Microarray technology in obstetrics and gynecology: a guide for clinicians

Enhancing Transcriptomic Insights into Neurological Disorders Through the Comparative Analysis of Shapley Values

Neurological disorders such as Autism Spectrum Disorder (ASD), Schizophrenia (SCH), Bipolar Disorder (BD), and Major Depressive Disorder (MDD) affect millions of people worldwide, yet their molecular mechanisms remain poorly understood. This study describes the application of the Comparative Analysis of Shapley values (CASh) to transcriptomic data from nine datasets associated with these complex disorders, demonstrating its effectiveness in identifying differentially expressed genes (DEGs). CASh, which combines Game Theory with Bootstrap resampling, offers a robust alternative to traditional statistical methods by assessing the contribution of each gene in the broader context of the complete dataset. Unlike conventional approaches, CASh is highly effective at detecting subtle but meaningful molecular patterns that are often missed. These findings highlight the potential of CASh to enhance the precision of transcriptomic analysis, providing a deeper understanding of the molecular mechanisms underlying these disorders and establishing a solid basis to improve diagnostic techniques and developing more targeted therapeutic interventions.

Comparative Analysis of Shapley Values Enhances Transcriptomics Insights across Some Common Uterine Pathologies

Uterine pathologies pose a challenge to women's health on a global scale. Despite extensive research, the causes and origin of some of these common disorders are not well defined yet. This study presents a comprehensive analysis of transcriptome data from diverse datasets encompassing relevant uterine pathologies such as endometriosis, endometrial cancer and uterine leiomyomas. Leveraging the Comparative Analysis of Shapley values (CASh) technique, we demonstrate its efficacy in improving the outcomes of the classical differential expression analysis on transcriptomic data derived from microarray experiments. CASh integrates the microarray game algorithm with Bootstrap resampling, offering a robust statistical framework to mitigate the impact of potential outliers in the expression data. Our findings unveil novel insights into the molecular signatures underlying these gynecological disorders, highlighting CASh as a valuable tool for enhancing the precision of transcriptomics analyses in complex biological contexts. This research contributes to a deeper understanding of gene expression patterns and potential biomarkers associated with these pathologies, offering implications for future diagnostic and therapeutic strategies.

Novel ploidy analysis in ectopic pregnancy

Objective

To study whether a single-nucleotide polymorphism (SNP) array could be used to test tissue from ectopic pregnancy to distinguish whether ectopic pregnancies were aneuploid.

Design

Case series report.

Setting

Academic medical center.

Patients

One hundred seventy-eight women who underwent surgery for ectopic pregnancy at Northwestern Memorial Hospital between 2015 and 2018 were eligible for participation; written consent was obtained from 33 patients. Eight subjects had sufficient DNA samples and were included in the analysis. Maternal and paternal DNA samples were self-collected by buccal swab. Archived paraffin tissue containing chorionic villi from each surgically removed ectopic specimen was analyzed using SNP microarray technology to determine chromosome number and evaluate for maternal cell contamination.

Interventions

None.

Main Outcome Measures

Prevalence of aneuploidy in ectopic pregnancy specimens as well as success of SNP array technology in formalin-fixed and paraffin-embedded specimens.

Results

Subjects had a mean (±SD) age of 33.4 ± 5.4 years, body mass index of 23.4 ± 5.7 kg/m², 3.3 ± 1.8 prior pregnancies, and 1.5 ± 1.4 live births. Genetic testing revealed that all eight tested samples were euploid, 6 female and 2 male (two arr(1-22)x2, (X,Y)x1 and 6 arr(1-22, X)x2); maternal cell contamination was ruled out in all cases.

Conclusions

This study showed proof of concept for the use of routinely stored formalin-fixed, paraffin-embedded tissue blocks with DNA extraction for SNP array to detect ploidy status of ectopic pregnancy. Although all tested samples were euploid, further research is needed to gain a definitive answer to this question and better understand the mechanism that leads to ectopic implantation.

Fetal postmortem imaging: an overview of current techniques and future perspectives

Fetal death because of miscarriage, unexpected intrauterine fetal demise, or termination of pregnancy is a traumatic event for any family. Despite advances in prenatal imaging and genetic diagnosis, conventional autopsy remains the gold standard because it can provide additional information not available during fetal life in up to 40% of cases and this by itself may change the recurrence risk and hence future counseling for parents. However, conventional autopsy is negatively affected by procedures involving long reporting times because the fetal brain is prone to the effect of autolysis, which may result in suboptimal examinations, particularly of the central nervous system. More importantly, fewer than 50%-60% of parents consent to invasive autopsy, mainly owing to the concerns about body disfigurement. Consequently, this has led to the development of noninvasive perinatal virtual autopsy using imaging techniques. Because a significant component of conventional autopsy involves the anatomic examination of organs, imaging techniques such as magnetic resonance imaging, ultrasound, and computed tomography are possible alternatives. With a parental acceptance rate of nearly 100%, imaging techniques as part of postmortem examination have become widely used in recent years in some countries. Postmortem magnetic resonance imaging using 1.5-Tesla magnets is the most studied technique and offers an overall diagnostic accuracy of 77%-94%. It is probably the best choice as a virtual autopsy technique for fetuses >20 weeks' gestation. However, for fetuses <20 weeks' gestation, its performance is poor. The use of higher magnetic resonance imaging magnetic fields such as 3-Tesla may slightly improve performance. Of note, in cases of fetal maceration, magnetic resonance imaging may offer diagnoses in a proportion of brain lesions wherein conventional autopsy fails. Postmortem ultrasound examination using a high-frequency probe offers overall sensitivity and specificity of 67%-77% and 74%-90%, respectively, with the advantage of easy access and affordability. The main difference between postmortem ultrasound and magnetic resonance imaging relates to their respective abilities to obtain images of sufficient quality for a confident diagnosis. The nondiagnostic rate using postmortem ultrasound ranges from 17% to 30%, depending on the organ examined, whereas the nondiagnostic rate using postmortem magnetic resonance imaging in most situations is far less than 10%. For fetuses ≤20 weeks' gestation, microfocus computed tomography achieves close to 100% agreement with autopsy and is likely to be the technique of the future in this subgroup. The lack of histology has always been listed as 1 limitation of all postmortem imaging techniques. Image-guided needle tissue biopsy coupled with any postmortem imaging can overcome this limitation. In addition to describing the diagnostic accuracy and limitations of each imaging technology, we propose a novel, stepwise diagnostic approach and describe the possible application of these techniques in clinical practice as an alternative or an adjunct or for triage to select cases that would specifically benefit from invasive examination, with the aim of reducing parental distress and pathologist workload. The widespread use of postmortem fetal imaging is inevitable, meaning that hurdles such as specialized training and dedicated financing must be overcome to improve access to these newer, well-validated techniques.

The molecular basis for sonographic cervical shortening at term: identification of differentially expressed genes and the epithelial-mesenchymal transition as a function of cervical length

OBJECTIVE

The purpose of this study was to determine whether cervical shortening of a ripe cervix at term is associated with changes in the cervical transcriptome.

STUDY DESIGN

Sonographically measured cervical lengths and biopsy specimens were obtained from 19 women at term who were not in labor with a ripe cervix. Affymetrix HG-U133 Plus 2.0 arrays (Affymetrix Inc, Santa Clara, CA) were used. Gene expression was analyzed as a function of cervical length. Gene Ontology, pathway analyses, quantitative real-time reverse transcription-polymerase chain reaction, and immunohistochemistry were performed.

RESULTS

Cervical length shortening was associated with differential expression of 687 genes. Fifty-four biologic processes, 22 molecular functions, and 9 pathways were enriched. Quantitative real-time reverse transcription-polymerase chain reaction analysis confirmed differential expression of 13 genes. Bone morphogenetic protein-7, claudin-1, integrin beta-6, and endometrial progesterone-induced protein messenger RNA, and protein expressions were down-regulated with cervical shortening.

CONCLUSION

Sonographic cervical shortening in patients at term who are not in labor with a ripe cervix is associated with changes in the uterine cervix transcriptome. The epithelial-mesenchymal transition may participate in the mechanism of cervical shortening at term.

Isobaric labeling and tandem mass spectrometry: a novel approach for profiling and quantifying proteins differentially expressed in amniotic fluid in preterm labor with and without intra-amniotic infection/inflammation

OBJECTIVE

Examination of the amniotic fluid (AF) proteome has been previously attempted to identify useful biomarkers in predicting the outcome of preterm labor (PTL). Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) labeling allows direct ratiometric comparison of relative abundance of identified protein species among multiplexed samples. The purpose of this study was to apply, for the first time, the combination of iTRAQ and tandem mass spectrometry to identify proteins differentially regulated in AF samples of women with spontaneous PTL and intact membranes with and without intra-amniotic infection/inflammation (IAI).

METHODS

A cross-sectional study was designed and included AF samples from patients with spontaneous PTL and intact membranes in the following groups: (1) patients without IAI who delivered at term (n = 26); (2) patients who delivered preterm without IAI (n = 25); and (3) patients with IAI (n = 24). Proteomic profiling of AF samples was performed using a workflow involving tryptic digestion, iTRAQ labeling and multiplexing, strong cation exchange fractionation, and liquid chromatography tandem mass spectrometry. Twenty-five separate 4-plex samples were prepared and analyzed.

RESULTS

Collectively, 123,011 MS(2) spectra were analyzed, and over 25,000 peptides were analyzed by database search (X!Tandem and Mascot), resulting in the identification of 309 unique high-confidence proteins. Analysis of differentially present iTRAQ reporter peaks revealed many proteins that have been previously reported to be associated with preterm delivery with IAI. Importantly, many novel proteins were found to be up-regulated in the AF of patients with PTL and IAI including leukocyte elastase precursor, Thymosin-like 3, and 14-3-3 protein isoforms. Moreover, we observed differential expression of proteins in AF of patients who delivered preterm in the absence of IAI in comparison with those with PTL who delivered at term including Mimecan precursor, latent-transforming growth factor beta-binding protein isoform 1L precursor, and Resistin. These findings have been confirmed for Resistin in an independent cohort of samples using ELISA. Gene ontology enrichment analysis was employed to reveal families of proteins participating in distinct biological processes. We identified enrichment for host defense, anti-apoptosis, metabolism/catabolism and cell and protein mobility, localization and targeting.

CONCLUSIONS

(1) Proteomics with iTRAQ labeling is a profiling tool capable of revealing differential expression of proteins in AF; (2) We discovered 82 proteins differentially expressed in three clinical subgroups of premature labor, 67 which were heretofore unknown. Of particular importance is the identification of proteins differentially expressed in AF from women who delivered preterm in the absence of IAI. This is the first report of the positive identification of biomarkers in this subgroup of patients.

Use of array comparative genomic hybridization for prenatal diagnosis of fetuses with sonographic anomalies and normal metaphase karyotype

OBJECTIVE

To prospectively study the addition of array comparative genomic hybridization (CGH) to the prenatal evaluation of fetal structural anomalies.

METHODS

Pregnant women carrying fetuses with a major structural abnormality were recruited at the time of invasive procedure for chromosome analysis. Only women whose fetuses had a normal karyotype (n = 50) were subsequently evaluated by array CGH using one of two arrays (1887 clones covering 622 loci or subsequently 4685 clones covering 1500 loci).

RESULTS

The mean gestational age of the fetuses was 24.5 weeks (range 11-38 weeks). The most prevalent anomalies were cardiac, central nervous system, skeletal, and urogenital. The median turnaround time for culturing and array CGH diagnosis was 18 days (range 2-72). Four of 50 fetuses had abnormal array results. One (2%) was clinically significant and three (6%) were inherited or benign variants.

CONCLUSIONS

Array CGH studies in fetuses with sonographic anomalies and normal metaphase karyotype detected clinically significant copy number alterations in 1 of 50 cases. This percentage (2%) is consistent with prior prenatal reports. Further studies are warranted to more precisely identify which fetal anomalies are associated with copy number alterations of clinical significance.

Proteomic analysis of amniotic fluid to identify women with preterm labor and intra-amniotic inflammation/infection: the use of a novel computational method to analyze mass spectrometric profiling

OBJECTIVE

Examination of the amniotic fluid proteome has been used to identify biomarkers for intra-amniotic inflammation as well as those that may be useful in predicting the outcome of preterm labor. The purpose of this study was to combine a novel computational method of pattern discovery with mass spectrometric proteomic profiling of amniotic fluid to discover biomarkers of intra-amniotic infection/inflammation (IAI).

METHODS

This cross-sectional study included patients with spontaneous preterm labor and intact membranes who delivered at term (n = 59) and those who delivered preterm with IAI (n = 60). Proteomic profiling was performed using surface-enhanced laser desorption/ionization (SELDI) mass spectrometry. A proteomic profile was acquired through multiple simultaneous SELDI conditions, which were combined in a single proteomic 'fingerprint' using a novel computational approach. Classification of patients based on their associated surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectra as belonging to either the class of individuals with preterm delivery with IAI or term delivery was accomplished by constructing an empirical model. The first phase in the construction of this empirical model involved the selection of adjustable parameters utilizing a training/testing subset of data. The second phase tested the generalization of the model by utilizing a blinded validation set of patients who were not employed in parameter selection.

RESULTS

Gestational age at amniocentesis was not significantly different between the groups. Thirty-nine unique mass spectrometric peaks discriminated patients with preterm labor/delivery with IAI from those with preterm labor and term delivery. In the testing/training dataset, the classification accuracies (averaged over 100 random draws) were: 91.4% (40.2/44) for patients with preterm delivery with IAI, and 91.2% (40.1/44) for term delivery. The overall accuracy of the classification of patients in the validation dataset was 90.3% (28/31).

CONCLUSIONS

Proteomic analysis of amniotic fluid allowed the identification of mass spectrometry features, which can distinguish patients with preterm labor with IAI from those with preterm labor without inflammation or infection who subsequently delivered at term.

Microarray technology applied to the complex disorder of preeclampsia

Preeclampsia is a life-threatening perinatal complication with unknown etiology. Microarray technology has characterized global gene expression in complex disorders such as preeclampsia. Nursing research and future practice may incorporate findings from microarray analyses to identify susceptibility to and prevent disease, to diagnose early, and to design and monitor personalized therapies. This overview of microarray technology, with emphasis on how it can inform genomics of preeclampsia, may provide concepts to improve future maternal-neonatal nursing care.

The use of high-dimensional biology (genomics, transcriptomics, proteomics, and metabolomics) to understand the preterm parturition syndrome

High-dimensional biology (HDB) refers to the simultaneous study of the genetic variants (DNA variation), transcription (messenger RNA [mRNA]), peptides and proteins, and metabolites of an organ, tissue, or an organism in health and disease. The fundamental premise is that the evolutionary complexity of biological systems renders them difficult to comprehensively understand using only a reductionist approach. Such complexity can become tractable with the use of "omics" research. This term refers to the study of entities in aggregate. The current nomenclature of "omics" sciences includes genomics for DNA variants, transcriptomics for mRNA, proteomics for proteins, and metabolomics for intermediate products of metabolism. Another discipline relevant to medicine is pharmacogenomics. The two major advances that have made HDB possible are technological breakthroughs that allow simultaneous examination of thousands of genes, transcripts, and proteins, etc., with high-throughput techniques and analytical tools to extract information. What is conventionally considered hypothesis-driven research and discovery-driven research (through "omic" methodologies) are complementary and synergistic. Here we review data which have been derived from: 1) genomics to examine predisposing factors for preterm birth; 2) transcriptomics to determine changes in mRNA in reproductive tissues associated with preterm labour and preterm prelabour rupture of membranes; 3) proteomics to identify differentially expressed proteins in amniotic fluid of women with preterm labour; and 4) metabolomics to identify the metabolic footprints of women with preterm labour likely to deliver preterm and those who will deliver at term. The complementary nature of discovery science and HDB is emphasised.

Analysis of microarray experiments of gene expression profiling

The study of gene expression profiling of cells and tissue has become a major tool for discovery in medicine. Microarray experiments allow description of genome-wide expression changes in health and disease. The results of such experiments are expected to change the methods employed in the diagnosis and prognosis of disease in obstetrics and gynecology. Moreover, an unbiased and systematic study of gene expression profiling should allow the establishment of a new taxonomy of disease for obstetric and gynecologic syndromes. Thus, a new era is emerging in which reproductive processes and disorders could be characterized using molecular tools and fingerprinting. The design, analysis, and interpretation of microarray experiments require specialized knowledge that is not part of the standard curriculum of our discipline. This article describes the types of studies that can be conducted with microarray experiments (class comparison, class prediction, class discovery). We discuss key issues pertaining to experimental design, data preprocessing, and gene selection methods. Common types of data representation are illustrated. Potential pitfalls in the interpretation of microarray experiments, as well as the strengths and limitations of this technology, are highlighted. This article is intended to assist clinicians in appraising the quality of the scientific evidence now reported in the obstetric and gynecologic literature.