Proteomics and irritable bowel syndrome.

INTRODUCTION: Irritable bowel syndrome (IBS) is a gastrointestinal disease that according to Rome IV criteria is subdivided into four subtypes. The pathophysiology of this disease is not well understood due to numerous factors playing multiple roles in disease development, such as diet, stress and hormones. IBS has a variety of symptoms and overlaps with many other gastrointestinal and non-gastrointestinal diseases. Area covered: This review aims to present an overview of implementation of proteomics in experimental studies in the field of IBS. Expert commentary: Proteomics is commonly used for biomarker discovery in and has also been extensively used in IBS research. The necessity of a sensitive and specific biomarker for IBS is apparent, but despite the intensive research performed in this field, an appropriate biomarker is not yet available.

Serum protein profiling of adults and children with Crohn disease.

OBJECTIVES: Crohn disease (CD) and ulcerative colitis (UC), known collectively as inflammatory bowel diseases (IBDs), are chronic immunoinflammatory pathologies of unknown aetiology. Despite the frequent use of biomarkers in medical practice, there is a relative lack of information regarding validated paediatric biomarkers for IBD. Furthermore, biomarkers proved to be efficacious in adults are frequently extrapolated to the paediatric clinical setting without considering that the pathogenesis of many diseases is distinctly different in children. In the present study, proteomics technology was used to monitor differences in protein expression among adult and young patients with CD, identify a panel of candidate protein biomarkers that may be used to improve prognostic-diagnostic accuracy, and advance paediatric medical care. METHODS: Male and female serum samples from 12 adults and 12 children with active CD were subjected to 2-dimensional gel electrophoresis. Following the relative quantitation of protein spots exhibiting a differential expression between the 2 groups by densitometry, the spots were further characterized by matrix-assisted laser desorption tandem time-of-flight mass spectrometer. The results were confirmed by Western blot analysis. RESULTS: Clusterin was found to be significantly overexpressed in adults with CD, whereas ceruloplasmin and apolipoprotein B-100 were found to be significantly overexpressed in children, indicating that the expression of these proteins may be implicated in the onset or progression of CD in these 2 subgroups of patients. CONCLUSIONS: Interestingly, we found a differential expression of several proteins in adults versus paediatric patients with CD. Undoubtedly, future experiments using a larger cohort of patients with CD are needed to evaluate the relevance of our preliminary findings.

The proteomics of pediatric brain tumors.

Pediatric tumors of the CNS are the leading cause of cancer-related mortality in children. In pediatric pathology, brain tumors constitute the most frequent solid malignancy. An unparalleled outburst of information in pediatric neuro-oncology research has been witnessed over the last few years, largely due to increased use of high-throughput technologies such as genomics, proteomics and meta-analysis tools. Input from these technologies gives scientists the advantage of early prognosis assessment, more accurate diagnosis and prospective curative intent in the pediatric brain tumor clinical setting. The present review aims to summarize current knowledge on research applying proteomics techniques or proteomics-based approaches performed on pediatric brain tumors. Proteins that can be used as potential disease markers or molecular targets, and their biological significance, are herein listed and discussed. Furthermore, future perspectives that proteomics technologies may offer regarding this devastating disorder are presented.

Proteomics Analysis of Pregnancy in Ewes under Heat Stress Conditions and Melatonin Administration.

Melatonin is an indoleamine with broad spectrum properties that acts as a regulator of antioxidant and immune response in organisms. In our previous studies, melatonin improved redox status and inflammatory response in pregnant ewes under heat stress conditions. In the present study, using proteomics, the proteins regulated by melatonin during different stages of pregnancy and lambing were assessed. Twenty-two ewes equally divided into two groups, the melatonin (M) (n = 11) and control (C) group (n = 11), participated in the study and were exposed to heat stress during the first months of pregnancy. In the M group, melatonin implants were administered throughout pregnancy, every 40 days, until parturition (a total of four implants per ewe). Blood samples were collected at the beginning of the study simultaneously with the administration of the first melatonin implant (blood samples M1, C1), mating (M2, C2), second implant (M3, C3), fourth implant (M4, C4) and parturition (M5, C5), and MALDI-TOF analysis was performed. The results revealed the existence of 42 extra proteins in samples M2, M3 and M4 and 53 in M5 (sample at parturition) that are linked to melatonin. The biological processes of these proteins refer to boosted immune response, the alleviation of oxidative and endoplasmic reticulum stress, energy metabolism, the protection of the maternal organism and embryo development. This proteomics analysis indicates that melatonin regulates protective mechanisms and controls cell proliferation under exogenous or endogenous stressful stimuli during pregnancy and parturition.

RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of SNCA transcripts.

Alpha-synuclein (SNCA) accumulation plays a central role in the pathogenesis of Parkinson's disease. Determining and interfering with the mechanisms that control SNCA expression is one approach to limiting disease progression. Currently, most of our understanding of SNCA regulation is protein-based. Post-transcriptional mechanisms directly regulating SNCA mRNA expression via its 3' untranslated region (3'UTR) were investigated here. Mass spectrometry of proteins pulled down from murine brain lysates using a biotinylated SNCA 3'UTR revealed multiple RNA-binding proteins, of which HNRNPD/AUF1 was chosen for further analysis. AUF1 bound both proximal and distal regions of the SNCA 3'UTR, but not the 5'UTR or CDS. In the nucleus, AUF1 attenuated SNCA pre-mRNA maturation and was indispensable for the export of SNCA transcripts. AUF1 destabilized SNCA transcripts in the cytosol, primarily those with shorter 3'UTRs, independently of microRNAs by recruiting the CNOT1-CNOT7 deadenylase complex to trim the polyA tail. Furthermore, AUF1 inhibited SNCA mRNA binding to ribosomes. These data identify AUF1 as a multi-tasking protein regulating maturation, nucleocytoplasmic shuttling, stability and translation of SNCA transcripts.

Prediction of SARS-CoV-2 Omicron Variant Immunogenicity, Immune Escape and Pathogenicity, through the Analysis of Spike Protein-Specific Core Unique Peptides.

The recently discovered Omicron variant of the SARS-CoV-2 coronavirus has raised a new, global, awareness. In this study, we identified the Core Unique Peptides (CrUPs) that reside exclusively in the Omicron variant of Spike protein and are absent from the human proteome, creating a new dataset of peptides named as SARS-CoV-2 CrUPs against the human proteome (C/H-CrUPs), and we analyzed their locations in comparison to the Alpha and Delta variants. In Omicron, 115 C/H-CrUPs were generated and 119 C/H-CrUPs were lost, almost four times as many compared to the other two variants. At the Receptor Binding Motif (RBM), 8 mutations were detected, resulting in the construction of 28 novel C/H-CrUPs. Most importantly, in the Omicron variant, new C/H-CrUPs carrying two or three mutant amino acids were produced, as a consequence of the accumulation of multiple mutations in the RBM. These C/H-CrUPs could not be recognized in any other viral Spike variant. Our findings indicated that the virus binding to the ACE2 receptor is facilitated by the herein identified C/H-CrUPs in contact point mutations and Spike cleavage sites, while the immunoregulatory NF9 peptide is not detectably affected. Thus, the Omicron variant could escape immune-system attack, while the strong viral binding to the ACE2 receptor leads to the highly efficient fusion of the virus to the target cell. However, the intact NF9 peptide suggests that Omicron exhibits reduced pathogenicity compared to the Delta variant.

Lipid rafts integrity is essential for prolactin-induced mitogenesis in mouse embryonic stem cells.

Embryonic stem cells, ESCs, retain the capacity to self-renew, yet, the protein machinery essential in maintaining this undifferentiated status remains largely undefined. Signalling interactions are initiated and enhanced at the plasma membrane lipid rafts, within constraints and regulations applied by the actin and tubulin cytoskeleton systems. First, we undertook a comprehensive approach using two-dimensional gel electrophoresis and mass spectrometry analysis combined with Western blotting and immunofluorescence analyses at the single cell level to compile the proteome profile of detergent-free preparations of lipid rafts of E14 mouse embryonic stem cells. In comparison with the proteomic profiles of other membrane fractions, recovery of actin and tubulin network proteins, including folding chaperones, was impressively high. At equally high frequency, we detected annexins, pleiotropic proteins that may bind membrane lipids and actin filaments to regulate important membrane processes, and we validated their expression in lipid rafts. Next, we tested whether lipid raft integrity is required for completion of mitogenic signalling pathways. Disruption of the rafts with the cholesterol sequestering methyl-ß-cyclodextrin (MCD) greatly downregulated the mitotic index of ESCs, in a dose- and time of exposure-dependent manner. Moreover, MCD greatly reduced the mitogenic actions of prolactin, a hormone known to stimulate proliferation in a great variety of stem and progenitor cells. Taken together, our data postulate that lipid rafts in ESCs act in close association with the actin and tubulin cytoskeletons to support signal compartmentalization, especially for signalling pathways pertinent to symmetric divisions for self-renewal.

High-throughput Proteomic Profiling of Male Breast Cancer Tissue.

BACKGROUND/AIM: Until now, little emphasis has been placed on the protein expression profile of male breast cancer (MBC) tumors, due to the rarity of the disease. The present study aimed to identify a proteomic pattern that is characteristic for malignant male breast tissue epithelium. MATERIALS AND METHODS: The protein content of four male breast tumors and corresponding adjacent healthy (control) tissues was analyzed by high-throughput nano-liquid chromatography-MS/MS technology. RESULTS: A total of 2,352 proteins were identified, that correspond to 1,249 single gene products, with diverse biological roles. Of those, a panel of 119 differentially expressed tissue proteins was identified in MBC samples compared to controls; 90 were found to be over-expressed in MBC tissues, while 29 were down-regulated. Concurrently, 844 proteins were detected only in MBC tumors and 197 were expressed exclusively in control mammary samples. CONCLUSION: Differential proteomic expression was found in MBC tissue, leading to improved understanding of MBC pathology and highlighting the need for personalized management of male patients.

Brain asymmetry: both sides of the story.

Biological systems demonstrate asymmetry, while lateralization has been observed from humans to lower animals structurally, functionally and behaviorally. This may be derived from evolutionary, genetic, developmental, epigenetic and pathologic factors. However, brain structure and function is complex, and macroscopic or microscopic asymmetries are hard to discern from random fluctuations. In this article, we discuss brain laterality and lateralization, beginning with a brief review of the literature on brain structural and functional asymmetries. We conclude with methods to detect and quantify asymmetry, focusing on neuroproteomics, for retrieval of protein-expression patterns, as a method of diagnosis and treatment monitoring. We suggest inter-hemispheric differential proteomics as a valid method to assess the experimental and biological variations in the healthy brain, and neurologic and neuropsychiatric disorders.

Serum Proteomic Signatures of Male Breast Cancer.

BACKGROUND: To date, the elucidation of serum protein alterations in male breast cancer (MBC) has not been extensively studied, due to the rarity of the disease. MATERIALS AND METHODS: In the present work, two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) were employed to detect differences in serum protein expression between patients with MBC and healthy controls. RESULTS: A panel of differentially expressed serum proteins was identified, including proteins involved in the regulation of the cell cycle [e.g. cell division cycle 7-related protein kinase (CDC7)], in mitochondrial function [e.g. mitochondrial aldehyde dehydrogenase (ALDH2) and dimethyladenosine transferase 1 (TFB1M)], in lipid metabolism and transport [e.g. apolipoprotein A-I (APOA1) and E (APOE)], in apoptosis and immune response [e.g. CD5 antigen-like (CD5L), clusterin (CLUS) and C-C motif chemokine 14 (CCL14)], in transcription (e.g. protein SSX3 and signal transducer and activator of transcription 3 (STAT3)], in invasion and metastasis (e.g. alpha-2-HS-glycoprotein (FETUA)], in estrogen synthesis [aromatase (CYP19A1)] and other diverse biological roles [e.g. actin-related protein 2/3 complex subunit 4 (ARPC4), dual specificity mitogen-activated protein kinase kinase 4 (MP2K4), ectoderm-neural cortex protein 1 (ENC1), and matrix metalloproteinase-27 (MMP27)]. CONCLUSION: These findings provide valuable insight into the distinct clinicopathological features of MBC and indicate that select serum proteomic markers may help improve MBC management.

The proteome profile of two cell lines and their xenografts isolated from a patient with clear cell sarcoma (soft tissue melanoma).

We report the establishment of two novel clear cell sarcoma (CCS) cell lines (soft tissue melanoma) from a patient and the production of the corresponding xenografts after xenotransplantation of those cells to NOD/SCID mice. As no comprehensive study on the relevant proteomes of this type of cancer has been reported to date, proteomics technologies were applied in a first attempt to analyze the proteins of the two cell lines and their corresponding primary xenografts. Total protein extracts were separated by two dimensional gel electrophoresis (2-DE) and analysed by MALDI-MS and MALDI-MS-MS following in-gel digestion with trypsin. Protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Comparative analysis revealed that 124 proteins were common between the cell lines and the xenografts; 249 proteins were found to be expressed only in the proteome of the cell lines, while 178 proteins were expressed only in the proteome of xenografts. Our results demonstrated that both cell lines and xenografts were positive for vimentin and S100 reported as markers for CCS. After functional analysis, 27 different protein groups were identified in the analysed proteomes, including apoptosis-related proteins, oncogenes and several proteins closely related to TP-53 and NF-kappa B pathways. Furthermore, the proteins nestin, stem cell growth factor CLC11 and mdr-1, closely related to malignant-melanoma-initiating cells, were found to be expressed in both the cell lines and their corresponding xenografts. Since there are no data concerning protein expression in CCS, this study may contribute to the understanding of the molecular basis of the disease, while the cell lines as well as the developed xenografts may be used as tools for the development of new therapeutic strategies to tackle this rare but fatal malignancy.

The proteome profile of the human osteosarcoma U2OS cell line.

The human osteosarcoma U2OS cell line is one of the first generated cell lines and is used in various areas of biomedical research. Knowledge of its protein expression is limited and no comprehensive study on the proteome of this cell line has been reported to date. Proteomics technology was used in order to analyse the proteins of the U2OS cell line. Total protein extracts were separated by two-dimensional gel electrophoresis (2-DE) and analysed by matrix-assisted laser desorption ionisation-mass spectrometry (MALDI-MS) and MALDI--MS-MS following in-gel digestion with trypsin and, finally, protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Approximately 3,000 spots were excised from two 2-DE gels and were analysed, resulting in the identification of 237 different gene products. The majority of the identified proteins were enzymes, regulatory proteins and RNA-associated proteins, while leukocyte markers and oncogenes were also present. Our findings include 11 protooncogenes (FKBP4, SRC8, PSD10, FUBP1, PARK7, NPM, PDIA1, OXRP, SET, TCTP and GRP75) related to the cancerous state of the U2OS cell line. The U2OS 2-DE database provides the basis for future protein studies.

Identification of serum proteome signature of irritable bowel syndrome: Potential utility of the tool for early diagnosis and patient's stratification.

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder with high incidence, and great heterogeneity of symptoms. Numerous factors are correlated with IBS development; however, the pathophysiology is not yet clear. In addition, there is no appropriate diagnostic tool available. The aim of this study was the identification of protein expression alterations in IBS patients compared to healthy individuals. Serum samples from 30 IBS patients (10 with IBS-Diarrhea, 10 IBS-Constipation and 10 IBS-Mixed) and 10 healthy individuals were subjected to proteomic analysis by 2-dimensional gel electrophoresis. Following evaluation of densitometrical data, protein spots exhibiting differential expression among the groups, were further characterized by matrix-assisted laser desorption tandem time-of-flight mass spectrometer and the results were confirmed by Western blot analysis. Eight significantly different expressed proteins were identified. Seven of them were overexpressed in IBS cases and only one was overexpressed in healthy individuals. These proteins were also differently expressed between the three IBS subgroups. IBS-D group overexpressed immunoglobulin light chain Lambda (LAC3) and apolipoprotein E (APOE), IBS-C group overexpressed apolipoprotein H (APOH) and collagen alpha-1 (XIV) chain (COEA1), and IBS-M group and healthy individuals overexpressed retinol-binding protein 4 (RET4). Our results show a different serum protein profile of IBS patients compared to healthy controls. Understanding the role of these eight proteins which are differently expressed in IBS patients, may contribute to a better clarification of IBS pathogenesis and to patient's stratification. SIGNIFICANCE: Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder with high incidence and great heterogeneity of symptoms without any appropriate diagnostic tool available. Eight significantly different expressed proteins were identified. Seven of them were overexpressed in IBS cases and only one was expressed in healthy individuals. These proteins were also differently expressed between the three IBS subgroups. Our results show that there is a different serum proteome signature in IBS compared to healthy individuals, as well as in IBS subgroups that could be used in the future for patient's stratification and as a diagnostic tool.

The Use of Proteomics in Assisted Reproduction.

Despite the explosive increase in the use of Assisted Reproductive Technologies (ART) over the last 30 years, their success rates remain suboptimal. Proteomics is a rapidly-evolving technology-driven science that has already been widely applied in the exploration of human reproduction and fertility, providing useful insights into its physiology and leading to the identification of numerous proteins that may be potential biomarkers and/or treatment targets of a successful ART pregnancy. Here we present a brief overview of the techniques used in proteomic analyses and attempt a comprehensive presentation of recent data from mass spectrometry-based proteomic studies in humans, regarding all components of ARTs, including the male and female gamete, the derived zygote and embryo, the endometrium and, finally, the ART offspring both pre- and postnatally.

Molecular Proteomic Characterization of a Pediatric Medulloblastoma Xenograft.

BACKGROUND/AIM: Medulloblastoma (MBL), an archetypal primitive neuroectodermal tumor of the cerebellum, is the most common pediatric central nervous system malignancy representing approximately 20% of all childhood brain tumors. Herein, we report on a new xenotransplantable tumor cell line, derived from a 6-year-old female patient with cerebellar medulloblastoma, and the completele proteome molecular characterization of subsequent tumors from MBL xenotrasplanted mice. MATERIALS AND METHODS: Tumors were grown in nude mice as subcutaneous xenografts (MBLX) composed of small round cells with hyperchromatic nuclei and scant cytoplasm. Tumor specimen were extracted from animals upon their sacrifice and their molecular proteomic content was analyzed by 2-DE coupled to MALDI-TOF MS analysis. RESULTS: Altogether 350 single-gene products were identified through the current approach, reported as the MBLX database. CONCLUSION: This new xenotransplantable tumor model, offers the scientific community valuable insight on the validity of xenografts altogether, while providing the means for a novel experimental model towards the study of human MBL.

The normal human amniotic fluid supernatant proteome.

Proteomic analysis combining two-dimentional electrophoresis (2DE) and mass spectrometry (MS) has the potential for a wide range of applications in biological and medical sciences, as protein screening in tissues obtained from healthy and diseased conditions can determine drug targets and diagnostic markers. Conventionally, amniotic fluid (AF) samples are routinely used for prenatal diagnosis of a wide range of fetal abnormalities. Proteomics have already been applied in the analysis of tissues from fetuses with Down's syndrome, in order to detect differences in their protein profile as compared to the normal profiles and to determine possible diagnostic tools. A detailed protein 2DE for the normal human AF has not been reported. In the present study, the 2D protein database of the normal human AF supernatant (AFS) was constructed. Ten AFS samples from women carrying normal fetuses were analysed by 2DE. A mean of 412 spots per gel were analyzed and protein identification was carried out by MALDI-MS and MALDI-MS-MS. A 2D protein map comprising of 136 different gene products was constructed. The majority of the identified proteins are regulatory proteins, enzymes, secreted proteins, carriers and immunoglobulins. Twelve hypothetical proteins were also included. The normal AFS proteome map is a valuable tool for the study of aberrant protein expression and the search for proteins as possible markers for the prediction of abnormal fetuses.

The rat brain hippocampus proteome.

The hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In humans, the CA1 area of hippocampus is one of the first brain areas to display pathology in Alzheimer's disease. A comprehensive analysis of the hippocampus proteome has not been accomplished yet. We applied proteomics technologies to construct a two-dimensional database for rat brain hippocampus proteins. Hippocampus samples from eight months old animals were analyzed by two-dimensional electrophoresis and the proteins were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The database comprises 148 different gene products, which are in the majority enzymes, structural proteins and heat shock proteins. It also includes 39 neuron specific gene products. The database may be useful in animal model studies of neurological disorders.

Proliferating fibroblasts and HeLa cells co-cultured in vitro reciprocally influence growth patterns, protein expression, chromatin features and cell survival.

AIM: to identify biological interactions between proliferating fibroblasts and HeLa cells in vitro. MATERIALS AND METHODS: Fibroblasts were isolated from both normal and tumour human tissues. Coverslip co-cultures of HeLa and fibroblasts in various ratios with medium replacement every 48 h were studied using fixed cell staining with dyes such as Giemsa and silver staining, with immunochemistry for Ki-67 and E-cadherin, with dihydrofolate reductase (DHFR) enzyme reaction, as well as live cell staining for non-specific esterases and lipids. Other techniques included carmine cell labeling, autoradiography and apoptosis assessment. RESULTS: Under conditions of feeding and cell: cell ratios allowing parallel growth of human fibroblasts and HeLa cells, co-cultured for up to 20 days, a series of phenomena occur consecutively: profound affinity between the two cell types and exchange of small molecules; encircling of the HeLa colonies by the fibroblasts and enhanced growth of both cell types at their contact areas; expression of carbonic anhydrase in both cell types and high expression of non-specific esterases and cytoplasmic argyrophilia in the surrounding fibroblasts; intense production and secretion of lipid droplets by the surrounding fibroblasts; development of a complex net of argyrophilic projections of the fibroblasts; E-cadherin expression in the HeLa cells; from the 10th day onwards, an increasing detachment of batches of HeLa cells at the peripheries of colonies and appearance of areas with many multi-nucleated and apoptotic HeLa cells, and small HeLa fragments; from the 17th day, appearance of fibroblasts blocked at the G2-M phase. Co-cultures at approximately 17-20 days display a cell-cell fight with foci of (a) sparse growth of both cell types, (b) overgrowth of the fibroblasts and (c) regrowth of HeLa in small colonies. These results indicate that during their interaction with HeLa cells in vitro, proliferating fibroblasts can be activated against HeLa. This type of activation is not observed if fibroblast proliferation is blocked by contact inhibition of growth at confluency, or by omitting replacement of the nutrient medium. CONCLUSION: The present observations show that: (a) interaction between proliferating fibroblasts and HeLa cells in vitro drastically influences each other's protein expression, growth pattern, chromatin features and survival; (b) these functions depend on the fibroblast/HeLa ratio, cell topology (cell-cell contact and the architectural pattern developed during co-culture) and frequent medium change, as prerequisites for fibroblast proliferation; (c) this co-culture model is useful in the study of the complex processes within the tumour microenvironment, as well as the in vitro reproduction and display of several phenomena conventionally seen in tumour cytological sections, such as desmoplasia, apoptosis, nuclear abnormalities; and (d) overgrown fibroblasts adhering to the boundaries of HeLa colonies produce and secrete lipid droplets.

Global Proteomic Profiling of Drosophila Ovary: A High-resolution, Unbiased, Accurate and Multifaceted Analysis.

BACKGROUND: Drosophila melanogaster ovary serves as an attractive model system for the investigation of the cell cycle, death, signaling, migration, differentiation, development and stemness. By employing the 3750/+ heterozygote fly strain that carries specific functions in the follicle cell compartment, and a reliable control in GAL4/UAS-based transgenic technology, we herein characterized the protein-expression profiling of D. melanogaster ovary by applying high-resolution proteomic tools and bioinformatics programs. MATERIALS AND METHODS: Whole-cell total protein extracts derived from 3750/+ fly ovaries were prepared under highly denaturing conditions and after tryptic digestion, their cognate peptides were processed to liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis in a high-resolution LTQ Orbitrap Elite instrument. Obtained protein data were analyzed through use of UniProt, DAVID, KEGG and PANTHER bioinformatics platforms. RESULTS: The 7,583 unique peptides identified show that fly ovary contains at least 2,103 single proteins, which are distributed to all egg chamber compartments, in cytoplasm, membrane and nucleus, compartmentalized into major cellular organelles, and categorized into critical macromolecular assemblies. Among the recognized specific functions, nucleic acid binding, hydrolase, oxidoreductase, transporter and vesicle-mediated trafficking activities were the most prevalent. Determinants implicated in cellular metabolism and gene expression are represented by ~41% and ~17% of the ovarian proteome, respectively. Surprisingly, several proteins were found engaged in aging, immune response and neurogenesis. All major signaling pathways were detected, while apoptotic and non-apoptotic cell death programs were also identified. Remarkably, proteins involved in tumor formation, neurodegenerative and inflammatory diseases were also recognized. The successful remodeling of the proteasome and nearly complete molecular reconstruction of the citrate cycle and fatty acid degradation pathways demonstrate the efficacy, accuracy and fidelity of our combined proteomics/bioinformatics approach. CONCLUSION: Global proteomic characterization of D. melanogaster ovary allows the discovery of novel regulators and pathways, and provides a systemic view of networks that govern ovarian pathophysiology and embryonic development in fly species as well in humans.