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428 results on '"Salmon-Divon, Mali"'

54. Homozygous MED25 mutation implicated in eye-intellectual disability syndrome

Author

Basel-Vanagaite, Lina, Smirin-Yosef, Pola, Essakow, Jenna, Tzur, Shay, Lagovsky, Irina, Maya, Idit, Pasmanik-Chor, Metsada, Yeheskel, Adva, Konen, Osnat, Orenstein, Naama, Weisz Hubshman, Monika, Drasinover, Valerie, Magal, Nurit, Peretz Amit, Gaby, Zalzstein, Yael, Zeharia, Avraham, Shohat, Mordechai, Straussberg, Rachel, Monté, Didier, Salmon-Divon, Mali, Behar, Doron, Basel-Vanagaite, Lina, Smirin-Yosef, Pola, Essakow, Jenna, Tzur, Shay, Lagovsky, Irina, Maya, Idit, Pasmanik-Chor, Metsada, Yeheskel, Adva, Konen, Osnat, Orenstein, Naama, Weisz Hubshman, Monika, Drasinover, Valerie, Magal, Nurit, Peretz Amit, Gaby, Zalzstein, Yael, Zeharia, Avraham, Shohat, Mordechai, Straussberg, Rachel, Monté, Didier, Salmon-Divon, Mali, and Behar, Doron

Abstract

Genetic syndromes involving both brain and eye abnormalities are numerous and include syndromes such as Warburg micro syndrome, Kaufman oculocerebrofacial syndrome, Cerebro-oculo-facio-skeletal syndrome, Kahrizi syndrome and others. Using exome sequencing, we have been able to identify homozygous mutation p.(Tyr39Cys) in MED25 as the cause of a syndrome characterized by eye, brain, cardiac and palatal abnormalities as well as growth retardation, microcephaly and severe intellectual disability in seven patients from four unrelated families, all originating from the same village. The protein encoded by MED25 belongs to Mediator complex or MED complex, which is an evolutionary conserved multi-subunit RNA polymerase II transcriptional regulator complex. The MED25 point mutation is located in the von Willebrand factor type A (MED25 VWA) domain which is responsible for MED25 recruitment into the Mediator complex; co-immunoprecipitation experiment demonstrated that this mutation dramatically impairs MED25 interaction with the Mediator complex in mammalian cells.

Published
2021

56. Topology of the human and mouse [m.sup.6]A RNA methylomes revealed by [m.sup.6]A-seq

Author

Dominissini, Dan, Moshitch-Moshkovit, Sharon, Schwartz, Schraga, Salmon-Divon, Mali, Ungar, Lior, Osenberg, Sivan, Cesarkas, Karen, Jacob-Hirsch, Jasmine, Amariglio, Ninette, Kupiec, Martin, Sorek, Rotem, and Rechavi, Gideon

Subjects
Gene expression -- Research, RNA -- Physiological aspects -- Structure -- Research, Methyltransferases -- Physiological aspects -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N6 -methyladenosine ([m.sup.6]A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse [m.sup.6]A modification landscape in a transcriptome-wide manner, using a novel approach,[m.sup.6]A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 [m.sup.6]A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks--around stop codons and within long internal exons--and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the [m.sup.6]A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by [m.sup.6]A has a fundamental role in regulation of gene expression., Although the multiple layers of epigenetic regulation that result from modification of DNA and proteins have been intensively explored, RNA modifications are still uncharted territory (1). The complex structure--function relationship [...]

Published
2012
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60. Influence of Maternal Age and Ovarian Reserve on the Decision to Continue or to Cancel IVF Cycles in Patients with One or Two Large Follicles: a Dual Effect

Author

Shrem, Guy, primary, Salmon-Divon, Mali, additional, Mahfoudh, Alina M., additional, Balayla, Jacques, additional, Volodarsky-Perel, Alexander, additional, Henderson, Sara, additional, Zeadna, Atif, additional, Son, Weon-Young, additional, Steiner, Naama, additional, and Dahan, Michael H., additional

Published
2021
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64. Reactive stroma and trastuzumab resistance in HER2-positive early breast cancer.

Author

Sonnenblick, Amir, Salmon-Divon, Mali, Salgado, Roberto, Dvash, Efrat, Pondé, Noam, Zahavi, Tamar, Salmon, Asher, Loibl, Sibylle, Denkert, Carsten, Joensuu, Heikki, Ameye, Lieveke, Van den Eynden, Gert, Kellokumpu-Lehtinen, Pirkko-Liisa, Azaria, Amos, Loi, Sherene, Michiels, Stefan, Richard, François, Sotiriou, Christos, Sonnenblick, Amir, Salmon-Divon, Mali, Salgado, Roberto, Dvash, Efrat, Pondé, Noam, Zahavi, Tamar, Salmon, Asher, Loibl, Sibylle, Denkert, Carsten, Joensuu, Heikki, Ameye, Lieveke, Van den Eynden, Gert, Kellokumpu-Lehtinen, Pirkko-Liisa, Azaria, Amos, Loi, Sherene, Michiels, Stefan, Richard, François, and Sotiriou, Christos

Abstract

We investigated the value of reactive stroma as a predictor for trastuzumab resistance in patients with early HER2-positive breast cancer receiving adjuvant therapy. The pathological reactive stroma and the mRNA gene signatures that reflect reactive stroma in 209 HER2-positive breast cancer samples from the FinHer adjuvant trial were evaluated. Levels of stromal gene signatures were determined as a continuous parameter, and pathological reactive stromal findings were defined as stromal predominant breast cancer (SPBC; ≥50% stromal) and correlated with distant disease-free survival. Gene signatures associated with reactive stroma in HER2-positive early breast cancer (N = 209) were significantly associated with trastuzumab resistance in estrogen receptor (ER)-negative tumors (hazard ratio [HR] = 1.27 p interaction = 0.014 [DCN], HR = 1.58, p interaction = 0.027 [PLAU], HR = 1.71, p interaction = 0.019 [HER2STROMA, novel HER2 stromal signature]), but not in ER-positive tumors (HR = 0.73 p interaction = 0.47 [DCN], HR = 0.71, p interaction = 0.73 [PLAU], HR = 0.84; p interaction = 0.36 [HER2STROMA]). Pathological evaluation of HER2-positive/ER-negative tumors suggested an association between SPBC and trastuzumab resistance. Reactive stroma did not correlate with tumor-infiltrating lymphocytes (TILs), and the expected benefit from trastuzumab in patients with high levels of TILs was pronounced only in tumors with low stromal reactivity (SPBC <50%). In conclusion, reactive stroma in HER2-positive/ER-negative early breast cancer tumors may predict resistance to adjuvant trastuzumab therapy., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2020

70. A study of normal copy number variations in Israeli population

Author

Maya, Idit, primary, Smirin-Yosef, Pola, additional, Kahana, Sarit, additional, Morag, Sne, additional, Yacobson, Shiri, additional, Agmon-Fishman, Ifaat, additional, Matar, Reut, additional, Bitton, Elisheva, additional, Shohat, Mordechai, additional, Basel-Salmon, Lina, additional, and Salmon-Divon, Mali, additional

Published
2020
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75. Abstract P4-10-16: Reactive stroma and trastuzumab resistance in HER2-positive early breast cancer

Author

Sonnenblick, Amir, primary, Salmon-Divon, Mali, additional, Salgado, Roberto, additional, Pondé, Noam, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Joensuu, Heikki, additional, Kellokumpu-Lehtinen, Pirkko-Liisa, additional, Azaria, Amos, additional, Loi, Sherene, additional, Michiels, Stefan, additional, and Sotiriou, Christos, additional

Published
2020
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76. Reactive stroma and trastuzumab resistance in HER2‐positive early breast cancer

Author

Sonnenblick, Amir, primary, Salmon‐Divon, Mali, additional, Salgado, Roberto, additional, Dvash, Efrat, additional, Pondé, Noam, additional, Zahavi, Tamar, additional, Salmon, Asher, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Joensuu, Heikki, additional, Ameye, Lieveke, additional, Van den Eynden, Gert, additional, Kellokumpu‐Lehtinen, Pirkko‐Liisa, additional, Azaria, Amos, additional, Loi, Sherene, additional, Michiels, Stefan, additional, Richard, François, additional, and Sotiriou, Christos, additional

Published
2020
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78. Uncommon side effects of common drugs in patients with familial dysautonomia.

Author

Perl, Liat, Hakimian, David, Maayan, Channa, Rekhtman, David, Fried, Elchanan, Salmon‐Divon, Mali, Sapozhnikov, Daniel Mark, and Cheishvili, David

Abstract

Purpose: Patients with the autosomal recessive disorder of familial dysautonomia typically exhibit exacerbated adverse side effects to many common drugs. We aimed to catalog these adverse effects – with a focus on common drugs that are frequently administered to FD patients and compare their incidences to those within the general population. Methods: We used data of 595 FD patients from an international database with information on drugs received and adverse effects. To investigate the molecular causes of reported differences in drug responses in FD patients, we used expression microarrays to compare the mRNA expression profiles in peripheral blood leukocytes of FD patients (n = 12) and healthy individuals (n = 10). Results: Several drug classes, including cholinergics, anti‐cholinergics, anti‐convulsants, methylxanthines, SSRIs, and antibiotics caused either unreported symptoms or elevated rates of adverse events in FD patients. FD patients experienced different or more frequent adverse side effects than the general population in 31/123 drugs. These side effects included blood cell dyscrasias, amenorrhea, gastrointestinal bleeding, and bronchospasm. New findings include enhanced reaction of FD patients to H2 antagonist agents and to serotonin receptor agonists. We also detected eight genes differentially expressed between FD patients and healthy individuals that may underlie the differential drug responses of FD patients. Conclusion: We provide evidence that suggests the use of several common drugs should be discontinued or reduced in FD patients. [ABSTRACT FROM AUTHOR]

Published
2022
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80. SYK expression level distinguishes control from BRCA1-mutated lymphocytes

Author

Zahavi, Tamar, Sonnenblick, Amir, Shimshon, Yael, Kadouri, Luna, Peretz, Tamar, Salmon, Asher Y, and Salmon-Divon, Mali

Subjects
endocrine system diseases, Cancer Management and Research, breast cancer susceptibility, RNA-Seq, peripheral blood, skin and connective tissue diseases, Original Research
Abstract

Tamar Zahavi,1,2,* Amir Sonnenblick,1,3,* Yael Shimshon,2 Luna Kadouri,1 Tamar Peretz,1 Asher Y Salmon,1,* Mali Salmon-Divon,2,* 1Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel; 2Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel; 3Sackler Faculty of Medicine, Sourasky Medical Center, Institute of Oncology, Tel Aviv University, Tel Aviv, Israel *These authors contributed equally to this work Background: About 5%–10% of breast cancer and 10%–15% of ovarian cancer are hereditary. BRCA1 and BRCA2 are the most common germline mutations found in both inherited breast and ovarian cancers. Once these mutations are identified and classified, a course of action to reduce the risk of developing either ovarian or breast cancer – including surveillance and surgery – is carried out. Purpose: The purpose of the current research is to characterize the gene expression differences between healthy cells harboring a mutation in BRCA1/2 genes and normal cells. This will allow detection of candidate genes and help identify women who carry functional BRCA1/2 mutations, which cannot always be detected by the available sequencing methods, for example, carriers of mutations found in regulatory sequences of the genes. Materials and methods: Our cohort consisted of 50 healthy women, of whom 24 were individuals with BRCA1 or BRCA2 heterozygous mutations and 26 were non-carrier controls. RNA purified from non-irradiated lymphocytes of nine BRCA1/2 mutation carriers versus four control mutation-negative individuals was utilized for RNA-Seq analysis. The selected RNA-Seq transcripts were validated, and the levels of spleen tyrosine kinase (SYK) mRNA were measured by using real-time quantitative polymerase chain reaction. Results: Differences in gene expression were found when comparing untreated lymphocytes of BRCA1/2 mutation carriers and controls. Among others, the SYK gene was identified as being differently expressed for BRCA1/2 mutation carriers. The expression level of SYK was significantly higher in untreated healthy lymphocytes of BRCA1 heterozygote carriers compared with controls, regardless of irradiation. In contrast to normal tissues, in cancerous breast tissues, the expression levels of the BRCA1 and SYK genes were not intercorrelated. Conclusion: Collectively, our observations demonstrate that SYK may prove to be a good candidate for better diagnosis, treatment, and prevention of BRCA1 mutation-associated breast cancer. Keywords: RNA-Seq, breast cancer susceptibility, peripheral blood

Published
2018

82. Influence of maternal age and ovarian reserve on the decision to continue or to cancel IVF cycles in patients with one or two large follicles

Author

Shrem, Guy, primary, Mahfoudh, Alina Mariana, additional, Balayla, Jacques, additional, Steiner, Naama, additional, Volodarsky-Perel, Alexander, additional, Henderson, Sara, additional, Zeadna, Atif, additional, Son, Weon-Young, additional, Salmon-Divon, Mali, additional, and Dahan, Michael H., additional

Published
2019
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85. PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Author

Tammoja Kairi, Dvinge Heidi, Salmon-Divon Mali, and Bertone Paul

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. Results PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. Conclusions PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.

Published
2010
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86. Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc

Author

Schnytzer, Yisrael, Simon-Blecher, Noa, Li, J., Ben-Asher, H. Waldman, Salmon-Divon, Mali, Achituv, Yair, Hughes, Michael E., Levy, Oren, Schnytzer, Yisrael, Simon-Blecher, Noa, Li, J., Ben-Asher, H. Waldman, Salmon-Divon, Mali, Achituv, Yair, Hughes, Michael E., and Levy, Oren

Abstract

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 4917, doi:10.1038/s41598-018-23167-y., Intertidal inhabitants are exposed to the 24-hour solar day, and the 12.4 hour rising and falling of the tides. One or both of these cycles govern intertidal organisms’ behaviour and physiology, yet little is known about the molecular clockworks of tidal rhythmicity. Here, we show that the limpet Cellana rota exhibits robust tidally rhythmic behaviour and gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with known circadian clock genes. Surprisingly, most of the putative circadian clock genes, lack a typical rhythmicity. We identified numerous tidally rhythmic genes and pathways commonly associated with the circadian clock. We show that not only is the behaviour of an intertidal organism in tune with the tides, but so too are many of its genes and pathways. These findings highlight the plasticity of biological timekeeping in nature, strengthening the growing notion that the role of ‘canonical’ circadian clock genes may be more fluid than previously thought, as exhibited in an organism which has evolved in an environment where tidal oscillations are the dominant driving force.

Published
2018

96. Corrigendum to “X-linked elliptocytosis with impaired growth is related to mutated AMMECR1” [Gene 606C (2017) 47–52]

Author

Basel-Vanagaite, Lina, primary, Pillar, Nir, additional, Isakov, Ofer, additional, Smirin-Yosef, Pola, additional, Lagovsky, Irina, additional, Orenstein, Naama, additional, Salmon-Divon, Mali, additional, Tamary, Hannah, additional, Zaft, Tami, additional, Bazak, Lily, additional, Meyerovitch, Joseph, additional, Pelli, Tal, additional, Botchan, Shay, additional, Farberov, Luba, additional, Weissglas-Volkov, Daphna, additional, and Shomron, Noam, additional

Published
2018
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98. Additional file 6: Figure S6. of Elucidating tissue specific genes using the Benford distribution

Author

Karthik, Deepak, Stelzer, Gil, Gershanov, Sivan, Baranes, Danny, and Salmon-Divon, Mali

Abstract

The effect of different technical parameters on the Benford pattern as calculated based on cell line-derived gene expression data described as raw counts. If not mentioned otherwise read length was 100Â bp and all reads were used in the analysis. Truncated reads (25 and 50Â bp) and lower coverage (30, 50 and 80Â % out of the total reads) appear in plot titles. The red line indicates the expected Benford distribution, symbol-marked lines are the distribution observed for three replicates. (PDF 17 kb)

Published
2016
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99. Additional file 1: Figure S1. of Elucidating tissue specific genes using the Benford distribution

Author

Karthik, Deepak, Stelzer, Gil, Gershanov, Sivan, Baranes, Danny, and Salmon-Divon, Mali

Abstract

The effect of different technical parameters on the Benford pattern as calculated based on brain-derived gene expression data described as raw counts. If not mentioned otherwise read length was 100Â bp and all reads were used in the analysis. Truncated reads (25 and 50Â bp) and lower coverage (30, 50 and 80Â % out of the total reads) appear in plot titles. The red line indicates the expected Benford distribution, symbol-marked lines are the distribution observed for three replicates. (PDF 10 kb)

Published
2016
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