scholarly journals Microarray technology offers a novel tool for the diagnosis and identification of therapeutic targets for male infertility

Reproduction ◽  
2006 ◽  
Vol 132 (1) ◽  
pp. 11-19 ◽  
Author(s):  
Zuping He ◽  
Wai-Yee Chan ◽  
Martin Dym
Keyword(s):  
Environmental Factors ◽  
Male Infertility ◽  
Expression Patterns ◽  
Environmental Pollutants ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Microarray Technology ◽  
Therapy Targets ◽  
Differential Gene

Male infertility is now a major reproductive health problem because of an increasing number of environmental pollutants and chemicals, which eventually result in gene mutations. Genetic alterations caused by environmental factors account for a significant percentage of male infertility. Microarray technology is a powerful tool capable of measuring simultaneously the expression of thousands of genes expressed in a single sample. Eventually, advances in genetic technology will allow for the diagnosis of patients with male infertility due to congenital reasons or environmental factors. Since its introduction in 1994, microarray technology has made significant advances in the identification and characterization of novel or known genes possibly correlated with male infertility in mice, as well as in humans. This provides a rational basis for the application of microarray to establishing molecular signatures for the diagnosis and gene therapy targets of male infertility. In this review, the differential gene expression patterns characterized by microarray in germ and somatic cells at different steps of development or in response to stimuli, as well as a number of novel or known genes identified to be associated with male infertility in mice and humans, are addressed. Moreover, issues pertaining to measurement reproducibility are highlighted for the application of microarray data to male infertility.

scholarly journals Updates on the Role of Molecular Alterations and NOTCH Signaling in the Development of Neuroendocrine Neoplasms

2019 ◽  
Author(s):  
Claudia von Arx ◽  
Monica Capozzi ◽  
Elena López-Jiménez ◽  
Alessandro Ottaiano ◽  
Fabiana Tatangelo ◽  
...  
Keyword(s):  
Notch Signaling ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Gene Mutations ◽  
Notch Signaling Pathway ◽  
Genetic Alterations ◽  
Neuroendocrine Cells ◽  
Neuroendocrine Neoplasms ◽  
Therapeutic Implications ◽  
Molecular Alterations

Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies mainly originated from hormones secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout MEN-1 gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development. Other molecular mechanisms, such as the NOTCH signaling pathway, have shown to play an important role in the pathogenesis of NENs. NOTCH receptors are expressed on neuroendocrine cells and generally, act as tumour suppressor proteins, but in some contexts can function as oncogenes. The biological heterogeneity of NENs suggests that to fully understand the roles and the potential therapeutic implications of gene mutations and NOTCH signaling in NENs, a comprehensive analysis of genetic alterations, NOTCH expression patterns and their potential roles across all NEN subtypes is required.

scholarly journals MSF: Modulated Sub-graph Finder

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1346
Author(s):  
Mariam R. Farman ◽  
Ivo L. Hofacker ◽  
Fabian Amman
Keyword(s):  
Expression Patterns ◽  
Differentially Expressed Gene ◽  
Data Interpretation ◽  
Differentially Expressed ◽  
Novel Approach ◽  
Differential Gene ◽  
External Stimuli ◽  
Flow Of Information

High throughput techniques such as RNA-seq or microarray analysis have proven tobe invaluable for the characterization of global transcriptional gene activity changesdue to external stimuli or diseases. Differential gene expression analysis (DGEA) is the first step in the course of data interpretation, typically producing lists of dozens to thousands of differentially expressed genes. To further guide the interpretation of these lists, different pathway analysis approaches have been developed. These tools typically rely on the classification of genes into sets of genes, such as pathways, based on the interactions between the genes and their function in a common biological process. Regardless of technical differences, these methods do not properly account for cross talk between different pathways and rely on binary separation into differentially expressed gene and unaffected genes based on an arbitrarily set p-value cut-off. To overcome this limitation, we developed a novel approach to identify concertedly modulated sub-graphs in the global cell signaling network, based on the DGEA results of all genes tested. To this end, expression patterns of genes are integrated according to the topology of their interactions and allow potentially to read the flow of information and identify the effectors. The described software, named Modulated Sub-graph Finder (MSF) is freely available at https://github.com/Modulated-Subgraph-Finder/MSF.

scholarly journals Correlation between the aberrant human testicular germ-cell gene expression and disruption of spermatogenesis leading to male infertility

2018 ◽  
Author(s):  
Arka Baksi ◽  
Ruchi Jain ◽  
Ravi Manjithaya ◽  
S S Vasan ◽  
Paturu Kondaiah ◽  
...  
Keyword(s):  
Gene Expression ◽  
Male Infertility ◽  
Differential Gene Expression ◽  
Germ Cells ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Obstructive Azoospermia ◽  
Sperm Retrieval ◽  
Testicular Germ Cell ◽  
Differential Gene

AbstractSpermatogenesis is characterized by sequential gene-expression at precise stages in progression of differentiation of the germ cells. Any alteration in expression of the critical genes is responsible for arrest of spermatogenesis associated with infertility. Inspite of advances the differential gene expression accompanying spermatogenesis, the corresponding regulatory mechanisms and their correlation to human infertility have not been clearly established. This study aims to identify the gene expression pattern of the human testicular germ cells from the patients either with obstructive azoospermia with complete intra-testicular spermatogenesis or non-obstructive azoospermia with spermatogenesis arrested at different stages and correlate the same to infertility. The testicular transcriptomes of 3 OA and 8 NOA patients and pooled testicular RNA (commercial source) were analyzed for their differential gene expression to identify potential regulators of spermatogenesis and the results were further validated in all of the 44 patients clinically diagnosed with azoospermia undergoing sperm retrieval surgery over the study period and 4 control samples included in this study. Analyses of the differential transcriptome led to identification of genes enriched in a specific testicular cell type and subsequently, several regulators of the diploid-double-diploid-haploid transitions in the human spermatogenesis were identified. Perturbations in the expression of these genes were identified as the potential causes of the spermatogenic arrest seen in azoospermia and thus the potential mediators of human male infertility. Another interesting observation was the increased autophagy in the testes of patients with non-obstructive azoospermia. The present study suggests that the regulation of the diploid-double-diploid-haploid transition is multigenic with the tandem alteration of several genes resulting in infertility. In conclusion, this study identified some of the genetic regulators controlling spermatogenesis using comparative transcriptome analyses of testicular tissues from azoospremic individuals and showed how alterations in several genes results in disruption of spermatogenesis and subsequent infertility. This study also provides interesting insights into the gene expression patterns of the Indian population that were not available earlier.

scholarly journals Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms

2019 ◽  
Vol 8 (9) ◽  
pp. 1277 ◽  
Author(s):  
Claudia von Arx ◽  
Monica Capozzi ◽  
Elena López-Jiménez ◽  
Alessandro Ottaiano ◽  
Fabiana Tatangelo ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Notch Signalling ◽  
Neuroendocrine Cells ◽  
Neuroendocrine Neoplasms ◽  
Therapeutic Implications ◽  
Molecular Alterations

Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies, mainly originating from hormone-secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout the multiple endocrine neoplasia type 1 (MEN-1) gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development. Other molecular mechanisms, such as the NOTCH signalling pathway, have shown to play an important role in the pathogenesis of NENs. NOTCH receptors are expressed on neuroendocrine cells and generally act as tumour suppressor proteins, but in some contexts can function as oncogenes. The biological heterogeneity of NENs suggests that to fully understand the role and the potential therapeutic implications of gene mutations and NOTCH signalling in NENs, a comprehensive analysis of genetic alterations, NOTCH expression patterns and their potential role across all NEN subtypes is required.

Implication of the Molecular Characterization of Acute Myeloid Leukemia

Hematology ◽  
2007 ◽  
Vol 2007 (1) ◽  
pp. 412-419 ◽  
Author(s):  
Hartmut Döhner
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Molecular Genetic ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Molecular Alterations ◽  
Binding Factor ◽  
Molecular Therapies ◽  
Acute Myeloid

AbstractThe identification of molecular genetic alterations such as gene mutations or deregulated gene expression in acute myeloid leukemia (AML) has greatly advanced our understanding of leukemogenesis. These markers now allow us to unravel the enormous heterogeneity seen within cytogenetically defined subgroups of AML. Furthermore, the molecular alterations are providing targets for molecular therapies. In this article, major molecular findings of prognostic and predictive significance are reviewed, with an emphasis on the discussion of gene mutations found in two major AML subgroups, cytogenetically normal and core-binding factor AML.

Characterization of the SIRT genes and their distinct expression patterns in Manila clams (Ruditapes philippinarum) exposed to air

Meta Gene ◽  
2021 ◽  
Vol 28 ◽  
pp. 100892
Author(s):  
Jingtian Wang ◽  
He Zhang ◽  
Shuang Xu ◽  
Ze Liu ◽  
Lu Yang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Ruditapes Philippinarum

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

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