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Article ; Online: Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer.

Bahl, Shalini / Carroll, Jason S / Lupien, Mathieu

Cold Spring Harbor perspectives in medicine

2022 Volume 12, Issue 10

Abstract: Breast cancer presents as multiple distinct disease entities. Each tumor harbors diverse cell populations defining a phenotypic heterogeneity that impinges on our ability to treat patients. To date, efforts mainly focused on genetic variants to find ... ...

Abstract	Breast cancer presents as multiple distinct disease entities. Each tumor harbors diverse cell populations defining a phenotypic heterogeneity that impinges on our ability to treat patients. To date, efforts mainly focused on genetic variants to find drivers of inter- and intratumor phenotypic heterogeneity. However, these efforts have failed to fully capture the genetic basis of breast cancer. Through recent technological and analytical approaches, the genetic basis of phenotypes can now be decoded by characterizing chromatin variants. These variants correspond to polymorphisms in chromatin states at DNA sequences that serve a distinct role across cell populations. Here, we review the function and causes of chromatin variants as they relate to breast cancer inter- and intratumor heterogeneity and how they can guide the development of treatment alternatives to fulfill the goal of precision cancer medicine.
MeSH term(s)	Carcinogenesis ; Cell Transformation, Neoplastic ; Chromatin/genetics ; Genetic Heterogeneity ; Humans ; Neoplasms ; Precision Medicine
Chemical Substances	Chromatin
Language	English
Publishing date	2022-10-03
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	2157-1422
ISSN (online)	2157-1422
DOI	10.1101/cshperspect.a041322
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Article ; Online: Targeting LSD1 and FOXA1 in prostate cancer.

Omarjee, Soleilmane / Carroll, Jason S

Nature genetics

2020 Volume 52, Issue 10, Page(s) 1002–1003

MeSH term(s)	Chromatin ; Demethylation ; Hepatocyte Nuclear Factor 3-alpha/genetics ; Hepatocyte Nuclear Factor 3-alpha/metabolism ; Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Humans ; Male ; Prostatic Neoplasms/genetics
Chemical Substances	Chromatin ; FOXA1 protein, human ; Hepatocyte Nuclear Factor 3-alpha ; Histone Demethylases (EC 1.14.11.-)
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-020-0702-6
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Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 46: Show issues

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Article ; Online: Steroids, nuclear receptors and breast cancer. Preface.

Carroll, Jason S

Molecular and cellular endocrinology

2014 Volume 382, Issue 1, Page(s) 623

MeSH term(s)	Breast Neoplasms/metabolism ; Female ; Humans ; Receptors, Cytoplasmic and Nuclear/metabolism ; Receptors, Estrogen/metabolism ; Steroids/metabolism
Chemical Substances	Receptors, Cytoplasmic and Nuclear ; Receptors, Estrogen ; Steroids
Language	English
Publishing date	2014-01-25
Publishing country	Ireland
Document type	Editorial ; Introductory Journal Article
ZDB-ID	187438-x
ISSN	1872-8057 ; 0303-7207
ISSN (online)	1872-8057
ISSN	0303-7207
DOI	10.1016/j.mce.2013.10.004
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Zs.A 1127: Show issues

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Article: Optical image and Vickers hardness dataset for repair of 1080 steel using additive friction stir deposition of Aermet 100

Chou, Kathleen / Eff, Michael / Cox, Chase D. / Saukas, Connor / Carroll, Jason

Data in Brief. 2022 Apr., v. 41

2022

Abstract: This article presents optical images, measurements of heat affected zone depths, and peak Vickers hardness values from the heat affected zone regions of a 1080 steel plate substrate with a machined groove “flaw” repaired using additive friction stir ... ...

Abstract	This article presents optical images, measurements of heat affected zone depths, and peak Vickers hardness values from the heat affected zone regions of a 1080 steel plate substrate with a machined groove “flaw” repaired using additive friction stir deposition of Aermet 100. The deposition of Aermet 100 was performed using a L3 Meld machine with 9.525 mm (0.375 inch) square bar profile Aermet 100 feedstock rods fed through a hollow, 10.16 mm (0.4 inch) diameter, rotating tool onto a 1.02 mm thick 1080 steel plate with a machined groove “flaw” along the plate's length and bisecting the plate's width. The depth of the machined groove “flaw” ranged from 4.7625, 6.35, and 9.525 mm. The data is categorized into four groups: multi-layer builds deposited at room temperature with and without a cooling plate, 2-layer builds deposited at room temperature without a cooling plate, single-layer builds deposited at room temperature without a cooling plate, and a design of experiments for single-layer builds that varied the spindle rotation speed (RPM), travel speed (mm/min), material feed rate (mm/min), and pre-heat temperature (°C) of the deposition. The data shows the parameter conditions that achieved flaw-free consolidated repairs and the associated depth and peak Vickers hardness of the heat affected zone. Optical images of cross-sectioned deposition regions were obtained using an optical microscope with Leco Olympus DP27 macro camera, and Vickers hardness line traces were measured along the depth of the deposited and heat affected zone extending into the substrate on cross-sectioned samples using a Leco LM 247AT microhardness tester. The depth of the heat affected zone is reported as the measured average of five individual data points. Peak values for Vickers hardness for the heat affected zone decreased for pre-heated conditions at 329°C compared to builds conducted at room temperature of 21°C. This dataset provides visual characterization and associated hardness measurements of as-deposited repairs of dissimilar steel alloys. This article can be used to inform parameter selection for additive friction stir deposition of dissimilar steel materials for repair and solid-state additive manufacturing applications.
Keywords	ambient temperature ; cameras ; data collection ; feedstocks ; friction ; hardness ; heat ; light microscopes ; steel
Language	English
Dates of publication	2022-04
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2022.107862
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs.

Minshall, Nicola / Chernukhin, Igor / Carroll, Jason S / Git, Anna

BioTechniques

2021 Volume 72, Issue 1, Page(s) 21–28

Abstract: Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq ... ...

Abstract	Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq protocol (ncRNAseq), allowing the capture and sequencing of mid-sized non-coding RNAs without detriment to the coverage of coding mRNAs. This protocol is coupled with a two-step alignment: a pre-alignment to a curated non-coding genome, passing only the non-mapping reads to a standard genomic alignment. ncRNAseq correctly assigns the highest read-numbers to established abundant non-coding RNAs and correctly identifies cytosolic and nuclear enrichment of known non-coding RNAs in two cell lines.
MeSH term(s)	Gene Library ; High-Throughput Nucleotide Sequencing/methods ; RNA, Untranslated ; RNA-Seq ; Sequence Analysis, RNA/methods
Chemical Substances	RNA, Untranslated
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	48453-2
ISSN	1940-9818 ; 0736-6205
ISSN (online)	1940-9818
ISSN	0736-6205
DOI	10.2144/btn-2021-0035
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Zs.A 2435: Show issues

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Article ; Online: Optical image and Vickers hardness dataset for repair of 1080 steel using additive friction stir deposition of Aermet 100.

Chou, Kathleen / Eff, Michael / Cox, Chase D / Saukas, Connor / Carroll, Jason

Data in brief

2022 Volume 41, Page(s) 107862

Abstract: This article presents optical images, measurements of heat affected zone depths, and peak Vickers hardness values from the heat affected zone regions of a 1080 steel plate substrate with a machined groove "flaw" repaired using additive friction stir ... ...

Abstract	This article presents optical images, measurements of heat affected zone depths, and peak Vickers hardness values from the heat affected zone regions of a 1080 steel plate substrate with a machined groove "flaw" repaired using additive friction stir deposition of Aermet 100. The deposition of Aermet 100 was performed using a L3 Meld machine with 9.525 mm (0.375 inch) square bar profile Aermet 100 feedstock rods fed through a hollow, 10.16 mm (0.4 inch) diameter, rotating tool onto a 1.02 mm thick 1080 steel plate with a machined groove "flaw" along the plate's length and bisecting the plate's width. The depth of the machined groove "flaw" ranged from 4.7625, 6.35, and 9.525 mm. The data is categorized into four groups: multi-layer builds deposited at room temperature with and without a cooling plate, 2-layer builds deposited at room temperature without a cooling plate, single-layer builds deposited at room temperature without a cooling plate, and a design of experiments for single-layer builds that varied the spindle rotation speed (RPM), travel speed (mm/min), material feed rate (mm/min), and pre-heat temperature (°C) of the deposition. The data shows the parameter conditions that achieved flaw-free consolidated repairs and the associated depth and peak Vickers hardness of the heat affected zone. Optical images of cross-sectioned deposition regions were obtained using an optical microscope with Leco Olympus DP27 macro camera, and Vickers hardness line traces were measured along the depth of the deposited and heat affected zone extending into the substrate on cross-sectioned samples using a Leco LM 247AT microhardness tester. The depth of the heat affected zone is reported as the measured average of five individual data points. Peak values for Vickers hardness for the heat affected zone decreased for pre-heated conditions at 329°C compared to builds conducted at room temperature of 21°C. This dataset provides visual characterization and associated hardness measurements of as-deposited repairs of dissimilar steel alloys. This article can be used to inform parameter selection for additive friction stir deposition of dissimilar steel materials for repair and solid-state additive manufacturing applications.
Language	English
Publishing date	2022-01-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2022.107862
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Article ; Online: Peroxide-cleavable linkers for antibody-drug conjugates.

Ashman, Nicola / Bargh, Jonathan D / Walsh, Stephen J / Greenwood, Ryan D / Tiberghien, Arnaud / Carroll, Jason S / Spring, David R

Chemical communications (Cambridge, England)

2023 Volume 59, Issue 13, Page(s) 1841–1844

Abstract: Antibody-drug conjugates containing peroxide-cleavable arylboronic acid linkers are described, which target the high levels of reactive oxygen species (ROS) in cancer. The arylboronic acid linkers rapidly release a payload in the presence of hydrogen ... ...

Abstract	Antibody-drug conjugates containing peroxide-cleavable arylboronic acid linkers are described, which target the high levels of reactive oxygen species (ROS) in cancer. The arylboronic acid linkers rapidly release a payload in the presence of hydrogen peroxide, but remain stable in plasma. Anti-HER2 and PD-L1 peroxide-cleavable ADCs exhibited potent cytotoxicity
MeSH term(s)	Immunoconjugates/pharmacology ; Peroxides ; Antineoplastic Agents/pharmacology ; Hydrogen Peroxide ; Acids
Chemical Substances	Immunoconjugates ; Peroxides ; Antineoplastic Agents ; Hydrogen Peroxide (BBX060AN9V) ; Acids
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d2cc06677g
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Article ; Online: Ultrasonic fatigue of unfilled and carbon nanotube (CNT) reinforced polyetheretherketone (PEEK).

Fitzka, Michael / Schönbauer, Bernd M / Stojanovic, Viktor / Rennhofer, Harald / Lichtenegger, Helga / Carroll, Jason W / Sanaei, Niloofar / Mapkar, Javed / Mayer, Herwig

Ultrasonics

2023 Volume 138, Page(s) 107236

Abstract: Fatigue properties of polyetheretherketone (PEEK) and multiwall carbon nanotube (CNT) reinforced PEEK were investigated with the ultrasonic fatigue testing method. Lifetimes were measured in the high and very high cycle fatigue regime at resonance ... ...

Abstract	Fatigue properties of polyetheretherketone (PEEK) and multiwall carbon nanotube (CNT) reinforced PEEK were investigated with the ultrasonic fatigue testing method. Lifetimes were measured in the high and very high cycle fatigue regime at resonance frequency 19 kHz and load ratio R = -1. Pulse-pause loading served to avoid specimen self-heating and led to effective cycling frequencies in the range from several hundred Hz to about two kHz. Stress amplitude for 50 % fracture probability at 10
Language	English
Publishing date	2023-12-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	200839-7
ISSN	1874-9968 ; 0041-624X
ISSN (online)	1874-9968
ISSN	0041-624X
DOI	10.1016/j.ultras.2023.107236
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Article ; Online: Comprehensive Genomic Analysis Reveals that the Pioneering Function of FOXA1 Is Independent of Hormonal Signaling.

Glont, Silvia-E / Chernukhin, Igor / Carroll, Jason S

Cell reports

2019 Volume 26, Issue 10, Page(s) 2558–2565.e3

Abstract: Considerable work has linked hormone receptors, such as estrogen receptor-alpha (ER), with the pioneer factor FOXA1. Altered FOXA1 levels contribute to endocrine-resistant breast cancer, where it maintains ER-chromatin interactions, even in contexts in ... ...

Abstract	Considerable work has linked hormone receptors, such as estrogen receptor-alpha (ER), with the pioneer factor FOXA1. Altered FOXA1 levels contribute to endocrine-resistant breast cancer, where it maintains ER-chromatin interactions, even in contexts in which cells are refractory to ER-targeted drugs. A recent study controversially suggests that FOXA1 binding can be induced by hormonal pathways, including the estrogen-ER complex. We now show that the vast majority (>99%) of FOXA1 binding events are unaffected by steroid activation. A small number (<1%) of FOXA1 binding sites appear to be induced by estrogen, but these are created from chromatin interactions between ER binding sites and adjacent FOXA1 binding sites and do not represent genuine new FOXA1-pioneering elements. FOXA1 is therefore not regulated by estrogen and remains a bone fide pioneer factor that is entirely upstream of the ER complex.
MeSH term(s)	Animals ; Cell Line ; Genomics/methods ; Hepatocyte Nuclear Factor 3-alpha/genetics ; Humans ; MCF-7 Cells ; Rabbits ; Signal Transduction
Chemical Substances	FOXA1 protein, human ; Hepatocyte Nuclear Factor 3-alpha
Language	English
Publishing date	2019-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2019.02.036
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Article ; Online: The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer.

Hosseinzadeh, Leila / Kikhtyak, Zoya / Laven-Law, Geraldine / Pederson, Stephen M / Puiu, Caroline G / D'Santos, Clive S / Lim, Elgene / Carroll, Jason S / Tilley, Wayne D / Dwyer, Amy R / Hickey, Theresa E

Genome biology

2024 Volume 25, Issue 1, Page(s) 44

Abstract: Background: The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, ...

Abstract	Background: The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, we employ an unbiased chromatin immunoprecipitation-based proteomic technique to identify endogenous AR interacting co-regulatory proteins in ER positive and negative models of breast cancer to gain new insight into mechanisms of AR signaling in this disease. Results: The DNA-binding factor GATA3 is identified and validated as a novel AR interacting protein in breast cancer cells irrespective of ER status. AR activation by the natural ligand 5α-dihydrotestosterone (DHT) increases nuclear AR-GATA3 interactions, resulting in AR-dependent enrichment of GATA3 chromatin binding at a sub-set of genomic loci. Silencing GATA3 reduces but does not prevent AR DNA binding and transactivation of genes associated with AR/GATA3 co-occupied loci, indicating a co-regulatory role for GATA3 in AR signaling. DHT-induced AR/GATA3 binding coincides with upregulation of luminal differentiation genes, including EHF and KDM4B, established master regulators of a breast epithelial cell lineage. These findings are validated in a patient-derived xenograft model of breast cancer. Interaction between AR and GATA3 is also associated with AR-mediated growth inhibition in ER positive and ER negative breast cancer. Conclusions: AR and GATA3 interact to transcriptionally regulate luminal epithelial cell differentiation in breast cancer regardless of ER status. This interaction facilitates the tumor suppressor function of AR and mechanistically explains why AR expression is associated with less proliferative, more differentiated breast tumors and better overall survival in breast cancer.
MeSH term(s)	Female ; Humans ; Breast Neoplasms/metabolism ; Cell Line, Tumor ; Epithelial Cells/metabolism ; GATA3 Transcription Factor/genetics ; GATA3 Transcription Factor/metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics ; Phenotype ; Proteomics ; Receptors, Androgen/genetics
Chemical Substances	GATA3 protein, human ; GATA3 Transcription Factor ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; KDM4B protein, human (EC 1.14.11.-) ; Receptors, Androgen
Language	English
Publishing date	2024-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-03161-y
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