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Article ; Online: Correction

E. Zeynep Erson-Omay / Shaurey Vetsa / Sagar Vasandani / Tanyeri Barak / Arushii Nadar / Neelan J. Marianayagam / Kanat Yalcin / Danielle Miyagishima / Stephanie Marie Aguilera / Stephanie Robert / Ketu Mishra-Gorur / Robert K. Fulbright / Declan McGuone / Murat Günel / Jennifer Moliterno

BMC Medical Genomics, Vol 15, Iss 1, Pp 1-

Genomic profiling of sporadic multiple meningiomas

2022 Volume 1

Keywords	Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic profiling of sporadic multiple meningiomas

E. Zeynep Erson-Omay / Shaurey Vetsa / Sagar Vasandani / Tanyeri Barak / Arushii Nadar / Neelan Marianayanam / Kanat Yalcin / Danielle Miyagishima / Stephanie Marie Aguilera / Stephanie Robert / Ketu Mishra-Gorur / Robert K. Fulbright / Declan McGuone / Murat Günel / Jennifer Moliterno

BMC Medical Genomics, Vol 15, Iss 1, Pp 1-

2022 Volume 9

Abstract: Abstract Background Multiple meningiomas (MMs) rarely occur sporadically. It is unclear whether each individual tumor in a single patient behaves similarly. Moreover, the molecular mechanisms underlying the formation of sporadic MMs and clonal formation ... ...

Abstract	Abstract Background Multiple meningiomas (MMs) rarely occur sporadically. It is unclear whether each individual tumor in a single patient behaves similarly. Moreover, the molecular mechanisms underlying the formation of sporadic MMs and clonal formation etiology of these tumors are poorly understood. Methods Patients with spatially separated MMs without prior radiation exposure or a family history who underwent surgical resection of at least two meningiomas were included. Unbiased, comprehensive next generation sequencing was performed, and relevant clinical data was analyzed. Results Fifteen meningiomas and one dural specimen from six patients were included. The majority of tumors (12/15) were WHO Grade I; one patient had bilateral MMs, one of which was Grade II, while the other was Grade I. We found 11/15 of our cohort specimens were of NF2-loss subtype. Meningiomas from 5/6 patients had a monoclonal origin, with the tumor from the remaining patient showing evidence for independent clonal formation. We identified a novel case of non-NF2 mutant MM with monoclonal etiology. MMs due to a monoclonal origin did not always display a homogenous genomic profile, but rather exhibited heterogeneity due to branching evolution. Conclusions Both NF2-loss and non-NF2 driven MMs can form due to monoclonal expansion and those tumors can acquire inter-tumoral heterogeneity through branched evolution. Grade I and II meningiomas can occur in the same patient. Thus, the molecular make-up and clinical behavior of one tumor in MMs, cannot reliably lend insight into that of the others and suggests the clinical management strategy for MMs should be tailored individually.
Keywords	Genomics ; Sporadic multiple meningiomas ; Clonal formation ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SomatiCA

Mengjie Chen / Murat Gunel / Hongyu Zhao

PLoS ONE, Vol 8, Iss 11, p e

identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.

2013 Volume 78143

Abstract: Whole genome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. However, analysis of somatic copy-number changes from sequencing data is still challenging because of insufficient sequencing coverage, unknown tumor ... ...

Abstract	Whole genome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. However, analysis of somatic copy-number changes from sequencing data is still challenging because of insufficient sequencing coverage, unknown tumor sample purity and subclonal heterogeneity. Here we describe a computational framework, named SomatiCA, which explicitly accounts for tumor purity and subclonality in the analysis of somatic copy-number profiles. Taking read depths (RD) and lesser allele frequencies (LAF) as input, SomatiCA will output 1) admixture rate for each tumor sample, 2) somatic allelic copy-number for each genomic segment, 3) fraction of tumor cells with subclonal change in each somatic copy number aberration (SCNA), and 4) a list of substantial genomic aberration events including gain, loss and LOH. SomatiCA is available as a Bioconductor R package at http://www.bioconductor.org/packages/2.13/bioc/html/SomatiCA.html.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2013-01-01T00:00:00Z
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: Functional synergy between cholecystokinin receptors CCKAR and CCKBR in mammalian brain development.

Sayoko Nishimura / Kaya Bilgüvar / Keiko Ishigame / Nenad Sestan / Murat Günel / Angeliki Louvi

PLoS ONE, Vol 10, Iss 4, p e

2015 Volume 0124295

Abstract: Cholecystokinin (CCK), a peptide hormone and one of the most abundant neuropeptides in vertebrate brain, mediates its actions via two G-protein coupled receptors, CCKAR and CCKBR, respectively active in peripheral organs and the central nervous system. ... ...

Abstract	Cholecystokinin (CCK), a peptide hormone and one of the most abundant neuropeptides in vertebrate brain, mediates its actions via two G-protein coupled receptors, CCKAR and CCKBR, respectively active in peripheral organs and the central nervous system. Here, we demonstrate that the CCK receptors have a dynamic and largely reciprocal expression in embryonic and postnatal brain. Using compound homozygous mutant mice lacking the activity of both CCK receptors, we uncover their additive, functionally synergistic effects in brain development and demonstrate that CCK receptor loss leads to abnormalities of cortical development, including defects in the formation of the midline and corpus callosum, and cortical interneuron migration. Using comparative transcriptome analysis of embryonic neocortex, we define the molecular mechanisms underlying these defects. Thus we demonstrate a developmental, hitherto unappreciated, role of the two CCK receptors in mammalian neocortical development.
Keywords	Medicine ; R ; Science ; Q
Subject code	571
Language	English
Publishing date	2015-01-01T00:00:00Z
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: The Effect of Using Different Multi Modal Representations within Writing to Learn Activities on Learning Force and Motion Unit at the Middle School Setting

Muhammed Ertaç ATİLA / Murat GÜNEL / Erdoğan BÜYÜKKASAP

Journal of Turkish Science Education, Vol 7, Iss 4, Pp 113-

2010 Volume 127

Abstract: The purpose of the present study is to investigate the effect of embedding different multi modal representation within the writing to learn activities on unit based academic achievement of primary education 6th grade students. The sampling of the study ... ...

Abstract	The purpose of the present study is to investigate the effect of embedding different multi modal representation within the writing to learn activities on unit based academic achievement of primary education 6th grade students. The sampling of the study consisted of 74 sixth grade (4 classes) students enrolled in a public school in Erzurum, province of Turkey. The students in 4 different 6th grade classes all studied the unit (force and motion) with the same lecturer using the same method, strategy, materials and spending same time on task. Upon completion of the unit, those 4 classes were selected into 4 random implementation groups. The first treatment group (class A) wrote a letter to 5th grade students including only text (other modes are not allowed) for the representation (only text); the second treatment group wrote a letter to 5th grade students including text and any other mode(s) of representation (any one or combination of picture, graphic, and mathematical modes of representation) (text + any mode); the third treatment group (class C) wrote a letter to 5th grade students including text and graphical modal representation (text + graphic); the fourth treatment group (class D) wrote a letter to 5th grade students including text and mathematical representation (text + mathematics). A quasi-experimental research method was used in this study. Post-test analyses indicated that there was no statistically significant difference between the students who only used text and the students who used any mode of representation. However, when the restricted groups were compared with free groups, it can be stated that unit based academic achievement of the students who have to use a certain mode of representation with textual mode of representation (text + mathematics and text + graphic) were higher than those who used any mode of representation.
Keywords	Writing-to-Learn ; Science Literacy ; Multimodal Representation ; Elementary Science Education ; Special aspects of education ; LC8-6691 ; Education ; L ; DOAJ:Education ; DOAJ:Social Sciences
Subject code	370
Language	Turkish
Publishing date	2010-12-01T00:00:00Z
Publisher	Ekip Ltd. Sti
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Functional differences between PD-1+ and PD-1- CD4+ effector T cells in healthy donors and patients with glioblastoma multiforme.

Brittany A Goods / Amanda L Hernandez / Daniel E Lowther / Liliana E Lucca / Benjamin A Lerner / Murat Gunel / Khadir Raddassi / Vlad Coric / David A Hafler / J Christopher Love

PLoS ONE, Vol 12, Iss 9, p e

2017 Volume 0181538

Abstract: Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) have been highly successful in the treatment of cancer. While PD-1 expression has been widely investigated, its role in CD4+ effector T cells in the setting of health and ... ...

Abstract	Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) have been highly successful in the treatment of cancer. While PD-1 expression has been widely investigated, its role in CD4+ effector T cells in the setting of health and cancer remains unclear, particularly in the setting of glioblastoma multiforme (GBM), the most aggressive and common form of brain cancer. We examined the functional and molecular features of PD-1+CD4+CD25-CD127+Foxp3-effector cells in healthy subjects and in patients with GBM. In healthy subjects, we found that PD-1+CD4+ effector cells are dysfunctional: they do not proliferate but can secrete large quantities of IFNγ. Strikingly, blocking antibodies against PD-1 did not rescue proliferation. RNA-sequencing revealed features of exhaustion in PD-1+ CD4 effectors. In the context of GBM, tumors were enriched in PD-1+ CD4+ effectors that were similarly dysfunctional and unable to proliferate. Furthermore, we found enrichment of PD-1+TIM-3+ CD4+ effectors in tumors, suggesting that co-blockade of PD-1 and TIM-3 in GBM may be therapeutically beneficial. RNA-sequencing of blood and tumors from GBM patients revealed distinct differences between CD4+ effectors from both compartments with enrichment in multiple gene sets from tumor infiltrating PD-1-CD4+ effectors cells. Enrichment of these gene sets in tumor suggests a more metabolically active cell state with signaling through other co-receptors. PD-1 expression on CD4 cells identifies a dysfunctional subset refractory to rescue with PD-1 blocking antibodies, suggesting that the influence of immune checkpoint inhibitors may involve recovery of function in the PD-1-CD4+ T cell compartment. Additionally, co-blockade of PD-1 and TIM-3 in GBM may be therapeutically beneficial.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2017-01-01T00:00:00Z
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: Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas

Mark W. Youngblood / Zeynep Erson-Omay / Chang Li / Hinda Najem / Süleyman Coșkun / Evgeniya Tyrtova / Julio D. Montejo / Danielle F. Miyagishima / Tanyeri Barak / Sayoko Nishimura / Akdes Serin Harmancı / Victoria E. Clark / Daniel Duran / Anita Huttner / Timuçin Avşar / Yasar Bayri / Johannes Schramm / Julien Boetto / Matthieu Peyre /

Maximilien Riche / Roland Goldbrunner / Nduka Amankulor / Angeliki Louvi / Kaya Bilgüvar / M. Necmettin Pamir / Koray Özduman / Türker Kilic / James R. Knight / Matthias Simon / Craig Horbinski / Michel Kalamarides / Marco Timmer / Amy B. Heimberger / Ketu Mishra-Gorur / Jennifer Moliterno / Katsuhito Yasuno / Murat Günel

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 16

Abstract: Abstract Hedgehog signaling mediates embryologic development of the central nervous system and other tissues and is frequently hijacked by neoplasia to facilitate uncontrolled cellular proliferation. Meningiomas, the most common primary brain tumor, ... ...

Abstract	Abstract Hedgehog signaling mediates embryologic development of the central nervous system and other tissues and is frequently hijacked by neoplasia to facilitate uncontrolled cellular proliferation. Meningiomas, the most common primary brain tumor, exhibit Hedgehog signaling activation in 6.5% of cases, triggered by recurrent mutations in pathway mediators such as SMO. In this study, we find 35.6% of meningiomas that lack previously known drivers acquired various types of somatic structural variations affecting chromosomes 2q35 and 7q36.3. These cases exhibit ectopic expression of Hedgehog ligands, IHH and SHH, respectively, resulting in Hedgehog signaling activation. Recurrent tandem duplications involving IHH permit de novo chromatin interactions between super-enhancers within DIRC3 and a locus containing IHH. Our work expands the landscape of meningioma molecular drivers and demonstrates enhancer hijacking of Hedgehog ligands as a route to activate this pathway in neoplasia.
Keywords	Science ; Q
Subject code	570
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical characteristics and outcomes for 7,995 patients with SARS-CoV-2 infection.

Jacob McPadden / Frederick Warner / H Patrick Young / Nathan C Hurley / Rebecca A Pulk / Avinainder Singh / Thomas J S Durant / Guannan Gong / Nihar Desai / Adrian Haimovich / Richard Andrew Taylor / Murat Gunel / Charles S Dela Cruz / Shelli F Farhadian / Jonathan Siner / Merceditas Villanueva / Keith Churchwell / Allen Hsiao / Charles J Torre /

Eric J Velazquez / Roy S Herbst / Akiko Iwasaki / Albert I Ko / Bobak J Mortazavi / Harlan M Krumholz / Wade L Schulz

PLoS ONE, Vol 16, Iss 3, p e

2021 Volume 0243291

Abstract: Objective Severe acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2. Design This was an observational, ... ...

Abstract	Objective Severe acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2. Design This was an observational, retrospective study based on real-world data for 7,995 patients with SARS-CoV-2 from a clinical data repository. Setting Yale New Haven Health (YNHH) is a five-hospital academic health system serving a diverse patient population with community and teaching facilities in both urban and suburban areas. Populations The study included adult patients who had SARS-CoV-2 testing at YNHH between March 1 and April 30, 2020. Main outcome and performance measures Primary outcomes were admission and in-hospital mortality for patients with SARS-CoV-2 infection as determined by RT-PCR testing. We also assessed features associated with the need for respiratory support. Results Of the 28605 patients tested for SARS-CoV-2, 7995 patients (27.9%) had an infection (median age 52.3 years) and 2154 (26.9%) of these had an associated admission (median age 66.2 years). Of admitted patients, 2152 (99.9%) had a discharge disposition at the end of the study period. Of these, 329 (15.3%) required invasive mechanical ventilation and 305 (14.2%) expired. Increased age and male sex were positively associated with admission and in-hospital mortality (median age 80.7 years), while comorbidities had a much weaker association with the risk of admission or mortality. Black race (OR 1.43, 95%CI 1.14-1.78) and Hispanic ethnicity (OR 1.81, 95%CI 1.50-2.18) were identified as risk factors for admission, but, among discharged patients, age-adjusted in-hospital mortality was not significantly different among racial and ethnic groups. Conclusions This observational study identified, among people testing positive for SARS-CoV-2 infection, older age and male sex as the most strongly associated risks for admission and in-hospital mortality in patients with SARS-CoV-2 infection. While minority racial and ethnic groups had increased burden of disease and risk of admission, age-adjusted in-hospital mortality for discharged patients was not significantly different among racial and ethnic groups. Ongoing studies will be needed to continue to evaluate these risks, particularly in the setting of evolving treatment guidelines.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
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: Correction

Akdes Serin Harmancı / Mark W. Youngblood / Victoria E. Clark / Süleyman Coşkun / Octavian Henegariu / Daniel Duran / E. Zeynep Erson-Omay / Leon D. Kaulen / Tong Ihn Lee / Brian J. Abraham / Matthias Simon / Boris Krischek / Marco Timmer / Roland Goldbrunner / S. Bülent Omay / Jacob Baranoski / Burçin Baran / Geneive Carrión-Grant / Hanwen Bai /

Ketu Mishra-Gorur / Johannes Schramm / Jennifer Moliterno / Alexander O. Vortmeyer / Kaya Bilgüvar / Katsuhito Yasuno / Richard A. Young / Murat Günel

Nature Communications, Vol 9, Iss 1, Pp 1-

Author Correction: Integrated genomic analyses of de novo pathways underlying atypical meningiomas

2018 Volume 1

Abstract: Nature Communications 8: Article number: 14433 (2017) Published online 14 February 2017; Updated 20 April 2018 In this Article, a subset of the H3K27ac ChIP-seq data (15 benign meningiomas and 2 dura samples (Sample IDs: MN-297, MN-288, MN-292, MN-163, ... ...

Abstract	Nature Communications 8: Article number: 14433 (2017) Published online 14 February 2017; Updated 20 April 2018 In this Article, a subset of the H3K27ac ChIP-seq data (15 benign meningiomas and 2 dura samples (Sample IDs: MN-297, MN-288, MN-292, MN-163, MN-1037, MN-105, MN-201, MN-249, MN-191, MN-1066, MN-169, MN-291, MN-24, MN-79, MN-1044, CONTROL1, CONTROL2) was reported previously in a publication by the corresponding author1.
Keywords	Science ; Q
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia

Weilai Dong / Sheng Chih Jin / August Allocco / Xue Zeng / Amar H. Sheth / Shreyas Panchagnula / Annie Castonguay / Louis-Étienne Lorenzo / Barira Islam / Geneviève Brindle / Karine Bachand / Jamie Hu / Agata Sularz / Jonathan Gaillard / Jungmin Choi / Ashley Dunbar / Carol Nelson-Williams / Emre Kiziltug / Charuta Gavankar Furey /

Sierra Conine / Phan Q. Duy / Adam J. Kundishora / Erin Loring / Boyang Li / Qiongshi Lu / Geyu Zhou / Wei Liu / Xinyue Li / Michael C. Sierant / Shrikant Mane / Christopher Castaldi / Francesc López-Giráldez / James R. Knight / Raymond F. Sekula, Jr. / J. Marc Simard / Emad N. Eskandar / Christopher Gottschalk / Jennifer Moliterno / Murat Günel / Jason L. Gerrard / Sulayman Dib-Hajj / Stephen G. Waxman / Fred G. Barker, II / Seth L. Alper / Mohamed Chahine / Shozeb Haider / Yves De Koninck / Richard P. Lifton / Kristopher T. Kahle

iScience, Vol 23, Iss 10, Pp 101552- (2020)

2020

Abstract: Summary: Trigeminal neuralgia (TN) is a common, debilitating neuropathic face pain syndrome often resistant to therapy. The familial clustering of TN cases suggests that genetic factors play a role in disease pathogenesis. However, no unbiased, large- ... ...

Abstract	Summary: Trigeminal neuralgia (TN) is a common, debilitating neuropathic face pain syndrome often resistant to therapy. The familial clustering of TN cases suggests that genetic factors play a role in disease pathogenesis. However, no unbiased, large-scale genomic study of TN has been performed to date. Analysis of 290 whole exome-sequenced TN probands, including 20 multiplex kindreds and 70 parent-offspring trios, revealed enrichment of rare, damaging variants in GABA receptor-binding genes in cases. Mice engineered with a TN-associated de novo mutation (p.Cys188Trp) in the GABAA receptor Cl− channel γ-1 subunit (GABRG1) exhibited trigeminal mechanical allodynia and face pain behavior. Other TN probands harbored rare damaging variants in Na+ and Ca+ channels, including a significant variant burden in the α-1H subunit of the voltage-gated Ca2+ channel Cav3.2 (CACNA1H). These results provide exome-level insight into TN and implicate genetically encoded impairment of GABA signaling and neuronal ion transport in TN pathogenesis.
Keywords	Neuroscience ; Structural Biology ; Genomics ; Science ; Q
Subject code	572
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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