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Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues

ABSTRACT: Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues

PROVIDER: PRJNA553244 | ENA |

REPOSITORIES: ENA

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Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues

Project description:Emerging work has demonstrated that histologically normal (non-tumor) tissue adjacent to breast tumor tissue shows evidence of molecular alterations related to tumorigenesis, referred to as field cancerization effects. Although changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumor DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumor. Matched tumor, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select breast epithelial cells from normal tissues, and neoplastic cells from tumor specimens for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal breast and tumor tissue (63,271 CpG loci q < 0.01), than between ipsilateral-normal tissue and tumor (38,346 CpG loci q < 0.01). In addition, we identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). Hypomethylated loci in ipsilateral normal relative to contralateral were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3. Hypermethylated loci in ipsilateral-normal relative to contralateral-normal tissue were significantly enriched for CpG island shore regions.

2020-07-10 | GSE133985 | GEO

Ipsilateral and contralateral retinal ganglion cells express distinct genes during decussation at the optic chiasm

Project description:The retinal projection neurons, retinal ganglion cells (RGCs), can be categorized into distinct morphological and functional subtypes and by the laterality of their projections. Here, we used a new method for purifying the sparse population of ipsilaterally projecting RGCs in mouse retina from their contralaterally-projecting counterparts during embryonic development through rapid retrograde labeling followed by fluorescence-activated cell sorting (FACS). Through microarray analysis, we have uncovered the distinct molecular signatures that define and distinguish ipsilateral and contralateral RGCs during the critical period of axonal outgrowth and decussation, with over three hundred genes differentially experienced within these two cell populations. Amongst the genes upregulated in ipsilateral RGCs are many that are known to be expresed in progenitors cells and mark “immaturity," including Math5 (Atoh7), Sox2, and cyclin D2. Many of these differentially regulated genes were subsequently validated via in vivo expression analysis. Thus, the molecular signatures of ipsilateral and contralateral RGCs and the mechanisms that regulate their differentiation are more diverse than previously expected.

2016-12-05 | GSE83461 | GEO

Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to Day 14 in cattle?

Project description:This study relates to embryo-maternal interaction. The aim was to compare the transcriptome and ability of the ipsilateral and contralateral uterine horns to support preimplantation conceptus survival and growth to Day 14. Although differences in gene expression exist between the endometrium of uterine horns ipsilateral and contralateral to the CL in cattle, they do not impact conceptus survival or length between Days 7 and 14.

2018-08-15 | GSE118507 | GEO

Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between repeat breeder and normal fertile cows

Project description:We investigated differential gene expression profiles of endometrium during the mid-luteal phase of the estrous cycle between repeat breeding (RB) and normally fertilized cows using microarray analysis. Caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and normally fertile cows on Day 15 of the estrous cycle. Global gene expression profiles of these endometrial samples were analyzed with a 15K custom-made oligo-microarray in cattle. Microarray analysis revealed that 405 and 397 genes were differentially expressed in CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with normal cows. In contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with normal cows. In the analysis of whole uterine (combining the above four portions), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3, PIPOX, CNGA1 and IGG1C and down-regulation of 39 genes including CHGA, KRT35, THBS4, CPXM2 and PRF1 compared with normal cows. Our results may suggest that local regulation of molecular mechanisms in each uterine portion contributes to normal uterine physiology.

2016-05-02 | GSE79367 | GEO

mRNA expression profiling in the spinal nerve ligation model of neuropathic pain in rats

Project description:Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain This series of samples comprises of contralateral and ipsilateral L4 and L5 DRG tissue collected 4 weeks after rats underwent a L5 spinal nerve ligation (SNL) or a sham operation with no L5 spinal nerve ligation. This defines 8 groups (i) contralateral L4 DRG from the sham cohort (n=5), (ii) ipsilateral L4 DRG from sham cohort (n=5), (iii) contralateral L4 DRG from SNL cohort (n=5), (iv) ipsilateral L4 DRG from the SNL chort (n=5), (v) contralateral L5 DRG from the sham cohort (n=5), (vi) ipsilateral L5 DRG from sham cohort (n=5), (vii) contralateral L5 DRG from SNL cohort (n=5), (viii) ipsilateral L5 DRG from the SNL cohort (n=5)

2011-10-17 | E-GEOD-24982 | biostudies-arrayexpress

Epigenome analysis of primary breast cancer tumors and different types of recurrences.

Project description:Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence.

2013-12-24 | GSE44870 | GEO

Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to Day 14 in cattle?

Project description:Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to Day 14 in cattle?

| PRJNA485877 | ENA

The neuronal tyrosine kinase receptor ligand ALKAL2 mediates persistent pain

Project description:To identify putative genes that could contribute to the phenotypic plasticity of TRPV1 nociceptors in inflammation-induced sensitization, we used the Complete Freund’s Adjuvant (CFA) model of chronic inflammatory pain. Three days post intraplantar injection of CFA, ipsilateral and contralateral lumbar DRG neurons were separated, and TRPV1-pHluorin neurons were purified by FACS and analyzed through the GeneChip™ Mouse Gene 2.0 ST Array. The array analysis provided a complete expression profile of mRNA between contralateral and ipsilateral TRPV1 neurons following inflammatory insult. In inflammatory condition, we found >100 genes to be up or down regulated in TRPV1 neurons.

2022-04-22 | GSE201227 | GEO

Reinnervation of rat muscle

Project description:Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks. All experiments were performed under Ketanest (ketamine hydrochloride, Essex Pharma GmbH, Munich, Germany; 100 mg/kg) and Rompun (xylazine hydrochloride, Bayer, Leverkusen, Germany; 10 mg/kg) anesthesia. Both substances were injected intraperitoneally. RNA was extracted from the ipsilateral and contralateral tibialis anterior muscles of each animal. The gene array analysis compared the ipsilateral muscle with the contralateral muscle of each animal. Keywords: parallel sample

2005-04-28 | GSE2566 | GEO

Acute STING signaling from microglia and peripheral white blood cells drive neutrophil infiltration influencing brain injury

Project description:To investigate transcriptomic changes 2 hours after injury in mice ablating STING in microglia after brain injury We then performed gene expression profiling analysis using data obtained from RNA-seq of ipsilateral and contralateral cortices.

2024-01-26 | GSE223784 | GEO

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