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Article ; Online: Chromatin Immunoprecipitation Assay for Analyzing Transcription Factor Activity at the Level of Peripheral Myelin Gene Promoters.

Makoukji, Joelle

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2011, Page(s) 647–658

Abstract: Disruption of epigenetic regulators of transcription is a central mechanism of oncogenesis. Differential gene expression is facilitated by transcriptional regulatory mechanisms and chromatin modifications through DNA-protein interactions. One of the ... ...

Abstract	Disruption of epigenetic regulators of transcription is a central mechanism of oncogenesis. Differential gene expression is facilitated by transcriptional regulatory mechanisms and chromatin modifications through DNA-protein interactions. One of the widely used assays to study this is chromatin immunoprecipitation (ChIP) assay, which enables the analysis of association between regulatory molecules, specific promoters, and histone modifications within the context of the cell. This is of immense value as ChIP assays can provide a glimpse of the regulatory mechanisms involved in gene expression in vivo. It is also a powerful technique for analyzing histone modifications as well as binding sites for proteins that bind either directly or indirectly to DNA. The basic steps in this protocol are fixation, sonication, immunoprecipitation, and analysis of the immunoprecipitated DNA. Although ChIP is a versatile tool, this procedure requires the optimization of the various reaction conditions. Here, we present a detailed application of the ChIP assay to study the differential recruitment of transcriptional factors at the level of peripheral myelin gene promoters.
MeSH term(s)	Animals ; Base Sequence ; Binding Sites ; Cell Line ; Chromatin Immunoprecipitation/methods ; Gene Expression Regulation ; Mice ; Myelin Sheath/genetics ; Myelin Sheath/metabolism ; Nucleotide Motifs ; Promoter Regions, Genetic ; Protein Binding ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2019-07-04
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9554-7_37
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Corrigendum to "Differential regulation of Wnt/beta-catenin signaling by Liver X Receptors in Schwann cells and oligodendrocytes" [Biochem. Pharmacol. 86 (2013) 106-114].

Shackleford, Ghjuvan'Ghjacumu / Makoukji, Joelle / Grenier, Julien / Liere, Philippe / Meffre, Delphine / Massaad, Charbel

Biochemical pharmacology

2020 Volume 175, Page(s) 113892

Language	English
Publishing date	2020-03-07
Publishing country	England
Document type	Published Erratum
ZDB-ID	208787-x
ISSN	1873-2968 ; 0006-2952
ISSN (online)	1873-2968
ISSN	0006-2952
DOI	10.1016/j.bcp.2020.113892
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Article ; Online: Sex differences in gene expression with galactosylceramide treatment in Cln3Δex7/8 mice.

Makoukji, Joelle / El-Sitt, Sally / Makhoul, Nadine J / Soueid, Jihane / Kadara, Humam / Boustany, Rose-Mary

PloS one

2020 Volume 15, Issue 10, Page(s) e0239537

Abstract: Background: CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease.: Methods: Differential gene expression in vehicle-exposed mouse brain ...

Abstract	Background: CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease. Methods: Differential gene expression in vehicle-exposed mouse brain was determined after intraperitoneal vehicle/Galactosylceramide (GalCer) injections for 40 weeks with GeneChip Mouse Genome 430 2.0 arrays. Results: Analysis identified 66 genes in male and 30 in female brains differentially expressed in GalCer-treated versus vehicle-exposed Cln3Δex7/8 mice. Gene ontology revealed aberrations of biological function including developmental, cellular, and behavioral processes. GalCer treatment altered pathways of long-term potentiation/depression, estrogen signaling, synaptic vesicle cycle, ErbB signaling, and prion diseases in males, but prolactin signaling, selenium compound metabolism and steroid biosynthesis in females. Gene-gene network analysis highlighted networks functionally pertinent to GalCer treatment encompassing motor dysfunction, neurodegeneration, memory disorder, inflammation and astrogliosis in males, and, cataracts, inflammation, astrogliosis, and anxiety in females. Conclusions: This study sheds light on global expression patterns following GalCer treatment of Cln3Δex7/8 mice. Understanding molecular effects of GalCer on mouse brain gene expression, paves the way for personalized strategies for treating this debilitating disease in humans.
MeSH term(s)	Animals ; Brain/drug effects ; Brain/metabolism ; Female ; Galactosylceramides/pharmacology ; Gene Expression Regulation/drug effects ; Gene Ontology ; Male ; Membrane Glycoproteins/genetics ; Mice ; Molecular Chaperones/genetics ; Oligonucleotide Array Sequence Analysis ; Sex Characteristics
Chemical Substances	CLN3 protein, mouse ; Galactosylceramides ; Membrane Glycoproteins ; Molecular Chaperones
Language	English
Publishing date	2020-10-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0239537
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exogenous Flupirtine as Potential Treatment for CLN3 Disease.

Maalouf, Katia / Makoukji, Joelle / Saab, Sara / Makhoul, Nadine J / Carmona, Angelica V / Kinarivala, Nihar / Ghanem, Noël / Trippier, Paul C / Boustany, Rose-Mary

Cells

2020 Volume 9, Issue 8

Abstract: CLN3 disease is a fatal neurodegenerative disorder affecting children. Hallmarks include brain atrophy, accelerated neuronal apoptosis, and ceramide elevation. Treatment regimens are supportive, highlighting the importance of novel, disease-modifying ... ...

Abstract	CLN3 disease is a fatal neurodegenerative disorder affecting children. Hallmarks include brain atrophy, accelerated neuronal apoptosis, and ceramide elevation. Treatment regimens are supportive, highlighting the importance of novel, disease-modifying drugs. Flupirtine and its new allyl carbamate derivative (compound 6) confer neuroprotective effects in CLN3-deficient cells. This study lays the groundwork for investigating beneficial effects in
MeSH term(s)	Aminopyridines/pharmacology ; Animals ; Apoptosis/drug effects ; Ceramides/metabolism ; Corticosterone/metabolism ; Female ; Gliosis/metabolism ; Immunoassay ; Immunohistochemistry ; Learning/drug effects ; Male ; Membrane Glycoproteins/genetics ; Membrane Glycoproteins/metabolism ; Memory/drug effects ; Mice ; Mice, Inbred C57BL ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Real-Time Polymerase Chain Reaction
Chemical Substances	Aminopyridines ; CLN3 protein, mouse ; Ceramides ; Membrane Glycoproteins ; Molecular Chaperones ; flupirtine (MOH3ET196H) ; Corticosterone (W980KJ009P)
Language	English
Publishing date	2020-08-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells9081872
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Article: Developmental Comparison of Ceramide in Wild-Type and

El-Sitt, Sally / Soueid, Jihane / Al Ali, Jamal / Makoukji, Joelle / Makhoul, Nadine J / Harati, Hayat / Boustany, Rose-Mary

Frontiers in neurology

2019 Volume 10, Page(s) 128

Abstract: CLN3 disease is a neurodevelopmental disease leading to early visual failure, motor decline, and death. CLN3 pathogenesis has been linked to dysregulation of ceramide, a key intracellular messenger impacting various biological functions. Ceramide is ... ...

Abstract	CLN3 disease is a neurodevelopmental disease leading to early visual failure, motor decline, and death. CLN3 pathogenesis has been linked to dysregulation of ceramide, a key intracellular messenger impacting various biological functions. Ceramide is upregulated in brains of CLN3 patients and activates apoptosis. Ceramide levels over the lifespan of WT and
Language	English
Publishing date	2019-02-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2019.00128
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Article ; Online: A Signature of Four Circulating microRNAs as Potential Biomarkers for Diagnosing Early-Stage Breast Cancer.

Itani, Maha M / Nassar, Farah J / Tfayli, Arafat H / Talhouk, Rabih S / Chamandi, Ghada K / Itani, Abdul Rahman S / Makoukji, Joelle / Boustany, Rose-Mary N / Hou, Lifang / Zgheib, Nathalie K / Nasr, Rihab R

International journal of molecular sciences

2021 Volume 22, Issue 11

Abstract: Breast cancer (BC) is the most predominant type of cancer among women. The aim of this study is to find new biomarkers that can help in early detection of BC, especially for those who are too young to be screened using mammography as per guidelines. ... ...

Abstract	Breast cancer (BC) is the most predominant type of cancer among women. The aim of this study is to find new biomarkers that can help in early detection of BC, especially for those who are too young to be screened using mammography as per guidelines. Using microRNA microarray, we previously showed dysregulation of 74 microRNAs in tumors from early BC patients as compared with normal adjacent tissues, which we were interested in studying in blood circulation. In this study, we investigated the expression of 12 microRNA (miR-21/miR-155/miR-23a/miR-130a/miR-145/miR-425-5p/miR-139-5p/miR-451/miR-195/miR-125b/miR-100, and miR-182) in the plasma of 41 newly diagnosed Lebanese BC patients with early invasive ductal carcinoma as compared with 32 healthy controls. Total RNA was extracted from plasma, and expression levels of miRNA of interest were measured using RT-qPCR followed by statistical analysis; miR-21, miR-155, miR-23a, miR-130a, miR-145, miR-425-5p, and miR-139-5p were significantly upregulated and miR-451 was significantly downregulated, in the plasma of BC patients as compared with healthy controls. The positively correlated miR-23a, miR-21, and miR-130a had a high diagnostic accuracy (86%). Importantly, the combination of miR-145/miR-425-5p/miR-139-5p/miR-130a scored the highest diagnostic accuracy of 95% with AUC = 0.97 (sensitivity 97% and specificity 91%). MicroRNAs are promising non-invasive diagnostic biomarkers for early-stage BC with the panel of miR-145/miR-425-5p/miR-139-5p/miR-130a having the highest diagnostic accuracy.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Breast Neoplasms/blood ; Breast Neoplasms/diagnosis ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Circulating MicroRNA/blood ; Circulating MicroRNA/genetics ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Middle Aged ; Neoplasm Staging ; Statistics, Nonparametric ; Young Adult
Chemical Substances	Biomarkers, Tumor ; Circulating MicroRNA
Language	English
Publishing date	2021-06-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22116121
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Article ; Online: LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population.

Awada, Zainab / Bouaoun, Liacine / Nasr, Rihab / Tfayli, Arafat / Cuenin, Cyrille / Akika, Reem / Boustany, Rose-Mary / Makoukji, Joelle / Tamim, Hani / Zgheib, Nathalie K / Ghantous, Akram

Environmental research

2021 Volume 197, Page(s) 111094

Abstract: Introduction: Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, ... ...

Abstract	Introduction: Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures. Purpose: We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)]. Methods: This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk. Results: In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = -0.04 [-0.07, -0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10 Conclusion: This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.
MeSH term(s)	Amino Acid Transport System ASC ; Body Mass Index ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Cross-Sectional Studies ; DNA Methylation ; Female ; Humans ; Long Interspersed Nucleotide Elements/genetics ; Minor Histocompatibility Antigens ; Pilot Projects ; Vesicular Transport Proteins
Chemical Substances	Amino Acid Transport System ASC ; Minor Histocompatibility Antigens ; SLC1A5 protein, human ; TXLNA protein, human ; Vesicular Transport Proteins
Language	English
Publishing date	2021-04-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2021.111094
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Sex differences in gene expression with galactosylceramide treatment in Cln3Δex7/8 mice.

Joelle Makoukji / Sally El-Sitt / Nadine J Makhoul / Jihane Soueid / Humam Kadara / Rose-Mary Boustany

PLoS ONE, Vol 15, Iss 10, p e

2020 Volume 0239537

Abstract: Background CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease. Methods Differential gene expression in vehicle-exposed mouse brain was ... ...

Abstract	Background CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease. Methods Differential gene expression in vehicle-exposed mouse brain was determined after intraperitoneal vehicle/Galactosylceramide (GalCer) injections for 40 weeks with GeneChip Mouse Genome 430 2.0 arrays. Results Analysis identified 66 genes in male and 30 in female brains differentially expressed in GalCer-treated versus vehicle-exposed Cln3Δex7/8 mice. Gene ontology revealed aberrations of biological function including developmental, cellular, and behavioral processes. GalCer treatment altered pathways of long-term potentiation/depression, estrogen signaling, synaptic vesicle cycle, ErbB signaling, and prion diseases in males, but prolactin signaling, selenium compound metabolism and steroid biosynthesis in females. Gene-gene network analysis highlighted networks functionally pertinent to GalCer treatment encompassing motor dysfunction, neurodegeneration, memory disorder, inflammation and astrogliosis in males, and, cataracts, inflammation, astrogliosis, and anxiety in females. Conclusions This study sheds light on global expression patterns following GalCer treatment of Cln3Δex7/8 mice. Understanding molecular effects of GalCer on mouse brain gene expression, paves the way for personalized strategies for treating this debilitating disease in humans.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sex differences in gene expression with galactosylceramide treatment in Cln3Δex7/8 mice

Joelle Makoukji / Sally El-Sitt / Nadine J. Makhoul / Jihane Soueid / Humam Kadara / Rose-Mary Boustany / Francisco J. Esteban

PLoS ONE, Vol 15, Iss

2020 Volume 10

Abstract	Background CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease. Methods Differential gene expression in vehicle-exposed mouse brain was determined after intraperitoneal vehicle/Galactosylceramide (GalCer) injections for 40 weeks with GeneChip Mouse Genome 430 2.0 arrays. Results Analysis identified 66 genes in male and 30 in female brains differentially expressed in GalCer-treated versus vehicle-exposed Cln3Δex7/8 mice. Gene ontology revealed aberrations of biological function including developmental, cellular, and behavioral processes. GalCer treatment altered pathways of long-term potentiation/depression, estrogen signaling, synaptic vesicle cycle, ErbB signaling, and prion diseases in males, but prolactin signaling, selenium compound metabolism and steroid biosynthesis in females. Gene-gene network analysis highlighted networks functionally pertinent to GalCer treatment encompassing motor dysfunction, neurodegeneration, memory disorder, inflammation and astrogliosis in males, and, cataracts, inflammation, astrogliosis, and anxiety in females. Conclusions This study sheds light on global expression patterns following GalCer treatment of Cln3Δex7/8 mice. Understanding molecular effects of GalCer on mouse brain gene expression, paves the way for personalized strategies for treating this debilitating disease in humans.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population

Awada, Zainab / Bouaoun, Liacine / Nasr, Rihab / Tfayli, Arafat / Cuenin, Cyrille / Akika, Reem / Boustany, Rose-Mary / Makoukji, Joelle / Tamim, Hani / Zgheib, Nathalie K / Ghantous, Akram

Environmental research. 2021 June, v. 197

2021

Abstract: Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly ... ...

Abstract	Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures.We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)].This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk.In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = −0.04 [−0.07, −0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10⁻¹⁴). This difference remained significant after adjustment for confounders (odds ratio (OR) [95% CI] = 9.75[3.74, 25.39]). Moreover, LINE-1 hypo-methylation mediated 83% of the inverse effect of BMI on breast cancer risk.This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.
Keywords	DNA methylation ; alcohol drinking ; biomarkers ; bisulfites ; blood ; body mass index ; breast neoplasms ; cigarettes ; confidence interval ; epigenetics ; high-throughput nucleotide sequencing ; mortality ; odds ratio ; research ; retrotransposons ; Lebanon
Language	English
Dates of publication	2021-06
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2021.111094
Database	NAL-Catalogue (AGRICOLA)

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