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  1. Article ; Online: Medulloblastoma: WHO 2021 and Beyond.

    Cotter, Jennifer A / Hawkins, Cynthia

    Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society

    2022  Volume 25, Issue 1, Page(s) 23–33

    Abstract: In 2016, medulloblastoma classification was restructured to allow for incorporation of updated data about medulloblastoma biology, genomics, and clinical behavior. For the first time, medulloblastomas were classified according to molecular ... ...

    Abstract In 2016, medulloblastoma classification was restructured to allow for incorporation of updated data about medulloblastoma biology, genomics, and clinical behavior. For the first time, medulloblastomas were classified according to molecular characteristics ("genetically defined" categories) as well as histologic characteristics ("histologically defined" categories). Current genetically-defined categories include WNT-activated, SHH-activated
    MeSH term(s) Cerebellar Neoplasms/diagnosis ; Cerebellar Neoplasms/genetics ; Humans ; Medulloblastoma/diagnosis ; Medulloblastoma/genetics ; World Health Organization
    Language English
    Publishing date 2022-02-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1463498-3
    ISSN 1615-5742 ; 1093-5266
    ISSN (online) 1615-5742
    ISSN 1093-5266
    DOI 10.1177/10935266211018931
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Evaluation and Diagnosis of Central Nervous System Embryonal Tumors (Non-Medulloblastoma).

    Cotter, Jennifer A / Judkins, Alexander R

    Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society

    2022  Volume 25, Issue 1, Page(s) 34–45

    Abstract: Since the 1990s, the sheer number of defined central nervous system (CNS) embryonal tumor entities has continuously increased, with the trend accelerating in the most recent editions of the World Health Organization (WHO) Classification of Tumours of the ...

    Abstract Since the 1990s, the sheer number of defined central nervous system (CNS) embryonal tumor entities has continuously increased, with the trend accelerating in the most recent editions of the World Health Organization (WHO) Classification of Tumours of the CNS. The introduction of increasingly specific tumor groups is an effort to create more internally homogeneous categories, to allow more precise prognostication, and potentially to develop targeted therapies. However, these ever-smaller categories within an already rare group of tumors pose a challenge for pediatric pathologists. In this article we review the current categorization of non-medulloblastoma CNS embryonal tumors (including atypical teratoid/rhabdoid tumor, cribriform neuroepithelial tumor, embryonal tumor with multilayered rosettes, CNS neuroblastoma,
    MeSH term(s) Central Nervous System ; Central Nervous System Neoplasms/diagnosis ; Cerebellar Neoplasms ; Child ; Forkhead Transcription Factors ; Humans ; Medulloblastoma/diagnosis ; Medulloblastoma/therapy ; Neoplasms, Germ Cell and Embryonal/diagnosis
    Chemical Substances FOXR2 protein, human ; Forkhead Transcription Factors
    Language English
    Publishing date 2022-02-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1463498-3
    ISSN 1615-5742 ; 1093-5266
    ISSN (online) 1615-5742
    ISSN 1093-5266
    DOI 10.1177/10935266211018554
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An update on the central nervous system manifestations of tuberous sclerosis complex.

    Cotter, Jennifer A

    Acta neuropathologica

    2019  Volume 139, Issue 4, Page(s) 613–624

    Abstract: The autosomal dominant disorder tuberous sclerosis complex (TSC) is characterized by an array of manifestations both within and outside of the central nervous system (CNS), including hamartomas and other malformations. TSC is caused by mutations in the ... ...

    Abstract The autosomal dominant disorder tuberous sclerosis complex (TSC) is characterized by an array of manifestations both within and outside of the central nervous system (CNS), including hamartomas and other malformations. TSC is caused by mutations in the TSC1 or TSC2 gene resulting in activation of the mechanistic target of rapamycin (mTOR) signaling pathway. Study of TSC has shed light on the critical role of the mTOR pathway in neurodevelopment. This update reviews the genetic basis of TSC, its cardinal phenotypic CNS features, and recent developments in the field of TSC and other mTOR-altered disorders.
    MeSH term(s) Central Nervous System Diseases/genetics ; Central Nervous System Diseases/pathology ; Genetic Predisposition to Disease ; Humans ; Tuberous Sclerosis/complications ; Tuberous Sclerosis/pathology
    Language English
    Publishing date 2019-04-11
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-019-02003-1
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  4. Article: Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.

    Mitchell, David / Cotter, Jennifer / Saleem, Irfana / Mustoe, Anthony M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a prominent role ... ...

    Abstract Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a prominent role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guanines
    Language English
    Publishing date 2023-04-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.10.536308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.

    Mitchell, David / Cotter, Jennifer / Saleem, Irfana / Mustoe, Anthony M

    Nucleic acids research

    2023  Volume 51, Issue 16, Page(s) 8744–8757

    Abstract: Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a pivotal role in ... ...

    Abstract Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a pivotal role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guanines in vitro at reduced accuracy. However, DMS remained unable to informatively probe guanines in cells. Here, we develop an improved DMS mutational profiling (MaP) strategy that leverages the unique mutational signature of N1-methylguanine DMS modifications to enable high-fidelity structure probing at all four nucleotides, including in cells. Using information theory, we show that four-base DMS reactivities convey greater structural information than current two-base DMS and SHAPE probing strategies. Four-base DMS experiments further enable improved direct base-pair detection by single-molecule PAIR analysis, and ultimately support RNA structure modeling at superior accuracy. Four-base DMS probing experiments are straightforward to perform and will broadly facilitate improved RNA structural analysis in living cells.
    MeSH term(s) Base Pairing ; Guanine ; Mutation ; Nucleic Acid Conformation ; RNA/genetics ; RNA/chemistry ; Mutagens/pharmacology ; Sulfuric Acid Esters/pharmacology
    Chemical Substances dimethyl sulfate (JW5CW40Z50) ; Guanine (5Z93L87A1R) ; RNA (63231-63-0) ; Mutagens ; Sulfuric Acid Esters
    Language English
    Publishing date 2023-06-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad522
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Show issues Location:
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  6. Article: Elevated liver enzymes: unusual presentation of anti-MDA5 antibody-associated juvenile dermatomyositis.

    Yi, Belina Y / Marrs, Joshua / Schenker, Rachel / Suddock, Jolee / Cotter, Jennifer A / Cidon, Michal

    Clinical and experimental rheumatology

    2023  Volume 42, Issue 2, Page(s) 456–457

    MeSH term(s) Humans ; Dermatomyositis/diagnosis ; Dermatomyositis/drug therapy ; Interferon-Induced Helicase, IFIH1 ; Lung Diseases, Interstitial ; Liver/diagnostic imaging ; Autoantibodies ; Prognosis
    Chemical Substances Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13) ; Autoantibodies
    Language English
    Publishing date 2023-06-06
    Publishing country Italy
    Document type Case Reports ; Letter
    ZDB-ID 605886-3
    ISSN 1593-098X ; 0392-856X
    ISSN (online) 1593-098X
    ISSN 0392-856X
    DOI 10.55563/clinexprheumatol/25znui
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Novel

    Hiemenz, Matthew C / Skrypek, Mary M / Cotter, Jennifer A / Biegel, Jaclyn A

    JCO precision oncology

    2022  Volume 3, Page(s) 1–6

    Language English
    Publishing date 2022-01-31
    Publishing country United States
    Document type Journal Article
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.18.00385
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  8. Article ; Online: Intraoperative Diagnosis for Pediatric Brain Tumors.

    Cotter, Jennifer A / Szymanski, Linda J / Pawel, Bruce R / Judkins, Alexander R

    Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society

    2022  Volume 25, Issue 1, Page(s) 10–22

    Abstract: Central nervous system (CNS) tumors are now the most common type of solid tumor in individuals aged 0-19 years, with an incidence rate in the United States around 5 per 100,000, accounting for about 1 out of 4 childhood cancers. Pediatric pathologists ... ...

    Abstract Central nervous system (CNS) tumors are now the most common type of solid tumor in individuals aged 0-19 years, with an incidence rate in the United States around 5 per 100,000, accounting for about 1 out of 4 childhood cancers. Pediatric pathologists encounter brain tumor cases with varying frequency, but many of these encounters begin in the context of intraoperative consultation or "frozen section." This review provides an overview of the technical aspects of intraoperative consultation specific to, or more helpful in, CNS tumors, emphasizing helpful cytologic and histologic features of the more commonly encountered pediatric CNS tumors, and illustrating some common diagnostic pitfalls and how these may be avoided.
    MeSH term(s) Adolescent ; Adult ; Brain Neoplasms/diagnosis ; Central Nervous System Neoplasms/diagnosis ; Child ; Child, Preschool ; Frozen Sections ; Humans ; Infant ; Infant, Newborn ; Referral and Consultation ; Young Adult
    Language English
    Publishing date 2022-02-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1463498-3
    ISSN 1615-5742 ; 1093-5266
    ISSN (online) 1615-5742
    ISSN 1093-5266
    DOI 10.1177/10935266211018932
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  9. Article ; Online: Spectrum of paired-like homeobox 2b immunoexpression in pediatric brain tumors with embryonal morphology.

    Alturkustani, Murad / Walker, Adam D / Tran, Ivy / Snuderl, Matija / Cotter, Jennifer A

    Pathology international

    2022  Volume 72, Issue 8, Page(s) 402–410

    Abstract: Paired-like homeobox 2b (PHOX2B) is an established immunomarker for peripheral neuroblastoma and autonomic nervous system cells. We aimed to evaluate the utility of PHOX2B immunostaining in central nervous system (CNS) tumors with embryonal morphology. ... ...

    Abstract Paired-like homeobox 2b (PHOX2B) is an established immunomarker for peripheral neuroblastoma and autonomic nervous system cells. We aimed to evaluate the utility of PHOX2B immunostaining in central nervous system (CNS) tumors with embryonal morphology. Fifty-one tumors were stained with PHOX2B and submitted for whole slide image analysis: 35 CNS tumors with embryonal morphology (31 CNS embryonal tumors and four gliomas); and 16 peripheral neuroblastomas were included for comparison. Diffuse nuclear immunopositivity was observed in all (16/16) neuroblastomas (primary and metastatic). Among CNS embryonal tumors, focal immunoreactivity for PHOX2B was observed in most (5/7) embryonal tumors with multilayered rosettes (ETMR) and a single high-grade neuroepithelial tumor (HGNET) with PLAGL2 amplification; the remaining 27 CNS tumors were essentially immunonegative (<0.05% positive). Among ETMR, PHOX2B expression was observed in a small overall proportion (0.04%-4.94%) of neoplastic cells but focally reached up to 39% in 1 mm 'hot spot' areas. In the PLAGL2-amplified case, 0.09% of the total neoplastic population was immunoreactive, with 0.53% in the 'hot spot' area. Care should be taken in interpreting PHOX2B immunopositivity in a differential diagnosis that includes metastatic neuroblastoma and CNS tumors; focal or patchy expression should not be considered definitively diagnostic of metastatic peripheral neuroblastoma.
    MeSH term(s) Brain Neoplasms/genetics ; Child ; DNA-Binding Proteins/metabolism ; Genes, Homeobox ; Homeodomain Proteins/genetics ; Humans ; Neoplasms, Germ Cell and Embryonal/genetics ; Neuroblastoma/genetics ; Neuroectodermal Tumors, Primitive/genetics ; RNA-Binding Proteins ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances DNA-Binding Proteins ; Homeodomain Proteins ; NBPhox protein ; PLAGL2 protein, human ; RNA-Binding Proteins ; Transcription Factors
    Language English
    Publishing date 2022-06-28
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 1194850-4
    ISSN 1440-1827 ; 1320-5463
    ISSN (online) 1440-1827
    ISSN 1320-5463
    DOI 10.1111/pin.13255
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  10. Article ; Online: Clinical, pathologic, and genomic characteristics of two pediatric glioneuronal tumors with a CLIP2::MET fusion.

    Chapman, Nicholas / Greenwald, Joshua / Suddock, Jolee / Xu, Dong / Markowitz, Alexander / Humphrey, Maeve / Cotter, Jennifer A / Krieger, Mark D / Hawes, Debra / Ji, Jianling

    Acta neuropathologica communications

    2024  Volume 12, Issue 1, Page(s) 63

    Abstract: Integration of molecular data with histologic, radiologic, and clinical features is imperative for accurate diagnosis of pediatric central nervous system (CNS) tumors. Whole transcriptome RNA sequencing (RNAseq), a genome-wide and non-targeted approach, ... ...

    Abstract Integration of molecular data with histologic, radiologic, and clinical features is imperative for accurate diagnosis of pediatric central nervous system (CNS) tumors. Whole transcriptome RNA sequencing (RNAseq), a genome-wide and non-targeted approach, allows for the detection of novel or rare oncogenic fusion events that contribute to the tumorigenesis of a substantial portion of pediatric low- and high-grade glial and glioneuronal tumors. We present two cases of pediatric glioneuronal tumors occurring in the occipital region with a CLIP2::MET fusion detected by RNAseq. Chromosomal microarray studies revealed copy number alterations involving chromosomes 1, 7, and 22 in both tumors, with Case 2 having an interstitial deletion breakpoint in the CLIP2 gene. By methylation profiling, neither tumor had a match result, but both clustered with the low-grade glial/glioneuronal tumors in the UMAP. Histologically, in both instances, our cases displayed characteristics of a low-grade tumor, notably the absence of mitotic activity, low Ki-67 labeling index and the lack of necrosis and microvascular proliferation. Glial and neuronal markers were positive for both tumors. Clinically, both patients achieved clinical stability post-tumor resection and remain under regular surveillance imaging without adjuvant therapy at the last follow-up, 6 months and 3 years, respectively. This is the first case report demonstrating the presence of a CLIP2::MET fusion in two pediatric low-grade glioneuronal tumors (GNT). Conservative clinical management may be considered for patients with GNT and CLIP2:MET fusion in the context of histologically low-grade features.
    MeSH term(s) Child ; Child, Preschool ; Female ; Humans ; Male ; Brain Neoplasms/genetics ; Brain Neoplasms/pathology ; Brain Neoplasms/diagnostic imaging ; Glioma/genetics ; Glioma/pathology ; Glioma/diagnostic imaging ; Microtubule-Associated Proteins/genetics ; Oncogene Proteins, Fusion/genetics ; Proto-Oncogene Proteins c-met/genetics
    Chemical Substances MET protein, human (EC 2.7.10.1) ; Microtubule-Associated Proteins ; Oncogene Proteins, Fusion ; Proto-Oncogene Proteins c-met (EC 2.7.10.1) ; cytoplasmic linker protein 115
    Language English
    Publishing date 2024-04-22
    Publishing country England
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2715589-4
    ISSN 2051-5960 ; 2051-5960
    ISSN (online) 2051-5960
    ISSN 2051-5960
    DOI 10.1186/s40478-024-01776-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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