Heng YJ, Lester SC, Tse GMK, Factor RE, Allison KH, Collins LC, Chen Y-Y, Jensen KC, Johnson NB, Jeong JC, et al. The molecular basis of breast cancer pathological phenotypes. J Pathol. 2017;241 (3) :375-391.Abstract
The histopathological evaluation of morphological features in breast tumours provides prognostic information to guide therapy. Adjunct molecular analyses provide further diagnostic, prognostic and predictive information. However, there is limited knowledge of the molecular basis of morphological phenotypes in invasive breast cancer. This study integrated genomic, transcriptomic and protein data to provide a comprehensive molecular profiling of morphological features in breast cancer. Fifteen pathologists assessed 850 invasive breast cancer cases from The Cancer Genome Atlas (TCGA). Morphological features were significantly associated with genomic alteration, DNA methylation subtype, PAM50 and microRNA subtypes, proliferation scores, gene expression and/or reverse-phase protein assay subtype. Marked nuclear pleomorphism, necrosis, inflammation and a high mitotic count were associated with the basal-like subtype, and had a similar molecular basis. Omics-based signatures were constructed to predict morphological features. The association of morphology transcriptome signatures with overall survival in oestrogen receptor (ER)-positive and ER-negative breast cancer was first assessed by use of the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset; signatures that remained prognostic in the METABRIC multivariate analysis were further evaluated in five additional datasets. The transcriptomic signature of poorly differentiated epithelial tubules was prognostic in ER-positive breast cancer. No signature was prognostic in ER-negative breast cancer. This study provided new insights into the molecular basis of breast cancer morphological phenotypes. The integration of morphological with molecular data has the potential to refine breast cancer classification, predict response to therapy, enhance our understanding of breast cancer biology, and improve clinical management. This work is publicly accessible at Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, et al. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017;28 (2) :167-176.Abstract
Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: (1) the development of new statistical methods to address etiologic heterogeneity; (2) the enhancement of causal inference; (3) the identification of previously unknown exposure-subtype disease associations; and (4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields.
Heng YJ, Pennell CE, McDonald SW, Vinturache AE, Xu J, Lee MWF, Briollais L, Lyon AW, Slater DM, Bocking AD, et al. Maternal Whole Blood Gene Expression at 18 and 28 Weeks of Gestation Associated with Spontaneous Preterm Birth in Asymptomatic Women. PLoS One. 2016;11 (6) :e0155191.Abstract
The heterogeneity of spontaneous preterm birth (SPTB) requires an interdisciplinary approach to determine potential predictive risk factors of early delivery. The aim of this study was to investigate maternal whole blood gene expression profiles associated with spontaneous preterm birth (SPTB, <37 weeks) in asymptomatic pregnant women. The study population was a matched subgroup of women (51 SPTBs, 114 term delivery controls) who participated in the All Our Babies community based cohort in Calgary (n = 1878). Maternal blood at 17-23 (sampling time point 1, T1) and 27-33 weeks of gestation (T2) were collected. Total RNA was extracted and microarray was performed on 326 samples (165 women). Univariate analyses determined significant clinical factors and differential gene expression associated with SPTB. Thirteen genes were validated using qRT-PCR. Three multivariate logistic models were constructed to identify gene expression at T1 (Model A), T2 (Model B), and gene expression fold change from T1 to T2 (Model C) associated with SPTB. All models were adjusted for clinical factors. Model C can predict SPTB with 65% sensitivity and 88% specificity in asymptomatic women after adjusting for history of abortion and anaemia (occurring before T2). Clinical data enhanced the sensitivity of the Models to predict SPTB. In conclusion, clinical factors and whole blood gene expression are associated with SPTB in asymptomatic women. An effective screening tool for SPTB during pregnancy would enable targeted preventive approaches and personalised antenatal care.
Heng YJ, Liong S, Permezel M, Rice GE, Di Quinzio MKW, Georgiou HM. Human cervicovaginal fluid biomarkers to predict term and preterm labor. Front Physiol. 2015;6 :151.Abstract
Preterm birth (PTB; birth before 37 completed weeks of gestation) remains the major cause of neonatal morbidity and mortality. The current generation of biomarkers predictive of PTB have limited utility. In pregnancy, the human cervicovaginal fluid (CVF) proteome is a reflection of the local biochemical milieu and is influenced by the physical changes occurring in the vagina, cervix and adjacent overlying fetal membranes. Term and preterm labor (PTL) share common pathways of cervical ripening, myometrial activation and fetal membranes rupture leading to birth. We therefore hypothesize that CVF biomarkers predictive of labor may be similar in both the term and preterm labor setting. In this review, we summarize some of the existing published literature as well as our team's breadth of work utilizing the CVF for the discovery and validation of putative CVF biomarkers predictive of human labor. Our team established an efficient method for collecting serial CVF samples for optimal 2-dimensional gel electrophoresis resolution and analysis. We first embarked on CVF biomarker discovery for the prediction of spontaneous onset of term labor using 2D-electrophoresis and solution array multiple analyte profiling. 2D-electrophoretic analyses were subsequently performed on CVF samples associated with PTB. Several proteins have been successfully validated and demonstrate that these biomarkers are associated with term and PTL and may be predictive of both term and PTL. In addition, the measurement of these putative biomarkers was found to be robust to the influences of vaginal microflora and/or semen. The future development of a multiple biomarker bed-side test would help improve the prediction of PTB and the clinical management of patients.
Heng YJ, Taylor L, Larsen BG, Chua HN, Pung SM, Lee MWF, Tucholska M, Tate S, Kupchak P, Pennell CE, et al. Albumin decrease is associated with spontaneous preterm delivery within 48 h in women with threatened preterm labor. J Proteome Res. 2015;14 (1) :457-66.Abstract
Threatened preterm labor (TPTL) accounts for ∼30% of pregnancy-related hospital admissions. Maternal peripheral leukocytes can be used to monitor a variety of physiological processes occurring in the body. Two high-throughput mass spectrometry methodologies, SWATH and iTRAQ, were used to study differentially expressed peripheral blood leukocyte lysate proteins in symptomatic women admitted for TPTL who had a preterm birth within 48 h (n = 16) and those who did not (n = 24). The SWATH spectral library consisted of 783 proteins. SWATH methodology quantified 258 proteins (using ≥2 peptides) and 5 proteins (ALBU, ANXA6, HNRPK, HSP90A, and PDIA1) were differentially expressed (p < 0.05, Mann-Whitney U). iTRAQ workflow identified 765 proteins; 354 proteins were quantified and 14 proteins (MIF, UBIQ, HXK3, ALBU, HNRPD, ST1A2, RS15A, RAP1B, CAN1, IQGA2, ST1A1, COX5A, ADDA, and UBQL1) were significantly different between the two groups of women (p < 0.05, Mann-Whitney U). Albumin was the only common differentially expressed protein in both SWATH (28% decrease) and iTRAQ studies (45% decrease). This decrease in albumin was validated using ELISA (11% decrease, p < 0.05, Mann-Whitney U) in another 23 TPTL women. This work suggests that albumin is a broad indicator of leukocyte activation with impending preterm birth and provides new future work directions to understand the pathophysiology of TPTL.
Heng YJ, Liong S, Permezel M, Rice GE, Di Quinzio MKW, Georgiou HM. The interplay of the interleukin 1 system in pregnancy and labor. Reprod Sci. 2014;21 (1) :122-30.Abstract
This work assessed the temporal coexpression of interleukin 1 (IL-1) and its inhibitor, IL-1 receptor antagonist (IL-1ra), in the cervicovaginal fluid (CVF) beyond 24 weeks gestation including women in spontaneous term labor. Two cohorts of women were recruited at 24 to 35 weeks' gestation (n = 65) and in late pregnancy (>36 weeks' gestation; n = 88). The CVF was serially collected either every 4 weeks between 24 and 35 weeks' gestation (n = 123 samples) or weekly during late pregnancy (n = 240 samples). The IL-1 and IL-1ra were quantitated by enzyme-linked immunosorbent assay, and the effect of vaginal microflora and unprotected sexual intercourse were also investigated. The IL-1β and IL-1ra remain unaltered between 24 and 35 weeks' gestation. At late pregnancy, IL-1α and β concentrations peak at 4 to 14 days prior to labor onset, while IL-1ra decreases with approaching spontaneous term labor (P < .05, 2-way analysis of variance). The IL-1 and IL-1ra were significantly correlated (P < .001, Pearson r). A combined biomarker model of IL-1α, IL-1β, and IL-1ra can predict term labor with 86% sensitivity and 92% specificity. This study indicates a shifting inflammatory balance in the gestational tissues prior to labor onset.
Heng YJ, Pennell CE, Chua HN, Perkins JE, Lye SJ. Whole blood gene expression profile associated with spontaneous preterm birth in women with threatened preterm labor. PLoS One. 2014;9 (5) :e96901.Abstract
Threatened preterm labor (TPTL) is defined as persistent premature uterine contractions between 20 and 37 weeks of gestation and is the most common condition that requires hospitalization during pregnancy. Most of these TPTL women continue their pregnancies to term while only an estimated 5% will deliver a premature baby within ten days. The aim of this work was to study differential whole blood gene expression associated with spontaneous preterm birth (sPTB) within 48 hours of hospital admission. Peripheral blood was collected at point of hospital admission from 154 women with TPTL before any medical treatment. Microarrays were utilized to investigate differential whole blood gene expression between TPTL women who did (n = 48) or did not have a sPTB (n = 106) within 48 hours of admission. Total leukocyte and neutrophil counts were significantly higher (35% and 41% respectively) in women who had sPTB than women who did not deliver within 48 hours (p<0.001). Fetal fibronectin (fFN) test was performed on 62 women. There was no difference in the urine, vaginal and placental microbiology and histopathology reports between the two groups of women. There were 469 significant differentially expressed genes (FDR<0.05); 28 differentially expressed genes were chosen for microarray validation using qRT-PCR and 20 out of 28 genes were successfully validated (p<0.05). An optimal random forest classifier model to predict sPTB was achieved using the top nine differentially expressed genes coupled with peripheral clinical blood data (sensitivity 70.8%, specificity 75.5%). These differentially expressed genes may further elucidate the underlying mechanisms of sPTB and pave the way for future systems biology studies to predict sPTB.
Liong S, Di Quinzio MKW, Heng YJ, Fleming G, Permezel M, Rice GE, Georgiou HM. Proteomic analysis of human cervicovaginal fluid collected before preterm premature rupture of the fetal membranes. Reproduction. 2013;145 (2) :137-47.Abstract
A significant obstetric complication facing contemporary materno-fetal medicine is preterm premature rupture of the fetal membranes (preterm PROM), which occurs in 30% of all preterm births. The objective of this study was to identify differentially expressed proteins in the cervicovaginal fluid of asymptomatic women before the clinical manifestation of preterm PROM. The preterm PROM group comprised of women with samples collected 6-23 days before PROM, who subsequently delivered preterm (n=5). Women who spontaneously delivered at term served as gestation-matched controls (n=10). Two-dimensional difference in-gel electrophoresis was used to distinguish differential expression between the pooled groups and fold changes were subsequently confirmed by two-dimensional PAGE of individual samples. Spots of interest were identified by mass spectrometry. Proteins that were significantly reduced with impending preterm PROM included the following: thioredoxin (2.7-fold), interleukin 1 receptor antagonist (1.7-fold), fatty acid-binding protein 5 (2.1-fold), cystatin A (dimer; 1.9-fold), monocyte/neutrophil elastase inhibitor (1.6-fold), squamous cell carcinoma antigen-1 (2.1-fold) and γ-glutamyl cyclotransferase (3.0-fold). By contrast, annexin A3 (3.7-fold) and vitamin D binding protein (3.9-fold) were significantly increased with impending preterm PROM. Western blot analysis was also performed on an independent cohort of preterm PROM and control samples to validate these candidate biomarkers. These proteins have known biological functions in oxidative balance, anti-inflammatory activity, metabolism or protease inhibition that may facilitate membrane rupture.
Heng YJ, Di Quinzio MKW, Liong S, Permezel M, Rice GE, Georgiou HM. Temporal investigation of matrix metalloproteinases and their inhibitors in human cervicovaginal fluid in late pregnancy and labor. Reprod Sci. 2012;19 (1) :55-63.Abstract
Temporal expression of matrix metalloproteinase (MMP)-1, -2, -3, -7, -8, -9, -12, and -13, and tissue inhibitors of metalloproteinases (TIMPs)-1 and -2 in human cervicovaginal fluid (CVF) in term pregnancy and labor was investigated. Term parous women provided CVF samples that were grouped into labor, 1 to 3, 6 to 8, and 12 to 16 days before labor onset. Both MMPs and TIMPs (n = 60) were quantified using multiplex solution array and enzyme-linked immunosorbent assays, respectively. Further analysis of TIMP-1 (n = 180) was undertaken. All MMPs and TIMPs except MMP-12 and -13 were detected in the CVF. Matrix metalloproteinase 7, TIMP-1, and TIMP-2 were significantly increased in labor. Tissue inhibitors of metalloproteinase 1 was significantly increased up to 7 days before spontaneous labor onset. The data suggest a role of MMP-7 in the remodeling and rupture of fetal membranes and may reflect the homeostatic regulation of extracellular matrix remodeling of MMP-7 by TIMP-1 and TIMP-2.
Georgiou HM, Thio YS, Russell C, Permezel M, Heng YJ, Lee S, Tong S. Association between maternal serum cytokine profiles at 7-10 weeks' gestation and birthweight in small for gestational age infants. Am J Obstet Gynecol. 2011;204 (5) :415.e1-415.e12.Abstract
OBJECTIVE: The purpose of this study was to investigate whether birth of a small-for-gestational-age (SGA) baby (birthweight, <10th percentile) is preceded by altered maternal serum cytokine profiles at early pregnancy, compared with control babies (birthweight, 30-80th percentile). STUDY DESIGN: A retrospective case-control study of maternal serum collected prospectively across 7-10 weeks of gestation from women attending their first prenatal visit (SGA, 57 cases; control subjects, 71 cases selected retrospectively). Serum concentrations of 27 cytokines were measured in each sample and analyzed by 2-way analysis of variance and nonparametric tests. Logistic regression was used for predictive modeling. RESULTS: Of 21 detectable cytokines/chemokines, 14 analytes varied significantly (P ≤ .030) among those women who were destined to deliver an SGA baby, when compared with control subjects. Of the cytokines that varied in association with SGA, interferon-γ concentrations increased, and major proinflammatory (interleukin [IL]-2, -7, -12) and antiinflammatory (IL-1 receptor antagonist, -4, -10, -13) cytokine concentrations decreased. Eotaxin and macrophage inflammatory protein-1α were higher; monocyte chemoattractant protein-1 and IL-8 were lower. CONCLUSION: SGA births may be preceded by altered immune cytokine profiles at 7-10 weeks of gestation.
Heng YJ, Di Quinzio MKW, Permezel M, Rice GE, Georgiou HM. Cystatin A protease inhibitor and cysteine proteases in human cervicovaginal fluid in term pregnancy and labor. Am J Obstet Gynecol. 2011;204 (3) :254.e1-7.Abstract
OBJECTIVE: The purpose of this study was to investigate the temporal changes in immunoreactive cystatin A and the enzymatic activity of cathepsins B, H, L, and S in human cervicovaginal fluid (CVF) in late pregnancy and spontaneous labor. STUDY DESIGN: CVF was collected weekly (n = 95 women) from 36 weeks gestation until spontaneous term labor. Cystatin A was quantified using enzyme-linked immunosorbent assay. The enzyme activity of cathepsins B, H, L, and S was measured with fluorometric enzyme assay kits. RESULTS: Cystatin A significantly decreased towards (P = .016, 2-way analysis of variance) and during labor (P < .001, 2-way analysis of variance). Enzymatic activity of cathepsins B, H, and S did not change with labor onset (P = .452, P = .703, P = .411, respectively, 2-way analysis of variance). CONCLUSION: In late gestation, CVF-decreased expression of the cysteine protease inhibitor, cystatin A, is associated with labor. Although the role and contribution of cystatin A to increased extracellular matrix remodeling has yet to be elucidated, the data that were obtained are consistent with this hypothesis.
Heng YJ, Saunders CIM, Kunde DA, Geraghty DP. TRPV1, NK1 receptor and substance P immunoreactivity and gene expression in the rat lumbosacral spinal cord and urinary bladder after systemic, low dose vanilloid administration. Regul Pept. 2011;167 (2-3) :250-8.Abstract
Transient receptor potential vanilloid 1 (TRPV1), neurokinin 1 (NK1) receptor and substance P (SP) immunoreactivity (-ir) and mRNA in the rat lumbosacral spinal cord and urinary bladder were measured 24h after s.c. injection of the vanilloids, capsaicin (50mg/kg) and resiniferatoxin (RTX, 100μg/kg), or vehicle (10% ethanol/10% Tween 80/saline). In the spinal cord, capsaicin significantly reduced TRPV1 and SP-ir (40-45%) in laminae I/II compared to controls, while RTX produced decreases of ~35%. NK1-ir in the spinal cord was unaffected by both vanilloid treatments. In the bladder, SP-ir was reduced in urothelial cells of some capsaicin- and RTX-treated rats, while SP-ir in the suburothelium and muscularis was significantly reduced by RTX. A significant increase in NK1-ir was observed in the urothelium and muscularis after capsaicin administration. Capsaicin significantly increased SP mRNA in the spinal cord, and TRPV1 and SP mRNA in the bladder, whereas RTX increased TRPV1, SP and NK1 mRNA in the spinal cord, and TRPV1 and SP mRNA in the bladder. These data suggest that stimulation of TRPV1 by low dose vanilloid administration can rapidly (within 24h) alter both transcription and translation of TRPV1 channels, SP and NK1 receptors in the rat urinary bladder and spinal cord.
Heng YJ, Di Quinzio MKW, Permezel M, Rice GE, Georgiou HM. Temporal expression of antioxidants in human cervicovaginal fluid associated with spontaneous labor. Antioxid Redox Signal. 2010;13 (7) :951-7.Abstract
Proteomic analysis of human cervicovaginal fluid (CVF) by 2D electrophoresis revealed significant differential expression of several major antioxidant enzymes during late pregnancy and term labor. Temporal quantitative changes of total antioxidant capacity (TAC), Cu,Zn superoxide dismutase (Cu,Zn SOD) and thioredoxin-1 (Trx-1) with impending term labor were investigated, and the potential of these biomarkers as individual and multiple predictors of labor was determined. The TAC of CVF (n = 193) was 8-fold significantly lower in labor, and approximately 2-fold significantly lower at 0-7, 8-14, 15-21, and 22-28 days, compared with >or=29 days prior to labor onset (p < 0.001). The expression of Cu,Zn SOD (n = 170) was 1.5- to 1.9-fold significantly decreased in labor (p < 0.001). Trx-1 (n = 163) was 2.8- to 5.1-fold significantly lower in labor (p = 0.002). The combination of TAC and Cu,Zn SOD produced the best predictive efficacy with 74% sensitivity and 95% specificity to predict term labor within 3 days of onset. These findings suggest that labor is associated with increased oxidative stress well before its onset and is reflected in the human CVF. The biomarkers identified in this study could serve as predictors of labor and offer potential strategies for novel therapeutics.
Heng YJ, Di Quinzio MKW, Permezel M, Ayhan M, Rice GE, Georgiou HM. Temporal proteomic analysis of human cervicovaginal fluid with impending term labor. J Proteome Res. 2010;9 (3) :1344-50.
Heng YJ, Di Quinzio MKW, Permezel M, Rice GE, Georgiou HM. Interleukin-1 receptor antagonist in human cervicovaginal fluid in term pregnancy and labor. Am J Obstet Gynecol. 2008;199 (6) :656.e1-7.Abstract
OBJECTIVE: The objective of the study was to investigate temporal changes in interleukin-1 receptor antagonist (IL-1ra) in human cervicovaginal fluid (CVF) in term pregnancy and labor. STUDY DESIGN: CVF was collected weekly from 155 multiparous women from 36 weeks' gestation until labor. High vaginal swabs were collected for microbiology assessment. RESULTS: IL-1ra was decreased in spontaneous term labor, compared with 15-21 and 22-28 days from labor, and was significantly lower at 0-7 days, compared with 15-21 days before labor (P < .05, 2-way ANOVA). After subdividing the women, IL-1ra concentrations were 6-fold lower in women who had prelabor rupture of membranes at term than women who had spontaneous labor with intact membranes at 8-14 and 15-21 days before labor (P < .05, Student t test). IL-1ra concentrations were not affected by the microbial status of the vagina. CONCLUSIONS: The changes in IL-1ra concentrations observed in the CVF may be linked to the remodeling of fetal membranes leading to rupture.
Di Quinzio MKW, Georgiou HM, Holdsworth-Carson SJ, Ayhan M, Heng YJ, Walker SP, Rice GE, Permezel M. Proteomic analysis of human cervico-vaginal fluid displays differential protein expression in association with labor onset at term. J Proteome Res. 2008;7 (5) :1916-21.Abstract
Human labor is characterized by dramatic physiological and structural alterations of the cervix and overlying fetal membranes, leading to myometrial activation and delivery. To investigate the potential mechanism of these changes, we performed 2D PAGE proteomic analysis on serial cervico-vaginal fluid samples obtained from women during late pregnancy and spontaneous labor. We identified 9 protein spots that were significantly altered ( p < 0.05) in association with spontaneous term labor. Eight protein spots were definitively characterized by electrospray ion-trap mass spectrometry yielding 7 different proteins: cystatin-A, interleukin-1 receptor antagonist, glutathione S-transferase P, peroxiredoxin-2, thioredoxin, copper-zinc superoxide dismutase, and epidermal fatty-acid binding protein. These proteins are involved in protease inhibition, anti-inflammatory cytokine activity, and oxidative stress defense. These findings may provide an insight into the biochemical processes and timing associated with extracellular matrix remodelling of the cervix, supracervical fetal membranes, and myometrial activation in association with spontaneous term labor. Application of these findings may lead to development of predictive biomarkers of labor onset.