and proteomes in saliva supernatants respectively. Significant variations of salivary transcriptomic and proteomic profiles were observed between breast cancer patients and healthy controls. Eleven transcriptomic biomarker candidates and two proteomic biomarker candidates were selected for a preclinical validation using an independent sample set. Transcriptomic biomarkers were validated by RT-qPCR and proteomic biomarkers were validated by quantitative protein immunoblot. Eight mRNA biomarkers and one protein biomarker have been validated for breast cancer detection, yielding ROC-plot AUC values between 0.665 and 0.959. This report provides proof of concept of salivary biomarkers for the non-invasive detection of breast cancer. The salivary biomarkersâ discriminatory power paves the way for a PRoBE-design definitive validation study. Keywords: Salivary biomarker, Breast cancer, Early detection, Salivary transcriptome, Salivary proteome This study, which was approved by the UCLA and Cedars-Sinai Medical Center Institutional Review Boards (#06-07-043 and #3870, respectively), started sample collection in February 2007. The sample collection followed the PRoBE principle (prospective specimen collection). The saliva bank for breast cancer project at the UCLA Dental Research Institute in collaboration with Cedars Sinai Medical Center has collected 200 saliva samples since 2007 with all subjects recruited from the Saul and Joyce Brandman Breast Cancer Center. Of these, 113 samples, including 41 breast cancer patients and 72 healthy control individuals, were selected for the discovery and validation phase of this study. Inclusion criteria of cancer patients consisted of a confirmed diagnosis of breast cancer. Exclusion criteria of cancer patients included therapy/surgery and/or a diagnosis of other malignancies within 5 years prior to saliva collection. Exclusion criteria of control patients included a diagnosis of any malignancies within 5 years prior to saliva collection. Written informed consents and questionnaire data sheets were obtained from all patients who agreed to serve as saliva donors. Unstimulated saliva samples were consistently collected, stabilized, and preserved as previously described. The sample supernatants were reserved at -80 C prior to assay. This study consisted of a discovery phase, followed by an independent preclinical validation phase. Of the 113 samples, 10 breast cancer samples and 10 healthy control samples were chosen for the discovery phase. All breast cancer cases are invasive ductal carcinoma (IDC), the most common type of breast cancer. Biomarkers identified from the discovery studies were first verified using the discovery sample set. An independent sample set, including 31 breast cancer patients and 62 healthy control subjects, was used for the biomarker validation phase.

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Correlates of chronic stress and their influence on the development of substance use in a population-based cohort of young adults (OYSUP)

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