GMP-Compliant Mesenchymal Stem Cell-Derived Exosomes for Cell-Free Therapy in Cancer

Cancer is categorized as one of the life-threatening disease in the world, which has recently been associated with a significant increase in the incidence and prevalence rate. Hence, the discovery of effective approaches for prevention, early diagnosis, and effective treatment for cancer has been prioritized by oncology researchers. In recent decades, mesenchymal stem cells show great potential to advance the field of regenerative medicine and oncology research due to representing prominent characteristics. Recently, studies indicate that mesenchymal stem cells can play an important role by secreting extracellular vesicles like exosomes in modulating the biological functions of target cells through paracrine regulation. Indeed, the exosomes derived from mesenchymal stem cells can represent the same therapeutic potential as parent cells with fewer side effects. Therefore, it can be demonstrated that exosomes can be a suitable drug delivery candidate in regenerative medicine and targeted therapy. It is also noteworthy that as the use of exosome therapy becomes more common in clinical studies, the importance of improving basic criteria such as safety, efficiency, and quality of stem cell products will also be highlighted. Based on this concept, the good manufacturing practice principles were put forward to examine the standard of cell products from different qualitative and quantitative aspects to progress the cell therapy. In other words, the principles of good manufacturing practice should be observed not only in the extraction and isolation of stem cells but also in the extraction of products related to stem cells such as exosomes in the field of treatment.

DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game

Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.

Targeted Amino Acids Profiling of Human Seminal Plasma from Teratozoospermia Patients Using LC-MS/MS

Identifying the metabolome of human seminal plasma (HSP) is a new research area to screen putative biomarkers of infertility. This case-control study was performed on HSP specimens of 15 infertile patients with teratozoospermia (defined as normal sperm morphology < 4%) and 12 confirmed fertile normozoospermic men as the control group to investigate the seminal metabolic signature and whether there are differences in the metabolome between two groups. HSPs were subjected to LC-MS-MS analysis. MetaboAnalyst5.0 software was utilized for statistical analysis. Different univariate and multivariate analyses were used, including T-tests, fold change analysis, random forest (RF), and metabolite set enrichment analysis (MSEA). Teratozoospermic samples contained seventeen significantly different amino acids. Upregulated metabolites include glutamine, asparagine, and glycylproline, whereas downregulated metabolites include cysteine, γ-aminobutyric acid, histidine, hydroxylysine, hydroxyproline, glycine, proline, methionine, ornithine, tryptophan, aspartic acid, argininosuccinic acid, α-aminoadipic acid, and β-aminoisobutyric acid. RF algorithm defined a set of 15 metabolites that constitute the significant features of teratozoospermia. In particular, increased glutamine, asparagine, and decreased cysteine, tryptophan, glycine, and valine were strong predictors of teratozoospemia. The most affected metabolic pathways in teratozoospermic men are the aminoacyl-tRNA, arginine, valine-leucine, and isoleucine biosynthesis. Altered metabolites detected in teratozoospermia were responsible for various roles in sperm functions that classified into four subgroups as follows: related metabolites to antioxidant function, energy production, sperm function, and spermatogenesis. The altered amino acid metabolome identified in this study may be related to the etiology of teratozoospermia, and may provide novel insight into potential biomarkers of male infertility for therapeutic targets.

GMP-Based Isolation of Full-Term Human Placenta-Derived NK Cells for CAR-NK Cell Therapy in Malignant Melanoma

Melanoma, a severe type of skin cancer, poses significant management challenges due to its resistance to available treatments. Despite this obstacle, the high immunogenicity of melanoma renders it amenable to immune therapy, and NK cells have been identified as possessing anti-tumor properties in immunotherapy. The development of chimeric antigen receptor (CAR)-modified NK cells, or CAR-NK cells, has shown potential in enhancing immunotherapeutic regimens. To achieve this, researchers have explored various sources of NK cells, including those derived from the placenta, which offers benefits compared to other sources due to their limited ex vivo expansion potential. Recent studies have indicated the capacity to expand functional NK cells from placenta-derived cells in vitro that possess anti-tumor cytolytic properties. This chapter discusses the isolation of full-term human placenta-derived NK cells using Good Manufacturing Practice-based methods for CAR-NK cell therapy in melanoma.

The Amino Acid Profile in Seminal Plasma of Normozoospermic Men: A Correlation Analysis with Spermiogram Parameters and Total Antioxidant Capacity

Background

Male infertility is usually determined by the manual evaluation of the semen, namely the standard semen analysis. It is currently impossible to predict sperm fertilizing ability based on the semen analysis alone. Therefore, a more sensitive and selective diagnosis tool is required.

Methods

Twelve fresh semen samples were collected from fertile volunteers attending the Avicenna Fertility Center (Tehran, Iran). The seminal plasma (SP) was prepared and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the total antioxidant capacity (TAC) was analysis. Thirty-four amino acids including essential amino acids (EAA), non-essential amino acids (NEAA), and non-proteinogenic amino acids (NPAA) relative concentration were determined, and the correlation between their concentration with spermiogram parameters and TAC of the SP was analyzed.

Results

Significant positive correlations have been found between selected amino acids with the motility (Met and Gln, rs=0.92; Cys, rs=0.72; and Asn, rs=0.82), normal sperm morphology (Met, rs=0.92; Cys, rs=0.72; Glu, rs=0.92; and Asn, rs=0.82), and sperm concentration (Trp, Phe, and Ala). In contrast, several AAs, including Gly, Ser, and Ile showed negative correlations with sperm concentration (rs=-0.93, r=-0.92, and r=-0.89, respectively). Furthermore, TAC showed a positive association only with Tyr (rs=0.79).

Conclusion

The strong positive/negative correlations between the seminal metabolic signature and spermiogram demonstrate the significance of determining metabolite levels under normal conditions for normal sperm functions. Combining the metabolome with the clinical characteristics of semen would enable clinicians to look beyond biomarkers toward the clinical interpretation of seminal parameters to explain the biological basis of sperm pathology.

Comparative proteomics analysis in different stages of urothelial bladder cancer for identification of potential biomarkers: highlighted role for antioxidant activity

BACKGROUND

Non-muscle-invasive bladder cancer (NMIBC) has a high recurrence rate and muscle-invasive bladder cancer (MIBC) has unfavorable outcomes in urothelial bladder cancer (UBC) patients. Complex UBC-related protein biomarkers for outcome prediction may provide a more efficient management approach with an improved clinical outcome. The aim of this study is to recognize tumor-associated proteins, which are differentially expressed in different stages of UBC patients compared non-cancerous tissues.

METHODS

The proteome of tissue samples of 42 UBC patients (NMIBC n = 25 and MIBC n = 17) was subjected to two-dimensional electrophoresis (2-DE) combined with Liquid chromatography-mass spectrometry (LC-MS) system to identify differentially expressed proteins. The intensity of protein spots was quantified and compared with Prodigy SameSpots software. Functional, pathway, and interaction analyses of identified proteins were performed using geneontology (GO), PANTHER, Reactome, Gene MANIA, and STRING databases.

RESULTS

Twelve proteins identified by LC-MS showed differential expression (over 1.5-fold, p < 0.05) by LC-MS, including 9 up-regulated in NMIBC and 3 up-regulated in MIBC patients. Proteins involved in the detoxification of reactive oxygen species and cellular responses to oxidative stress showed the most significant changes in UBC patients. Additionally, the most potential functions related to these detected proteins were associated with peroxidase, oxidoreductase, and antioxidant activity.

CONCLUSION

We identified several alterations in protein expression involved in canonical pathways which were correlated with the clinical outcomes suggested might be useful as promising biomarkers for early detection, monitoring, and prognosis of UBC.

Proteome Analysis of Adult Acute Lymphoblastic Leukemia by Two-dimensional Blue Native/Sodium Dodecyl Sulfate Gel Electrophoresis

Background

Despite the significant progress in the treatment of Acute Lymphoblastic Leukemia (ALL) in children, it still remains as one of the most challenging malignancies in adults. Identification of new biomarkers may improve the management of adult ALL. Proteins expressed on the cell surface can be considered as disease-associated biomarkers with potential for diagnosis and targeted therapies. Thus, membrane proteome studies give essential information about the disease-related biomarkers.

Methods

We applied 2-dimensional blue-native SDS-PAGE technique followed by MALDI-TOF/TOF-mass spectrometry to study the cell membrane proteome of peripheral blood mononuclear cells of adult B-ALL patients in comparison to that of the healthy controls.

Results

Sixty seven differentially expressed protein spots were detected, among them 52 proteins were found to be up-regulated but the other 15 proteins were down-regulated in B-ALL. Five differentially expressed proteins, involved in energy metabolism pathways, were detected in B-ALL patients compared to the healthy control group.

Conclusion

Differentially expressed proteins provide an insight into the molecular biology of B-ALL. Further studies must be done to confirm our data to be considered as potential targets for detection and treatment of B-ALL.

Sperm Morphology Assessment in the Era of Intracytoplasmic Sperm Injection: Reliable Results Require Focus on Standardization, Quality Control, and Training

Semen analysis is the first, and frequently, the only step in the evaluation of male fertility. Although the laboratory procedures are conducted according to the World Health Organization (WHO) guidelines, semen analysis and especially sperm morphology assessment is very difficult to standardize and obtain reproducible results. This is mainly due to the highly subjective nature of their evaluation. ICSI is the choice of treatment when sperm morphology is severely abnormal (teratozoospermic). Hence, the standardization of laboratory protocols for sperm morphology evaluation represents a fundamental step to ensure reliable, accurate and consistent laboratory results that avoid misdiagnoses and inadequate treatment of the infertile patient. This article aims to promote standardized laboratory procedures for an accurate evaluation of sperm morphology, including the establishment of quality control and quality assurance policies. Additionally, the clinical importance of sperm morphology results in assisted reproductive outcomes is discussed, along with the clinical management of teratozoospermic patients.

P-055 Evaluation of seminal plasma targeted metabolomics (amino acids) following untargeted antioxidant therapy in asthenozoospermia patients: A proposed approach for Personalized Medicine

Study question

To evaluate amino acids profile of Seminal Plasma following untargeted antioxidant therapy in asthenozoospermia patients.

Summary answer

Random Antioxidant therapy in asthenozoospermia could alter seminal plasma amino acids profile,and any prescribed antioxidant therapy should be based on individual human seminal plasma profile.

What is known already

The mitochondria of Spermatozoa perform aerobic metabolism and generate reactive oxygen species (ROS). When ROS production exceeds the antioxidant capacity of cells, they cause deleterious effects on sperm functions. Asthenozoospermia patient is defined based on 5th WHO (2010) as having normal morphology &gt;4%, count &gt;15 × 106/ ml, and motility&lt; 32%. One of the important aspects of sperm functions that are affected by ROS is sperm motility. Oral antioxidants seem to be one of the latest trends in counteracting high ROS levels and improving sperm motility for this group of patients.

Study design, size, duration

Semen samples of asthenozoospermia patients (n = 51) with a mean age (36.3 ±6) were collected after 3 – 5 days of abstention. Routine antioxidant supplementation (Vitamin E 400 IU / day + Selenium 60 mg / day + Folic acid 5 mg / day) was prescribed daily for 3 months.

Participants/materials, setting, methods

Semen analysis was done before and after antioxidant therapy. The seminal plasma amino acids profile was analyzed by using HILIC-LC-MS/MS. In detail, 34 amino acids were evaluated quantitatively before and after administrating supplementation.

Main results and the role of chance

In our study MetaboAnalyst, software was utilized for metabolomics investigations. The volcano plot appeared a noteworthy diminish in 12 amino acids after antioxidant treatment. The foremost noticeable decrease was seen in Beta-Aminoisobutyric and L-tryptophan as Improvers of sperm motility, also hydroxyproline which has to be present within the normal semen had a significant decrease after antioxidant therapy. Interestingly, after antioxidant treatment, only sperm count increased (163 × 106 ± 9) compared with the pre-treatment group (104 × 106 ± 6) but not sperm motility. Moreover based on the Enrichment Analysis information; Urea Cycle, Ammonia Recycling, and Aspartate Metabolism are the foremost prevailing cycles in asthenozoospermia patients. The literature recommends that the Urea cycle has a negative correlation with sperm count and Ammonia Recycling contains a negative relationship with sperm motility in infertile men. Our findings propose that the most important cause of sperm count increase after the mentioned treatment is suppression of the Urea cycle without having any effect on Ammonia Recycling to improve sperm motility, which was in contrast with our objectives. thereupon any prescribed antioxidant treatment ought to be based on individual human seminal plasma profiles and metabolomics pathways to have the desired result at the end.

Limitations, reasons for caution

The main limitations of this study are the exact patient selection and involving the pure asthenozoospermia patients in the study.

Wider implications of the findings

Knowing the exact etiology of each affected semen parameter and normal metabolomics of sperm and seminal plasma can prepare important data for personalized medicine and the administration of suitable interventions to improve sperm quality and male fertility status.

Trial registration number

not applicable

P-052 Targeted metabolomics (amino acids) profiling of seminal plasma distinguished teratozoospermia from normozoospermic samples

Study question

Is there a difference in metabolic composition between teratozoospermia and normozoospermic seminal samples?

Summary answer

Teratozoospermia and normozoospermia in humans are distinguished by seminal fluid metabolome markers especially amino acid content.

What is known already

Metabolomic profiling is the study of metabolites as downstream gene expression products in physiological and pathological circumstances. Identifying the metabolome of human seminal plasma (HSP) is a new research area to screen putative (in)fertility biomarkers. Knowing the semen metabolic signature and whether there are differences in metabolic composition between the teratozoospermia sample and semen with normal morphology could enhance our understanding of aspects associated with poor sperm quality and consequent male infertility.

Study design, size, duration

The Ethics Committee of Islamic Azad Tehran Medical Sciences University-Pharmacy and Pharmaceutical Branches approved the case-control study. Teratozoospermia was defined based on 5th WHO (2010) as normal morphology&lt;4%, count&gt;15*106/ml, progressive and non-progressive motility≥40%. In contrast, in normozoospermic samples from fertile men (who had at least one child), normal morphology was greater than 4%. HSP specimens were obtained from 15 infertile patients with teratozoospermia, and 12 confirmed fertile men as the control group.

Participants/materials, setting, methods

Fresh semen samples were obtained through masturbation following 3–4 days of abstention. A portion of each sample was used for routine semen analysis. Remained seminal plasma was isolated by centrifugation and stored; following post-thaw, HSPs were subjected to LC-MS-MSanalysis. MetaboAnalyst 5.0 software(www.metaboanalyst.ca) was utilized to identify fundamental metabolism alterations related to the morphology status of spermatozoa. In addition, different uni/multivariate analysis was performed to ascertain the group of metabolites responsible for the overall discrimination ability.

Main results and the role of chance

Seventeen significantly differentially metabolites (14 decreased and three increased) were observed in teratozoospermia samples vs. fertile control. Down-regulated metabolites include Cysteine, Gamma-aminobutyric acid, Glycine, Histidine, Hydroxylysine, Hydroxyproline, Methionine, Ornithine, Proline, Tryptophan, Aspartic acid, Argininosuccinic acid, Alpha-aminoadipic acid, and Beta-aminoisobutyric acid; whereas up. In contrast, up-regulatedlutamine, Asparagine, and Glycylproline.

The PLS-DA score plot demonstrated the clear separation obtained according to the sperm morphological status. The two distinct groups were well-clustered, with distinct metabolic profiles for each group.

The random forest (RF) algorithm was utilized to select relevant variables for teratozoospermia status classification by estimating the importance of each metabolite to teratozoospermia. The RF analysis defined a set of 15 metabolites that constitute the best predictors of teratozoospermia. In particular, increased Glutamine, Asparagine, and decreased Cysteine, Tryptophan, Glycine, and Valine were strong predictors of teratozoospermia. Interestingly, pathway enrichment analysis revealed that the most affected metabolic pathways in teratozoospermia men were the Aminoacyle-tRANA, arginine, valine-leucine, and isoleucine biosynthesis.

Among 34 metabolites, Asparagine, Glutamine, and Glycylproline negatively correlated with sperm morphology status; whereas 21 metabolites were positively correlated with morphology, including Alanine, Argininesuccinic, Aspartic, Cystine, Gamma-aminobutyric acid, Glutamic, Glycine, Histidine, Homocitrulline, Hydroxylysine, Hydroxyproline, Isoleucine, Leucine, Methionine, Ornithine, Phenylalanine, Proline, Threonine, Tryptophan, Tyrosine, and Valine.

Limitations, reasons for caution

Since the strict criteria were considered for teratozoospermia patients, these results are preliminary and need to be confirmed with more sample size.

Wider implications of the findings

The possible cause of metabolite difference in seminal plasma of teratozoospermia patients comes from the disability of spermatozoa for selectively absorption or secretion of specific amino acids into/out of the cell, which is critical for sperm function and maturation and reflects the potential of fertility.

Trial registration number

Not Applicable

Corrigendum: Molecular Docking as a Therapeutic Approach for Targeting Cancer Stem Cell Metabolic Processes

[This corrects the article DOI: 10.3389/fphar.2022.768556.].

Molecular Docking as a Therapeutic Approach for Targeting Cancer Stem Cell Metabolic Processes

Cancer stem cells (CSCs) are subpopulation of cells which have been demonstrated in a variety of cancer models and involved in cancer initiation, progression, and development. Indeed, CSCs which seem to form a small percentage of tumor cells, display resembling characteristics to natural stem cells such as self-renewal, survival, differentiation, proliferation, and quiescence. Moreover, they have some characteristics that eventually can demonstrate the heterogeneity of cancer cells and tumor progression. On the other hand, another aspect of CSCs that has been recognized as a central concern facing cancer patients is resistance to mainstays of cancer treatment such as chemotherapy and radiation. Owing to these details and the stated stemness capabilities, these immature progenitors of cancerous cells can constantly persist after different therapies and cause tumor regrowth or metastasis. Further, in both normal development and malignancy, cellular metabolism and stemness are intricately linked and CSCs dominant metabolic phenotype changes across tumor entities, patients, and tumor subclones. Hence, CSCs can be determined as one of the factors that correlate to the failure of common therapeutic approaches in cancer treatment. In this context, researchers are searching out new alternative or complementary therapies such as targeted methods to fight against cancer. Molecular docking is one of the computational modeling methods that has a new promise in cancer cell targeting through drug designing and discovering programs. In a simple definition, molecular docking methods are used to determine the metabolic interaction between two molecules and find the best orientation of a ligand to its molecular target with minimal free energy in the formation of a stable complex. As a comprehensive approach, this computational drug design method can be thought more cost-effective and time-saving compare to other conventional methods in cancer treatment. In addition, increasing productivity and quality in pharmaceutical research can be another advantage of this molecular modeling method. Therefore, in recent years, it can be concluded that molecular docking can be considered as one of the novel strategies at the forefront of the cancer battle via targeting cancer stem cell metabolic processes.

COVID-19 Pathology on Various Organs and Regenerative Medicine and Stem Cell-Based Interventions

Severe acute respiratory syndrome-coronavirus 2, a novel betacoronavirus, has caused the global outbreak of a contagious infection named coronavirus disease-2019. Severely ill subjects have shown higher levels of pro-inflammatory cytokines. Cytokine storm is the term that can be used for a systemic inflammation leading to the production of inflammatory cytokines and activation of immune cells. In coronavirus disease-2019 infection, a cytokine storm contributes to the mortality rate of the disease and can lead to multiple-organ dysfunction syndrome through auto-destructive responses of systemic inflammation. Direct effects of the severe acute respiratory syndrome associated with infection as well as hyperinflammatory reactions are in association with disease complications. Besides acute respiratory distress syndrome, functional impairments of the cardiovascular system, central nervous system, kidneys, liver, and several others can be mentioned as the possible consequences. In addition to the current therapeutic approaches for coronavirus disease-2019, which are mostly supportive, stem cell-based therapies have shown the capacity for controlling the inflammation and attenuating the cytokine storm. Therefore, after a brief review of novel coronavirus characteristics, this review aims to explain the effects of coronavirus disease-2019 cytokine storm on different organs of the human body. The roles of stem cell-based therapies on attenuating cytokine release syndrome are also stated.

Using Metabolomics to Differentiate Player Positions in Elite Male Basketball Games: A Pilot Study

Purpose: The current study compared metabolic profiles and movement patterns between different player positions and explored relationships between indicators of internal and external loads during elite male basketball games.

Methods: Five main players from 14 basketball teams (n = 70) were selected as subjects and defined as backcourt (positions 1–3) or frontcourt (positions 4–5) players. Video-based time motion analysis (VBTMA) was performed based on players’ individual maximal speeds. Movements were classified into high and low intensity running with and without ball, high and low intensity shuffling, static effort and jumps. Saliva samples were collected before and after 40-min basketball games with metabolomics data being analyzed by multivariate statistics. Independent t-tests were used to compare VBTMA.

Results: Frequency, duration, and distance of high and low intensity running and -shuffling were higher in backcourt players, whereas static effort duration and frequency as well as jump frequency were higher in frontcourt players (all p ≤ 0.05). The levels of taurine, succinic acid, citric acid, pyruvate, glycerol, acetoacetic acid, acetone, and hypoxanthine were higher in backcourt players, while lactate, alanine, 3-methylhistidine were higher and methionine was lower in frontcourt players (all p < 0.05). High intensity running with ball was significantly associated by acetylecholine, hopoxanthine, histidine, lactic acid and leucine in backcourt players (p < 0.05).

Conclusion: We demonstrate different metabolic profiles of backcourt and frontcourt players during elite male basketball games; while aerobic metabolic changes are more present in backcourt players, frontcourt players showed lager changes in anaerobic metabolic pathways due to more static movements.

Identification of Celecoxib-Targeted Proteins Using Label-Free Thermal Proteome Profiling on Rat Hippocampus

Celecoxib, or Celebrex, a nonsteroidal anti-inflammatory drug, is one of the most common medicines for treating inflammatory diseases. Recently, it has been shown that celecoxib is associated with implications in complex diseases, such as Alzheimer disease and cancer as well as with cardiovascular risk assessment and toxicity, suggesting that celecoxib may affect multiple unknown targets. In this project, we detected targets of celecoxib within the nervous system using a label-free thermal proteome profiling method. First, proteins of the rat hippocampus were treated with multiple drug concentrations and temperatures. Next, we separated the soluble proteins from the denatured and sedimented total protein load by ultracentrifugation. Subsequently, the soluble proteins were analyzed by nano-liquid chromatography tandem mass spectrometry to determine the identity of the celecoxib-targeted proteins based on structural changes by thermal stability variation of targeted proteins toward higher solubility in the higher temperatures. In the analysis of the soluble protein extract at 67°C, 44 proteins were uniquely detected in drug-treated samples out of all 478 identified proteins at this temperature. Ras-associated binding protein 4a, 1 out of these 44 proteins, has previously been reported as one of the celecoxib off targets in the rat central nervous system. Furthermore, we provide more molecular details through biomedical enrichment analysis to explore the potential role of all detected proteins in the biologic systems. We show that the determined proteins play a role in the signaling pathways related to neurodegenerative disease-and cancer pathways. Finally, we fill out molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets. SIGNIFICANCE STATEMENT: This study determined 44 off-target proteins of celecoxib, a nonsteroidal anti-inflammatory and one of the most common medicines for treating inflammatory diseases. It shows that these proteins play a role in the signaling pathways related to neurodegenerative disease and cancer pathways. Finally, the study provides molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets.

Fast diagnosis of men's fertility using Raman spectroscopy combined with chemometric methods: An experimental study

Background

Idiopathic infertile men suffer from unexplained male infertility; they are infertile despite having a normal semen analysis, a normal history, and physical examination, and when female infertility factor has been ruled out.

Objective

The present study aimed to develop a metabolic fingerprinting methodology using Raman spectroscopy combined with Chemometrics to detect idiopathic infertile men vs. fertile ones by seminal plasma.

Materials and Methods

In this experimental study, the seminal plasma of 26 men including 13 fertile and 13 with unexplained infertility who reffered to, Avicenna Infertility Clinic, 2018, Tehran, Iran, have been investigated. The seminal metabolomic fingerprinting was evaluated using Raman spectrometer from 100 to 4250 cm-1. The principal component analysis and discriminate analysis methods were used.

Results

The total of 26 samples were divided into 20 training and 6 test sets. The Principal component analysis score plot of the training set showed that the data were perfectly divided into two sides of the plot, which statistically approves the direct effect of semen metabolome changes on the Raman spectra. A classification model was constructed by linear discriminant analysis using the training set and evaluated by the test group which resulted in completely correct classification. While three of the six test samples appeared in the fertile group, the rest appeared in the infertile as expected.

Conclusion

Metabolic fingerprinting of seminal plasma using Raman spectroscopy combined with chemometric classification methods accurately discriminated between the idiopathic infertile men and the fertile ones and predicted their fertility type.

Reanalysis of discarded blastocysts for autosomal aneuploidy after sex selection in cleavage-stage embryos

Objective

The goal of the present study was to investigate the rate of chromosomal aneuploidies in surplus embryos after sex determination at the cleavage stage. Then, the same chromosomal aneuploidies were evaluated in blastocysts after extended culture.

Methods

Sixty-eight surplus embryos were biopsied at the cleavage stage and incubated for an additional 3 days to allow them to reach the blastocyst stage. The embryos were reanalyzed via fluorescence in situ hybridization (FISH) to examine eight chromosomes (13, 15, 16, 18, 21, 22, X, and Y) in both cleavage-stage embryos and blastocysts.

Results

Although the total abnormality rate was lower in blastocysts (32.35%) than in cleavage-stage embryos (45.58%), the difference was not significant (p=0.113). However, when we restricted the analysis to autosomal abnormalities, we observed a significant difference in the abnormality rate between the cleavage-stage embryos (44.11%) and the blastocysts (17.64%, p=0.008). A higher rate of sex chromosomal abnormalities was also observed in cleavage-stage embryos (29.4%) than in blastocysts (14.70%, p=0.038).

Conclusion

The data indicated that embryo biopsy should be conducted at the blastocyst stage rather than the cleavage stage. The results also emphasized that examination of common chromosomal aneuploidies apart from sex selection cycles can be conducted in the blastocyst stage with the FISH method.

Metabolic load comparison between the quarters of a game in elite male basketball players using sport metabolomics

Purpose: A basketball match is characterized by intermittent high-intensity activities, thereby relying extensively on both aerobic and anaerobic metabolic pathways. Here, we aimed to compare the metabolic fluctuations between the four 10-min quarters of high-level basketball games using metabolomics analyses. Methods: 70 male basketball players with at least 3 years of experience in the Iran national top-league participated. Before and after each quarter, saliva samples were taken for subsequent untargeted metabolomics analyses, where Principal component analysis (PCA) and Partial least squares-discriminant analysis (PLS-DA) were employed for statistical analysis. Results: Quarters 1 and 3 showed similar metabolic profiles, with increased levels of ATP turnover (higher Lactate, Pyruvate, Succinic Acid, Citric Cid, Glucose and Hypoxanthine), indicating more reliance on anaerobic energy systems than quarters 2 and 4. In comparison, quarters 2 and 4 showed a reduction in Valine and Lucien and an increase in Alanine, Glycerol, AcetoAcetic Acid, Acetone, Succinic Acid, Citric Acid, Acetate and Taurine that was not present in quarters 1 and 3, indicating greater reliance of aerobic energy contribution, fat metabolism and gluconeogenesis. Conclusion: Our data demonstrate that the higher intensity of movements in the first quarter, where players are more rested, induce an increase in anaerobic energy contribution. This seems to be the case also for the third quarter that follows 15 min of rest, whereas the accumulated fatigue and reduction of high-intensity movements in the second and fourth quarters also reduces the speed of energy production and players thereby utilize more aerobic energy.

Prospect of Stem Cell Therapy and Regenerative Medicine in Osteoporosis

The field of cell therapy and regenerative medicine can hold the promise of restoring normal tissues structure and function. Additionally, the main targets of stem cell-based therapies are chronic diseases and lifelong disabilities without definite cures such as osteoporosis. Osteoporosis as one of the important causes of morbidity in older men and post-menopausal women is characterized by reduced bone quantity or skeletal tissue atrophy that leads to an increased risk of osteoporotic fractures. The common therapeutic methods for osteoporosis only can prevent the loss of bone mass and recover the bone partially. Nevertheless, stem cell-based therapy is considered as a new approach to regenerate the bone tissue. Herein, mesenchymal stem cells as pivotal candidates for regenerative medicine purposes especially bone regeneration are the most common type of cells with anti-inflammatory, immune-privileged potential, and less ethical concerns than other types of stem cells which are investigated in osteoporosis. Based on several findings, the mesenchymal stem cells effectiveness near to a great extent depends on their secretory function. Indeed, they can be involved in the establishment of normal bone remodeling via initiation of specific molecular signaling pathways. Accordingly, the aim herein was to review the effects of stem cell-based therapies in osteoporosis.

OMICS insights into cancer histology; Metabolomics and proteomics approach

Metabolomics as a post-genomic research area comprising different analytical methods for small molecules analysis. One of the underlying applications of metabolomics technology for better disease diagnosis and prognosis is discovering the metabolic pathway differences between healthy individuals and patients. On the other hand, the other noteworthy applications of metabolomics include its effective role in biomarker screening for cancer detection, monitoring, and prediction. In other words, emerging of the metabolomics field can be hopeful to provide a suitable alternative for the common current cancer diagnostic methods especially histopathological tests. Indeed, cancer as a major global issue places a substantial burden on the health care system. Hence, proper management can be beneficial. In this respect, formalin-fixed paraffin-embedded tissue specimens (in histopathological tests) are considered as a valuable source for metabolomics investigations. Interestingly, formalin-fixed paraffin-embedded tissue specimens can provide informative data for cancer management. In general, using these specimens, determining the cancer stage, individual response to the different therapies, personalized risk prediction are possible and high-quality clinical services are the promise of OMICS technologies for cancer disease. However, considering all of these beneficial characteristics, there are still some limitations in this area that need to be addressed in order to optimize the metabolomics utilizations and advancement.

Metabolomics Analysis of Mesenchymal Stem Cells

Various mesenchymal stem cells as easily accessible and multipotent cells can share different essential signaling pathways related to their stemness ability. Understanding the mechanism of stemness ability can be useful for controlling the stem cells for regenerative medicine targets. In this context, OMICs studies can analyze the mechanism of different stem cell properties or stemness ability via a broad range of current high-throughput techniques. This field is fundamentally directed toward the analysis of whole genome (genomics), mRNAs (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in biological samples. According to several studies, metabolomics is more effective than other OMICs ّfor various system biology concerns. Metabolomics can elucidate the biological mechanisms of various mesenchymal stem cell function by measuring their metabolites such as their secretome components. Analyzing the metabolic alteration of mesenchymal stem cells can be useful to promote their regenerative medicine application.

Metabolomics and Cell Therapy in Diabetes Mellitus

Diabetes with a broad spectrum of complications has become a global epidemic metabolic disorder. Till now, several pharmaceutical and non-pharmaceutical therapeutic approaches were applied for its treatment. Cell-based therapies have become promising methods for diabetes treatment. Better understanding of diabetes pathogenesis and identification of its specific biomarkers along with evaluation of different treatments efficacy, can be possible by clarification of specific metabolic modifications during the diabetes progression. Subsequently, metabolomics technology can support this goal as an effective tool. The present review tried to show how metabolomics quantifications can be useful for diabetic monitoring before and after cell therapy. Cell therapy is an alternative approach to achieve diabetes treatments goals including insulin resistance amelioration, insulin independence reparation, and control of glycemia. OMICs approaches provide a comprehensive insight into the molecular mechanisms of cells features and functional mechanism of their genomics, transcriptomics, proteomics, and metabolomics profile which can be useful for their therapeutic application. As a modern technology for the detection and analysis of metabolites in biological samples, metabolomica can identify many of the metabolic and molecular pathways associated with diabetes and its following complications.

Oncometabolites as biomarkers in thyroid cancer: a systematic review

Introduction

Thyroid cancer (TC) is an important common endocrine malignancy, and its incidence has increased in the past decades. The current TC diagnosis and classification tools are fine-needle aspiration (FNA) and histological examination following thyroidectomy. The metabolite profile alterations of thyroid cells (oncometabolites) can be considered for current TC diagnosis and management protocols.

Methods

This systematic review focuses on metabolite alterations within the plasma, FNA specimens, and tissue of malignant TC contrary to benign, goiter, or healthy TC samples. A systematic search of MEDLINE (PubMed), Scopus, Embase, and Web of Science databases was conducted, and the final 31 studies investigating metabolite biomarkers of TC were included.

Results

A total of 15 targeted studies and 16 untargeted studies revealed several potential metabolite signatures of TC such as glucose, fructose, galactose, mannose, 2-keto-d-gluconic acid and rhamnose, malonic acid and inosine, cholesterol and arachidonic acid, glycosylation (immunoglobulin G [IgG] Fc-glycosylation), outer mitochondrial membrane 20 (TOMM20), monocarboxylate transporter 4 (MCT4), choline, choline derivatives, myo-/scyllo-inositol, lactate, fatty acids, several amino acids, cell membrane phospholipids, estrogen metabolites such as 16 alpha-OH E1/2-OH E1 and catechol estrogens (2-OH E1), and purine and pyrimidine metabolites, which were suggested as the TC oncometabolite.

Conclusion

Citrate was suggested as the first most significant biomarker and lactate as the second one. Further research is needed to confirm these biomarkers as the TC diagnostic oncometabolite.

Reactive oxygen species-induced alterations in H19-Igf2 methylation patterns, seminal plasma metabolites, and semen quality

PURPOSE

This study was conducted in order to investigate the effects of reactive oxygen species (ROS) levels on the seminal plasma (SP) metabolite milieu and sperm dysfunction.

METHODS

Semen specimens of 151 normozoospermic men were analyzed for ROS by chemiluminescence and classified according to seminal ROS levels [in relative light units (RLU)/s/106 sperm]: group 1 (n = 39): low (ROS < 20), group 2 (n = 38): mild (20 ≤ ROS < 40), group 3 (n = 31): moderate (40 ≤ ROS < 60), and group 4 (n = 43): high (ROS ≥ 60). A comprehensive analysis of SP and semen parameters, including conventional semen characteristics, measurement of total antioxidant capacity (TAC), sperm DNA fragmentation index (DFI), chromatin maturation index (CMI), H19-Igf2 methylation status, and untargeted seminal metabolic profiling using nuclear magnetic resonance spectroscopy (1H-NMR), was carried out.

RESULT(S)

The methylation status of H19 and Igf2 was significantly different in specimens with high ROS (P < 0.005). Metabolic fingerprinting of these SP samples showed upregulation of trimethylamine N-oxide (P < 0.001) and downregulations of tryptophan (P < 0.05) and tyrosine/tyrosol (P < 0.01). High ROS significantly reduced total sperm motility (P < 0.05), sperm concentration (P < 0.001), and seminal TAC (P < 0.001) but increased CMI and DFI (P < 0.005). ROS levels have a positive correlation with Igf2 methylation (r = 0.19, P < 0.05), DFI (r = 0.40, P < 0.001), CMI (r = 0.39, P < 0.001), and trimethylamine N-oxide (r = 0.45, P < 0.05) and a negative correlation with H19 methylation (r = - 0.20, P < 0.05), tryptophan (r = - 0.45, P < 0.05), sperm motility (r = - 0.20, P < 0.05), sperm viability (r = - 0.23, P < 0.01), and sperm concentration (r = - 0.30, P < 0.001).

CONCLUSION(S)

Results showed significant correlation between ROS levels and H19-Igf2 gene methylation as well as semen parameters. These findings are critical to identify idiopathic male infertility and its management through assisted reproduction technology (ART).

Metabolomics of Male Infertility: A New Tool for Diagnostic Tests

Infertility is a major health issue worldwide. Males and females contribute equally to this problem. Diagnostic semen analysis fails to identify 50% of male infertility disorders. In this regard, metabolomics as a new field of omics has been suggested to have the potential of solving and diagnosis of the male infertility problems. Metabo-lome has a history of around 20 years. However, there are only limited metabolomics studies carried out regarding male infertility. In this review, the current metabolomics researches that have been done in infertile men were reviewed. Based on our own results, using human seminal plasma for metabolomics studies is highly recommended to find potential biomarkers and developing diagnosis tests for detection of main deficiencies in infertile men.

The Horizon of Gene Therapy in Modern Medicine: Advances and Challenges

Gene therapy as a novel study in molecular medicine will have a significant impact on human health in the near future. In recent years, the scope of gene therapy has been developed and is now beginning to revolutionize therapeutic approaches. Accordingly, many types of diseases are now being studied and treated in clinical trials through various gene delivery vectors. The emergence of recombinant DNA technology which provides the possibility of fetal genetic screening and genetic counseling is a good case in point. Therefore, gene therapy advances are being applied to correct inherited genetic disorders such as hemophilia, cystic fibrosis, and familial hypercholesterolemia as well as acquired diseases like cancer, AIDS, Alzheimer's disease, Parkinson's disease, and infectious diseases like HIV. As a result, gene therapy approaches have the ability to help the vast majority of newborns with different diseases. Since these ongoing treatments and clinical trials are being developed, many more barriers and challenges have been created. In order to continue this positive growth, these challenges need to be recognized and addressed. Accordingly, safety, efficiency and also risks and benefits of gene therapy trials for each disease should be considered. As a result, sustained manufacturing of the therapeutic gene product without any harmful side effects is the least requirement for gene therapy. Herein, different aspects of gene therapy, an overview of the progress, and also the prospects for the future have been discussed for the successful practice of gene therapy.

The Design and Application of an Appropriate Parkinson's Disease Animal Model in Regenerative Medicine

OBJECTIVES

Aging as an inevitable and complex physiological process occurs through a progressive decrease in the potential of tissue regeneration. Given the increasing global outbreak of aging and age-related disorders, it is important to control this phenomenon. Parkinson's disease (one of the age-related neurodegenerative and progressive disorders) resulted from predominant dopaminergic neurons deficiency. Usual Parkinson's disease treatments just can lead to symptomatically relieving. Recently, cell therapy and regenerative medicine a great promise in the treatment of several types of disorders including Parkinson's disease. Herein, before starting clinical trials, preclinical studies should be performed to answer some fundamental questions about the safety and efficacy of various treatments. Additionally, developing a well-designed and approved study is required to provide an appropriate animal model with strongly reliable validation methods. Hereupon, this review will discuss about the design and application of an appropriate Parkinson's disease animal model in regenerative medicine.

EVIDENCE ACQUISITION

In order to conduct the present review, numbers of Parkinson's disease preclinical studies, as well as literatures related to the animal modeling, were considered.

RESULTS

Appropriate animal models which approved by related authorize committees should have a high similarity to humans from anatomical, physiological, behavioral, and genetic characteristics view of point.

CONCLUSION

It is concluded that animal studies before starting clinical trials have an important role in answering the crucial questions about the various treatments safety and efficacy. Therein, it is recommended that all of animal modeling stages be assessed by animal ethics and welfare guidelines and also evaluated by different validation tests. However, it is better to find some alternatives to replacement, refinement, and, reduction of animals. Nowadays, some novel technologies such as using imaging methods have been introduced.

The molecular cues for the biological effects of ionizing radiation dose and post-irradiation time on human breast cancer SKBR3 cell line: A Raman spectroscopy study

Radiotherapy is one of the main modalities of cancer treatment. The utility of Raman spectroscopy (RS) for detecting the distinct radiobiological responses in human cancer cells is currently under investigation. RS holds great promises to provide good opportunities for personalizing radiotherapy treatments. Here, we report the effects of the radiation dose and post-irradiation time on the molecular changes in the human breast cancer SKBR3 cells, using RS. The SKBR3 cells were irradiated by gamma radiation with different doses of 0, 1, 2, 4, and 6 Gy. The Raman signals were acquired 24 and 48 h after the gamma radiation. The collected Raman spectra were analyzed by different statistical methods such as principal component analysis, linear discriminant analysis, and genetic algorithm. A thorough analysis of the obtained Raman signals revealed that 2 Gy of gamma radiation induces remarkable molecular and structural changes in the SKBR3 cells. We found that the wavenumbers in the range of 1000-1400 cm^-1 in Raman spectra are selective for discriminating between the effects of the different doses of irradiation. The results also revealed that longer post-irradiation time leads to the relaxation of the cells to their initial state. The molecular changes that occurred in the 2Gy samples were mostly reversible. On the other hand, the exposure to doses higher than 4Gy induced serious irreversible changes, mainly seen in 2700-2800 cm^-1 in Raman spectra. The classification models developed in this study would help to predict the radiation-based molecular changes induced in the cancer cells by only using RS. Also, this designed framework may facilitate the process of biodosimetry.

Adipose Tissue-Derived Stromal Cells for Wound Healing

Skin as the outer layer covers the body. Wounds can affect this vital organ negatively and disrupt its functions. Wound healing as a biological process is initiated immediately after an injury. This process consists of three stages: inflammation, proliferation, remodeling. Generally, these three stages occur continuously and timely. However, some factors such as infection, obesity and diabetes mellitus can interfere with these stages and impede the normal healing process which results in chronic wounds. Financial burden on both patients and health care systems, negative biologic effect on the patient's general health status and reduction in quality of life are a number of issues which make chronic wounds as a considerable challenge. During recent years, along with advances in the biomedical sciences, various surgical and non-surgical therapeutic methods have been suggested. All of these suggested treatments have their own advantages and disadvantages. Recently, cell-based therapies and regenerative medicine represent promising approaches to wound healing. Accordingly, several types of mesenchymal stem cells have been used in both preclinical and clinical settings for the treatment of wounds. Adipose-derived stromal cells are a cost-effective source of mesenchymal stem cells in wound management which can be easily harvest from adipose tissues through the less invasive processes with high yield rates. In addition, their ability to secrete multiple cytokines and growth factors, and differentiation into skin cells make them an ideal cell type to use in wound treatment. This is a concise overview on the application of adipose-derived stromal cells in wound healing and their role in the treatment of chronic wounds.

Metabolic Fingerprinting of Seminal Plasma from Non-obstructive Azoospermia Patients: Positive Versus Negative Sperm Retrieval

BACKGROUND

Non-obstructive azoospermia (NOA) occurs in approximately 10% of infertile men. Retrieval of the spermatozoa from the testicle of NOA patients is an invasive approach. Seminal plasma is an excellent source for exploring to find the biomarkers for presence of spermatozoa in testicular tissue. The present discovery phase study aimed to use metabolic fingerprinting to detect spermatogenesis from seminal plasma in NOA patients as a non-invasive method.

METHODS

In this study, 20 men with NOA were identified based on histological analysis who had their first testicular biopsy in 2015 at Avicenna Fertility Center, Tehran, Iran. They were divided into two groups, a positive testicular sperm extraction (TESE(+)) and a negative testicular sperm extraction (TESE(-)). Seminal plasma of NOA patients was collected before they underwent testicular sperm extraction (TESE) operation. The metabolomic fingerprinting was evaluated by Raman spectrometer. Principal component analysis (PCA) and an unsupervised statistical method, was used to detect outliers and find the structure of the data. The PCA was analyzed by MATLAB software.

RESULTS

Metabolic fingerprinting of seminal plasma from NOA showed that TESE (+) versus TESE(-) patients were classified by PCA. Furthermore, a possible subdivision of TESE(-) group was observed. Additionally, TESE(-) patients were in extreme oxidative imbalance compared to TESE(+) patients.

CONCLUSION

Metabolic fingerprinting of seminal plasma can be considered as a breakthrough, an easy and cheap method for prediction presence of spermatogenesis in NOA.

Male Infertility, Precision Medicine and Systems Proteomics

Precision medicine (PM) is an approach that has the power to create the best effect and safety of medicine and treatment with the least side effects for each person. PM is very helpful as sometimes due to inaccurate or late diagnosis or toxicities of the drugs irreversible side effect for patient's health are generated. This seemingly new and emerging science is also effective in preventing disease, due to differences in the genes, environment, and lifestyles of any particular person. PM can be a prominent criterion in infertility research. To achieve this goal, there should be information from a healthy human body, including genetic and molecular information. A PM is an evolution in health care, which is very helpful even economically. The guarantor of the PM success is the examination of the molecular profile of the patient, including genes, proteins, metabolites, etc. Therefore, genomics, proteomics, and metabolomics-based techniques are very important in this regard. Unfortunately, despite extensive studies on PM practice in various fields, male infertility has remained unresponsive. Given that around 20% of couples around the world suffer from infertility, and almost half of them are related to men's problems, the PM approach has a high potential for male infertility. In this study, with the help of proteomics and metabolomics, PM information on male infertility was explored.

The Challenge of Human Spermatozoa Proteome: A Systematic Review

Currently, there are 20,197 human protein-coding genes in the most expertly curated database (UniProtKB/Swiss-Pro). Big efforts have been made by the international consortium, the Chromosome-Centric Human Proteome Project (C-HPP) and independent researchers, to map human proteome. In brief, anno 2017 the human proteome was outlined. The male factor contributes to 50% of infertility in couples. However, there are limited human spermatozoa proteomic studies. Firstly, the development of the mapping of the human spermatozoa was analyzed. The human spermatozoa have been used as a model for missing proteins. It has been shown that human spermatozoa are excellent sources for finding missing proteins. Y chromosome proteome mapping is led by Iran. However, it seems that it is extremely challenging to map the human spermatozoa Y chromosome proteins based on current mass spectrometry-based proteomics technology. Post-translation modifications (PTMs) of human spermatozoa proteome are the most unexplored area and currently the exact role of PTMs in male infertility is unknown. Additionally, the clinical human spermatozoa proteomic analysis, anno 2017 was done in this study.

Two-Way Gene Interaction From Microarray Data Based on Correlation Methods

Background

Gene networks have generated a massive explosion in the development of high-throughput techniques for monitoring various aspects of gene activity. Networks offer a natural way to model interactions between genes, and extracting gene network information from high-throughput genomic data is an important and difficult task.

Objectives

The purpose of this study is to construct a two-way gene network based on parametric and nonparametric correlation coefficients. The first step in constructing a Gene Co-expression Network is to score all pairs of gene vectors. The second step is to select a score threshold and connect all gene pairs whose scores exceed this value.

Materials and Methods

In the foundation-application study, we constructed two-way gene networks using nonparametric methods, such as Spearman’s rank correlation coefficient and Blomqvist’s measure, and compared them with Pearson’s correlation coefficient. We surveyed six genes of venous thrombosis disease, made a matrix entry representing the score for the corresponding gene pair, and obtained two-way interactions using Pearson’s correlation, Spearman’s rank correlation, and Blomqvist’s coefficient. Finally, these methods were compared with Cytoscape, based on BIND, and Gene Ontology, based on molecular function visual methods; R software version 3.2 and Bioconductor were used to perform these methods.

Results

Based on the Pearson and Spearman correlations, the results were the same and were confirmed by Cytoscape and GO visual methods; however, Blomqvist’s coefficient was not confirmed by visual methods.

Conclusions

Some results of the correlation coefficients are not the same with visualization. The reason may be due to the small number of data.

Estimating complicated baselines in analytical signals using the iterative training of Bayesian regularized artificial neural networks

The present work deals with the development of a new baseline correction method based on the comparative learning capabilities of artificial neural networks. The developed method uses the Bayes probability theorem for prevention of the occurrence of the over-fitting and finding a generalized baseline. The developed method has been applied on simulated and real metabolomic gas-chromatography (GC) and Raman data sets. The results revealed that the proposed method can be used to handle different types of baselines with cave, convex, curvelinear, triangular and sinusoidal patterns. For further evaluation of the performances of this method, it has been compared with benchmarking baseline correction methods such as corner-cutting (CC), morphological weighted penalized least squares (MPLS), adaptive iteratively-reweighted penalized least squares (airPLS) and iterative polynomial fitting (iPF). In order to compare the methods, the projected difference resolution (PDR) criterion has been calculated for the data before and after the baseline correction procedure. The calculated values of PDR after the baseline correction using iBRANN, airPLS, MPLS, iPF and CC algorithms for the GC metabolomic data were 4.18, 3.64, 3.88, 1.88 and 3.08, respectively. The obtained results in this work demonstrated that the developed iterative Bayesian regularized neural network (iBRANN) method in this work thoroughly detects the baselines and is superior over the CC, MPLS, airPLS and iPF techniques. A graphical user interface has been developed for the suggested algorithm and can be used for easy implementation of the iBRANN algorithm for the correction of different chromatography, NMR and Raman data sets.

Exploring the human seminal plasma proteome: an unexplored gold mine of biomarker for male infertility and male reproduction disorder

BACKGROUND

The human seminal fluid is a complex body fluid. It is not known how many proteins are expressed in the seminal plasma; however in analog with the blood it is possible up to 10,000 proteins are expressed in the seminal plasma. The human seminal fluid is a rich source of potential biomarkers for male infertility and reproduction disorder.

METHODS

In this review, the ongoing list of proteins identified from the human seminal fluid was collected. To date, 4188 redundant proteins of the seminal fluid are identified using different proteomics technology, including 2-DE, SDS-PAGE-LC-MS/MS, MudPIT. However, this was reduced to a database of 2168 non-redundant protein using UniProtKB/Swiss-Prot reviewed database.

RESULTS

The core concept of proteome were analyzed including pI, MW, Amino Acids, Chromosome and PTM distribution in the human seminal plasma proteome. Additionally, the biological process, molecular function and KEGG pathway were investigated using DAVID software. Finally, the biomarker identified in different male reproductive system disorder was investigated using proteomics platforms so far.

CONCLUSION

In this study, an attempt was made to update the human seminal plasma proteome database. Our finding showed that human seminal plasma studies used to date seem to have converged on a set of proteins that are repeatedly identified in many studies and that represent only a small fraction of the entire human seminal plasma proteome.

Fourier transform infrared spectroscopy: a potential technique for noninvasive detection of spermatogenesis

BACKGROUND

The seminal plasma is an excellent source for noninvasive detection of spermatogenesis. The seminal plasma of normospermic and azoospermic men has been analyzed for detection of spermatogenesis.

METHODS

Optical spectroscopy (Attenuated Total Reflectance-Infrared spectroscopy (ATR-IR) and Fourier Transform infrared spectroscopy (FT-IR) has been used to analyze the seminal plasma and the metabolome of seminal plasma for detection of spermatogenesis.

RESULTS

The seminal plasma of normospermic and azoospermic men has been analyzed by ATR-IR. The results show that there is a pattern variation in the azoospermic men compared to normospermic men. However, the seminal plasma is too complex to show significant pattern variation. Therefore, the metabolome which is a subcomponent of the seminal plasma was analyzed. The seminal plasma metabolome of normospermic and azoospermic men has been analyzed by FT-IR. A significant pattern change was observed. The data combined with chemometrics analysis showed that significant changes are observed at metabolome level.

CONCLUSION

We suggest that FT-IR has the potential as a diagnostic tool instead of testicular biopsy.

The Profile of Human Sperm Proteome; A Mini-review

New advances in mass spectrometry-based proteomics technology are having a major impact on our understanding of how human spermatozoa acquire their capacity for fertilization. A complete analysis of the proteins found in the human spermatozoa is essential for understanding the events leading up to, and including, fertilization and early embryo development. In this short review, we have collected the human sperm proteome from the literature and analyzed it by the Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Bioinformatics analysis demonstrated that the collected 1,300 proteins were involved in various metabolic pathways including catabolic processes. Additionally, the majority of the collected human sperm proteome belonged to cytoplasm. Application of the multi-dimensional protein identification technology (MudPIT) for obtaining a better coverage of the hydrophobic and basic proteins of the human sperm proteome is recommended.

Effects of selenite and tellurite on growth, physiology, and proteome of a moderately halophilic bacterium

We isolated a moderately halophilic bacterium with high level of tolerance to two toxic oxyanions, selenite and tellurite, from hypersaline soil in Garmsar, Iran. 16s rRNA sequence analysis revealed that the isolate, strain MAM, had 98% similarity with Halomonas elongate, and is closely related to other species of the genus Halomonas. We observed that the tolerance to tellurite and its removal increased significantly when both selenite and tellurite were added to the culture media, suggesting a positive synergism of selenite on tellurite tolerance and removal. We applied a proteomic approach to study the proteome response of Halomonas sp. strain MAM to selenite, tellurite, and selenite + tellurite. Out of approximately 800 protein spots detected on 2-DE gels, 208 spots were differentially expressed in response to at least one of treatments. Of them, 70 CBB stained spots were analyzed by MALDI TOF/TOF mass spectrometry, leading to identification of 36 proteins. Our results revealed that several mechanisms including fatty acid synthesis, energy production, cell transport, oxidative stress detoxification, DNA replication, transcription and translation contributed in bacterial response and/or adaptation. These results provided new insights into the general mechanisms on the tolerance of halophilic bacteria to these two toxic oxyanions and the use of them for bioremediation of contaminated saline soils and wastes discharge sites.

A comparative proteome approach to decipher the mechanism of rice adaptation to phosphorous deficiency

Mineral deficiency limits crop production in most soils and in Asia alone, about 50% of rice lands are phosphorous deficient. In an attempt to determine the mechanism of rice adaptation to phosphorous deficiency, changes in proteome patterns associated with phosphorous deficiency have been investigated. We analyzed the parental line Nipponbare in comparison to its near isogenic line (NIL6-4) carrying a major phosphorous uptake QTL (Pup1) on chromosome 12. Using 2-DE, the proteome pattern of roots grown under 1 and 100 microM phosphorous were compared. Out of 669 proteins reproducibly detected on root 2-DE gels, 32 proteins showed significant changes in the two genotypes. Of them, 17 proteins showed different responses in two genotypes under stress condition. MS resulted in identification of 26 proteins involved in major phosphorous deficiency adaptation pathways including reactive oxygen scavenging, citric acid cycle, signal transduction, and plant defense responses as well as proteins with unknown function. Our results highlighted a coordinated response in NIL in response to phosphorous deficiency which may confer higher adaptation to nutrient deficiency.

The hemoglobins of the trematodes Fasciola hepatica and Paramphistomum epiclitum: a molecular biological, physico-chemical, kinetic, and vaccination study

The trematode Fasciola hepatica (Fa.he.) is a common parasite of human and livestock. The hemoglobin (Hb) of Fa.he., a potential immunogen, was chosen for characterization in the search for an effective vaccine. Characterization of trematode Hbs show that they are intracellular single-domain globins with the following remarkable features: (1) Fa.he. expresses two Hb isoforms that differ at two amino acid sites (F1: 119Y/123Q; F2: 119F/123L). Both isoforms are monoacetylated at their N-termini; (2) the genes coding for Fa.he. and Paramphistomum epiclitum (Pa.ep.) Hbs are interrupted by two introns at the conserved positions B12.2 and G7.0.; (3) UV/VIS and resonance Raman spectroscopy identify the recombinant Fa.he. HbF2 as a pentacoordinated high-spin ferrous Hb; (4) electron paramagnetic resonance spectroscopy of cyano-met Fa.he. HbF2 proves that the endogenously bound imidazole has no imidazolate character; (5) the major structural determinants of the globin fold are present, they contain a TyrB10/TyrE7 residue pair on the distal side. Although such distal-site pair is a signature for high oxygen affinity, as shown for Pa.ep. Hb, the oxygen-binding rate parameters for Fa.he. Hb are intermediate between those of myoglobin and those of other trematode Hbs; (6) the three-dimensional structure of recombinant Fa.he. HbF2 from this study closely resembles the three-dimensional structure of Pa.ep. determined earlier. The set of distal-site polar interactions observed in Pa.ep. Hb is matched with small but significant structural adjustments; (7) despite the potential immunogenic character of the fluke Hb, vaccination of calves with recombinant Fa.he. HbF2 failed to promote protection against parasitic infection.

The role of the S1 binding site of carboxypeptidase M in substrate specificity and turn-over

The influence of the P1 amino acid on the substrate selectivity, the catalytic parameters K(m) and k(cat), of carboxypeptidase M (CPM) (E.C. 3.4.17.12) was systematically studied using a series of benzoyl-Xaa-Arg substrates. CPM had the highest catalytic efficiency (k(cat)/K(m)) for substrates with Met, Ala and aromatic amino acids in the penultimate position and the lowest with amino acids with branched side-chains. Substrates with Pro in P1 were not cleaved in similar conditions. The P1 substrate preference of CPM differed from that of two other members of the carboxypeptidase family, CPN (CPN/CPE subfamily) and CPB (CPA/CPB subfamily). Aromatic P1 residues discriminated most between CPM and CPN. The type of P2 residue also influenced the k(cat) and K(m) of CPM. Extending the substrate up to P7 had little effect on the catalytic parameters. The substrates were modelled in the active site of CPM. The results indicate that P1-S1 interactions play a role in substrate binding and turn-over.