Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)–based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

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What can we learn from gene expression profiling of mouse oocytes?

Reproduction ◽

10.1530/rep-07-0430 ◽

2008 ◽

Vol 135 (5) ◽

pp. 581-592 ◽

Cited By ~ 22

Author(s):

Toshio Hamatani ◽

Mitsutoshi Yamada ◽

Hidenori Akutsu ◽

Naoaki Kuji ◽

Yoshiyuki Mochimaru ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Oocyte Quality ◽

Preimplantation Development ◽

Preimplantation Embryos ◽

Gene Expressions ◽

Oocyte Competence

Mammalian ooplasm supports the preimplantation development and reprograms the introduced nucleus transferred from a somatic cell to confer pluripotency in a cloning experiment. However, the underlying molecular mechanisms of oocyte competence remain unknown. Recent advances in microarray technologies have allowed gene expression profiling of such tiny specimens as oocytes and preimplantation embryos, generating a flood of information about gene expressions. So, what can we learn from it? Here, we review the initiative global gene expression studies of mouse and/or human oocytes, focusing on the lists of maternal transcripts and their expression patterns during oogenesis and preimplantation development. Especially, the genes expressed exclusively in oocytes should contribute to the uniqueness of oocyte competence, driving mammalian development systems of oocytes and preimplantation embryos. Furthermore, we discuss future directions for oocyte gene expression profiling, including discovering biomarkers of oocyte quality and exploiting the microarray data for ‘making oocytes’.

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Prediction of Docetaxel Response in Human Breast Cancer by Gene Expression Profiling

Journal of Clinical Oncology ◽

10.1200/jco.2005.09.078 ◽

2005 ◽

Vol 23 (3) ◽

pp. 422-431 ◽

Cited By ~ 202

Author(s):

Kyoko Iwao-Koizumi ◽

Ryo Matoba ◽

Noriko Ueno ◽

Seung Jin Kim ◽

Akiko Ando ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Side Effects ◽

Gene Expression Profiling ◽

Clinical Response ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Redox System ◽

Response To Therapy

Purpose Docetaxel is one of the most effective anticancer drugs available in the treatment of breast cancer. Nearly half of the treated patients, however, do not respond to chemotherapy and suffer from side effects. The ability to reliably predict a patient's response based on tumor gene expression will improve therapeutic decision making and save patients from unnecessary side effects. Patients and Methods A total of 44 breast tumor tissues were sampled by biopsy before treatment with docetaxel, and the response to therapy was clinically evaluated by the degree of reduction in tumor size. Gene expression profiling of the biopsy samples was performed with 2,453 genes using a high-throughput reverse transcriptase polymerase chain reaction technique. Using genes differentially expressed between responders and nonresponders, a diagnostic system based on the weighted-voting algorithm was constructed. Results This system predicted the clinical response of 26 previously unanalyzed samples with over 80% accuracy, a level promising for clinical applications. Diagnostic profiles in nonresponders were characterized by elevated expression of genes controlling the cellular redox environment (ie, redox genes, such as thioredoxin, glutathione-S-transferase, and peroxiredoxin). Overexpression of these genes protected cultured mammary tumor cells from docetaxel-induced cell death, suggesting that enhancement of the redox system plays a major role in docetaxel resistance. Conclusion These results suggest that the clinical response to docetaxel can be predicted by gene expression patterns in biopsy samples. The results also suggest that one of the molecular mechanisms of the resistance is activation of a group of redox genes.

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Can molecular mechanisms be revealed by large-scale gene expression profiling?

10.1240/sav_gbm_2005_h_001156 ◽

2005 ◽

Vol 2005 (Fall) ◽

Author(s):

Zlatko Trajanoski ◽

Hubert Hackl ◽

Thomas Burkard ◽

Frank Eisenhaber

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Large Scale ◽

Molecular Mechanisms

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278: Gene Expression Profiling of Prostatic Epithelial Cells in Two-Dimensional Versus Three-Dimensional Cultures

The Journal of Urology ◽

10.1016/s0022-5347(18)30543-3 ◽

2007 ◽

Vol 177 (4S) ◽

pp. 93-93

Author(s):

Toshiyuki Tsunoda ◽

Junichi Inocuchi ◽

Darren Tyson ◽

Seiji Naito ◽

David K. Ornstein

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Three Dimensional ◽

Two Dimensional

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Identification of molecular mechanisms underlying mood stabilization through genome-wide gene expression profiling

The International Journal of Neuropsychopharmacology ◽

10.1017/s1461145705006176 ◽

2005 ◽

Vol 9 (03) ◽

pp. 263 ◽

Cited By ~ 3

Author(s):

Rulun Zhou ◽

Carlos A. Zarate ◽

Husseini K. Manji

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Genome Wide ◽

Mood Stabilization ◽

Genome Wide Gene Expression

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Three Years Follow-Up Study Showed Prenatal Methamphetamine Exposure May Cause Chronic Abnormalities In Transcriptomic Pattern

10.21203/rs.3.rs-668566/v1 ◽

2021 ◽

Author(s):

Arvin Haghighatfard ◽

Soha Seifollahi ◽

Pegah Rajabi ◽

Niloofar Rahmani ◽

Rojin Ghannadzadeh

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Expression Profiles ◽

Expression Patterns ◽

Rna Extraction ◽

Childbearing Age ◽

Methamphetamine Use ◽

Methamphetamine Use Disorder

Abstract Background: The high rate of methamphetamine use disorder among young adults and women of childbearing age makes it imperative to clarify the long-term effects of Methamphetamine exposure on the offspring. Behavioral and cognitive problems had been reported in children with parental Methamphetamine exposure (PME). The present study aimed to assess the acute and chronic effects of PME in molecular regulations and gene expression profiles of children during their first years of life.Methods: All subjects were recruited before birth, and sampling was conducted from the first ten days of birth, twelve months, twenty months, and thirty-six months of age. Finally, 2658 children with PME and 3573 normal children had been finished the follow-up. RNA extraction was operated from blood samples and gene expression profiling was conducted by using the Affymetrix GeneChip Human Genome U133 plus 2.0 Array Platform. Gene expression data were confirmed by Real-time PCR. Results: Gene expression profiling during thirty-six months showed several constant mRNA level alterations in children with PME compared with normal. These genes are involved in several gene ontologies and pathways involved with the immune system, neuronal functions, and bioenergetic metabolism. It seems that Methamphetamine use disorder before and during the pregnancy period may affect the expression profile of children, and these changes could remain years after birth. Affected genes have some similarities with the gene expression patterns of addiction, psychiatric disorders, neurodevelopmental disabilities, and immune deficiencies. Conclusion: Findings may shed light on the molecular effects of prenatal methamphetamine exposure and may lead to new psychological and somatic caring protocols for these children based on their potential abnormalities.

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Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

Neural Plasticity ◽

10.1155/2013/605079 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 11

Author(s):

Ettore Tiraboschi ◽

Ramon Guirado ◽

Dario Greco ◽

Petri Auvinen ◽

Jose Fernando Maya-Vetencourt ◽

...

Keyword(s):

Gene Expression ◽

Visual Cortex ◽

Large Scale ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Monocular Deprivation ◽

Adult Brain ◽

Gene Expression Patterns ◽

Postnatal Life ◽

Critical Periods

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

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