Human Spermatozoa Quantitative Proteomic Signature Classifies Normo- and Asthenozoospermia.

Scarcely understood defects lead to asthenozoospermia, which results in poor fertility outcomes. Incomplete knowledge of these defects hinders the development of new therapies and reliance on interventional therapies, such as in vitro fertilization, increases. Sperm cells, being transcriptionally and translationally silent, necessitate the proteomic approach to study the sperm function. We have performed a differential proteomics analysis of human sperm and seminal plasma and identified and quantified 667 proteins in sperm and 429 proteins in seminal plasma data set, which were used for further analysis. Statistical and mathematical analysis combined with pathway analysis and self-organizing maps clustering and correlation was performed on the data set.It was found that sperm proteomic signature combined with statistical analysis as opposed to the seminal plasma proteomic signature can differentiate the normozoospermic versus the asthenozoospermic sperm samples. This is despite the results that some of the seminal plasma proteins have big fold changes among classes but they fall short of statistical significance. S-Plot of the sperm proteomic data set generated some high confidence targets, which might be implicated in sperm motility pathways. These proteins also had the area under the curve value of 0.9 or 1 in ROC curve analysis.Various pathways were either enriched in these proteomic data sets by pathway analysis or they were searched by their constituent proteins. Some of these pathways were axoneme activation and focal adhesion assembly, glycolysis, gluconeogenesis, cellular response to stress and nucleosome assembly among others. The mass spectrometric data is available via ProteomeXchange with identifier PXD004098.

Recycling factors for ribosome disassembly in the apicoplast and mitochondrion of Plasmodium falciparum.

The reduced genomes of the apicoplast and mitochondrion of the malaria parasite Plasmodium falciparum are actively translated and antibiotic-mediated translation inhibition is detrimental to parasite survival. In order to understand recycling of organellar ribosomes, a critical step in protein translation, we identified ribosome recycling factors (RRF) encoded by the parasite nuclear genome. Targeting of PfRRF1 and PfRRF2 to the apicoplast and mitochondrion respectively was established by localization of leader sequence-GFP fusions. Unlike any RRF characterized thus far, PfRRF2 formed dimers with disulphide interaction(s) and additionally localized in the cytoplasm, thus suggesting adjunct functions for the factor. PfRRF1 carries a large 108-amino-acid insertion in the functionally critical hinge region between the head and tail domains of the protein, yet complemented Escherichia coli RRF in the LJ14frr(ts) mutant and disassembled surrogate E. coli 70S ribosomes in the presence of apicoplast-targeted EF-G. Recombinant PfRRF2 bound E. coli ribosomes and could split monosomes in the presence of the relevant mitochondrial EF-G but failed to complement the LJ14frr(ts) mutant. Although proteins comprising subunits of P. falciparum organellar ribosomes are predicted to differ from bacterial and mitoribosomal counterparts, our results indicate that the essential interactions required for recycling are conserved in parasite organelles.

Dichotomy of complement system: Tumorigenesis or destruction.

Complement system proteins, their regulators and endpoint effector complex significantly promote tumor growth by upregulation of oncogenic growth factors, activation of mitogenic signalling pathways and breakage of normal cell cycle. Contrastingly, complement cascades, initiated by anti-tumor therapeutic antibodies, also play a pivotal role in therapy response. This contradictory role of complement system possibly be a very crucial factor for the outcomes of antibody mediated immunotherapies. Herein, we reviewed the twin role of the complement system in cancer and also the genetic variations in complement system genes. Future studies should be focused on the biomarker discovery for the personalised cancer immunotherapies.

Proteomic analyses reveal lower expression of TEX40 and ATP6V0A2 proteins related to calcium ion entry and acrosomal acidification in asthenozoospermic males.

AIMS: Idiopathic nature of male infertility disorder needs to be investigated by different horizons of molecular biology for its treatment and to device male contraceptive. Further, it can also aid in advancement of assisted reproductive technology (ART), as nowadays the failure and disquiets of ART are consistent. Herein, we have attempted to find out proteins responsible for male infertility by comparing proteome profile of sperms collected from normal control and asthenozoospermic (AS) males. MAIN METHODS: Differential proteome profiles were studied by 2-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry. The confirmation of proteome profiling results was done by western blotting and ELISA. Quantitative reverse-transcription-PCR was also performed in an independent cohort of AS and normal individuals to investigate the transcriptional regulation of proteins. KEY FINDINGS: Although seven differentially regulated proteins were identified, highpoints of the study were two proteins, TEX40 and ATP6V0A2. Lower expression of a crucial sperm motility related protein, TEX40 is reported for the first time in clinically diagnosed AS males in the present investigation. Most likely with reference to previous findings the down regulation of TEX40 leads to fewer entries of calcium ions in the sperm and lower expression of ATP6V0A2 is responsible for acrosomal de-acidification. SIGNIFICANCE: Conclusively, the down regulation of these two proteins in AS males might result in diminished sperm motility. The findings can be worthwhile for male contraception and ART management besides their use for male infertility therapy.

Proteomics in clinical interventions: achievements and limitations in biomarker development.

Development of toxicological and clinical biomarkers for disease diagnosis, quantification of toxicant/drug responses and rapid patient care are major concerns in modern biology. Even after human genome sequencing, identification of specific molecular signatures for unambiguous correlation with toxicity and clinical interventions is a challenging task. Differential protein expression patterns and protein-protein interaction studies have started unraveling rigorous molecular explanation of multi-factorial and toxicant borne diseases. Proteome profiling is extensively used to investigate etiology of diseases, develop predictive biomarkers for toxicity and therapeutic interventions and potential strategies for treatment of complex and toxicant mediated diseases. In this review, achievements and limitations of proteomics in developing predictive biomarkers for toxicological and clinical interventions have been discussed.

Identification of differentially expressed proteins in striatum of maneb-and paraquat-induced Parkinson's disease phenotype in mouse.

Behavioral, phenotypic and biochemical changes induced by maneb+paraquat (MB+PQ) in experimental animals have shown their role in the etiologies of Parkinson's disease (PD); however, MB+PQ induced neuronal damage at genome and proteome level have not yet been clearly understood. The present study was undertaken to investigate the differential protein expression patterns in control and MB+PQ treated mouse striatum and to identify differentially expressed proteins. Animals were treated with and without MB+PQ, twice a week for three, six and nine weeks and proteome profiles of striatum were compared. Three differentially expressed proteins were identified as complexin-I, alpha-enolase and glia maturation factor-beta (GMF-beta) using 2D-PAGE and mass spectrometry. The differential expressions were also confirmed at transcription level by semi-quantitative RT-PCR. The results suggest the involvement of complexin-I, alpha-enolase and GMF-beta in MB+PQ induced PD phenotype in mouse.

Multi-omics and male infertility: status, integration and future prospects.

Within the cell, gene expression analysis is the key to gain information about  different cellular and physiological events. The multifaceted route of fertilization is a combination of different processes, which include production, maturation and ejaculation of the sperm, its travel through the female genital tract, followed by the ultimate fusion of the fertile sperm with the egg. Early embryogenesis and gametogenesis as well as gene expression at tissue level and global gene silencing are under different levels of stringent epigenetic checks. Moreover, transcriptome (expressed segment of the genome in form of RNA) and the proteome (expressed set of genomic proteins) contribute uniformly to the overall cellular gene expression. In both normal and pathophysiological environments, this gene expression is altered across various levels viz., genome variations, post-transcriptional modifications, protein expression and post translational modifications. Consequently, more informative conclusions can be drawn through a new 'omics' approach of system biology, which takes into account all the genomics, epigenomics, proteomics, and metabolomics findings under one roof, thus computing the alterations in all the entities (genes, proteins, metabolites) concurrently.

Identification of differentially displayed proteins in cerebrospinal fluid of Parkinson's disease patients: a proteomic approach.

BACKGROUND: Clinical proteomics has been widely used to identify differentially displayed proteins in blood and cerebrospinal fluid (CSF) to understand the molecular and cellular events leading to Parkinson's disease (PD). The close connection between CSF and the brain offers reliable and reproducible way to assess the majority of changes in the brain proteome profile directly into CSF throughout the course of neurodegeneration. METHODS: We identified the differentially displayed proteins in CSF of PD patients as compared with controls using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry. RESULTS: Comparative 2-D PAGE electrophoretograms of CSF of PD patients with case controls and/or neurological controls revealed significant differential display of six protein spots. The differentially displayed proteins were identified as serum albumin precursor, serum albumin chain-A, hemoglobin beta fragment, mutant globin, proline rich repeat 14 (PRR 14) and serum transferrin N-terminal lobe. Although the level of hemoglobin beta fragment and mutant globin was attenuated, serum albumin precursor, serum albumin chain-A, PRR 14 and serum transferrin N-terminal lobe were augmented in PD patients as compared with case controls. The level of serum albumin chain-A, PRR 14 and serum transferrin N-terminal lobe was not significantly altered when compared with neurological controls. CONCLUSIONS: The results obtained thus suggest that differential display of CSF serum albumin precursor, serum albumin chain-A, PRR 14 and serum transferrin N-terminal lobe could be associated with neuronal dysfunction and hemoglobin/globin with the onset/progression of PD in humans.

A study on the association of cytochrome-P450 1A1 polymorphism and breast cancer risk in north Indian women.

Cytochrome P-450 1A1 (CYP1A1) is involved in the 2-hydroxylation of estrogens and mammary carcinogens into 2-hydroxy catechol metabolites. Many commonly occurring single nucleotide polymorphism (SNP) are reported in CYP1A1 in various populations that include, isoleucine to valine substitution at 462 codon in heme binding region in exon 7 (A to G transition at position 2455; M2), threonine to asparagine substitution at codon 461 (C to A transversion at position 2453; M4), T to C transition at 3801 position (M1) and T to C transition at position 3205 (M3) in 3' non-coding region. Epidemiological studies have shown inconsistent patterns between CYP1A1 polymorphism and breast cancer risk among various populations. Most of the studies have shown significant association between CYP1A1 genotype polymorphism and breast cancer risk. The present investigation was therefore undertaken to investigate the association of M1, M2, M3 and M4 polymorphisms and their subsequent contribution in premenopausal and postmenopausal women with breast cancer risk in north Indian women. Genomic DNA was isolated from case controls and breast cancer patients, specific segments of genomic DNA were amplified and restriction fragment length polymorphism (RFLP) was performed. CYP1A1 expression and catalytic activity were also assessed in premenopausal and postmenopausal case controls and patients. Polymorphism at M1, M2 and M4 alleles was detected and odds ratio for W/M1 and M1/M1 was calculated as 1.07 (95% CI, 0.59-1.87) and 0.74 (95% CI, 0.28-1.96) respectively. Odds ratio for W/M1 and M1/M1 alleles in premenopausal and postmenopausal women was 1.09 (95% CI, 0.45-2.49)/0.62 (95% CI, 0.10-2.66) and 1.60 (95% CI, 0.60-4.22)/1.06 (95% CI, 0.22-7.33) respectively. Odds ratio for W/M4 and M4/M4 allele was 1.20 (95% CI, 0.65-2.24)/4.55 (95% CI, 0.44-226.2) and 0.96 (95% CI, 0.36-2.64)/4.51 (95% CI, 0.23-273.0) respectively in total and premenopausal women. In postmenopausal women odds ratio was calculated as 1.16 (95% CI, 0.45-2.94) for M4/W but it could not be detected for M4/M4 since this genotype was not found in any postmenopausal case controls. Odds ratio for W/M2 genotype was calculated 0.57 (95% CI, 0.28-1.02), 1.06 (95% CI, 0.40-2.47) and 0.33 (95% CI, 0.12-0.89) respectively for total, premenopausal and postmenopausal women, however, in any group the odds ratio for M2/M2 could not be detected as M2/M2 genotype was not found in breast cancer patients. Polymorphism at M1 and M4 alleles was not found significantly associated with breast cancer risk and only wild type genotype was found in case controls and patients for M3 allele. Lack of protective association between CYP1A1 M2 genotype was also observed, however, in postmenopausal women a significant protective association with breast cancer risk was found (odds ratio, 0.33; 95% CI, 0.12-0.89; P-value 0.03). Similarly, no significant alteration in CYP1A1 expression and catalytic activity was observed in wild type and variant genotypes both in premenopausal and postmenopausal patients as compared with their respective controls. The results obtained from the present investigation thus suggest that probably CYP1A1 (M1, M2, M3, and M4) polymorphism alone does not play a significant role in the breast cancer risk in north Indian women.