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  1. Article ; Online: GLI1 Coamplification in Well-Differentiated/Dedifferentiated Liposarcomas: Clinicopathologic and Molecular Analysis of 92 Cases.

    Sharma, Aarti E / Dickson, Mark / Singer, Samuel / Hameed, Meera R / Agaram, Narasimhan P

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2024  Volume 37, Issue 6, Page(s) 100494

    Abstract: GLI1(12q13.3) amplification is identified in a subset of mesenchymal neoplasms with a distinct nested round cell/epithelioid phenotype. MDM2 and CDK4 genes are situated along the oncogenic 12q13-15 segment, amplification of which defines well- ... ...

    Abstract GLI1(12q13.3) amplification is identified in a subset of mesenchymal neoplasms with a distinct nested round cell/epithelioid phenotype. MDM2 and CDK4 genes are situated along the oncogenic 12q13-15 segment, amplification of which defines well-differentiated liposarcoma (WDLPS)/dedifferentiated liposarcoma (DDLPS). The 12q amplicon can occasionally include GLI1, a gene in close proximity to CDK4. We hereby describe the first cohort of GLI1/MDM2/CDK4 coamplified WD/DDLPS. The departmental database was queried retrospectively for all cases of WD/DDLPS having undergone next-generation (MSK-IMPACT) sequencing with confirmed MDM2, CDK4, and GLI1 coamplification. Clinicopathologic data was obtained from a review of the medical chart and available histologic material. Four hundred eighty-six WD/DDLPS cases underwent DNA sequencing, 92 (19%) of which harbored amplification of the GLI1 locus in addition to that of MDM2 and CDK4. These included primary tumors (n = 60), local recurrences (n = 29), and metastases (n = 3). Primary tumors were most frequently retroperitoneal (47/60, 78%), mediastinal (4/60, 7%), and paratesticular (3/60, 5%). Average age was 63 years, with a male:female ratio of 3:2. The cohort was comprised of DDLPS (86/92 [93%], 6 of which were WDLPS with early dedifferentiation) and WDLPS without any longitudinal evidence of dedifferentiation (6/92, 7%). One-fifth (13/86, 17%) of DDLPS cases showed no evidence of a well-differentiated component in any of the primary, recurrent, or metastatic specimens. Dedifferentiated areas mostly showed high-grade undifferentiated pleomorphic sarcoma-like (26/86,30%) and high-grade myxofibrosarcoma-like (13/86,16%) morphologies. A disproportionately increased incidence of meningothelial whorls with/without osseous metaplasia was observed as the predominant pattern in 16/86 (19%) cases, and GLI1-altered morphology as described was identified in a total of 10/86 (12%) tumors. JUN (1p32.1), also implicated in the pathogenesis of WD/DDLPS, was coamplified with all 3 of MDM2, CDK4, and GLI1 in 7/91 (8%) cases. Additional loci along chromosomal arms 1p and 6q, including TNFAIP3, LATS1, and ESR1, were also amplified in a subset of cases. In this large-scale cohort of GLI1 coamplified WD/DDLPS, we elucidate uniquely recurrent features including meningothelial whorl-like and GLI-altered morphology in dedifferentiated areas. Assessment of tumor location (retroperitoneal or mediastinal), identification of a well-differentiated liposarcoma component, and coamplification of other spatially discrete genomic segments (1p and 6q) might aid in distinction from tumors with true driver GLI1 alterations.
    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1016/j.modpat.2024.100494
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Toward Deploying a Deep Learning Model for Diagnosis of Rhabdomyosarcoma.

    Ho, David Joon / Agaram, Narasimhan P / Frankel, Arthur O / Lathara, Melvin / Catchpoole, Daniel / Keller, Charles / Hameed, Meera R

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2024  Volume 37, Issue 3, Page(s) 100421

    MeSH term(s) Humans ; Deep Learning ; Rhabdomyosarcoma/diagnosis ; Rhabdomyosarcoma/pathology ; Diagnosis, Differential
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Letter
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1016/j.modpat.2024.100421
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Mesenchymal chondrosarcoma: imaging features and clinical findings.

    Ghafoor, Soleen / Hameed, Meera R / Tap, William D / Hwang, Sinchun

    Skeletal radiology

    2020  Volume 50, Issue 2, Page(s) 333–341

    Abstract: Objective: To describe imaging and clinical features of primary mesenchymal chondrosarcoma (MCS) and evaluate for presence of a distinct biphasic pattern on imaging.: Material and methods: Patients with a pathologic diagnosis of MCS were identified ... ...

    Abstract Objective: To describe imaging and clinical features of primary mesenchymal chondrosarcoma (MCS) and evaluate for presence of a distinct biphasic pattern on imaging.
    Material and methods: Patients with a pathologic diagnosis of MCS were identified along with imaging of their primary tumor. Size, location, appearance (lytic, sclerotic, or mixed), presence, extent and distribution of calcifications, cortical destruction, soft tissue extension, periosteal reaction, contrast enhancement, and radiotracer uptake were recorded. The presence of T2-hyperintense tumor lobules on MRI and a biphasic morphology (distinct calcified and non-calcified components) on CT were assessed. Presence and location of metastases were documented.
    Results: Twenty-three patients (mean age 28.0 ± 13.8 years) were reviewed (13 skeletal, 10 extraskeletal). Overall mean tumor size was 10.2 ± 7.2 cm, 7.1 ± 7.3 cm in non-metastatic and 13.2 ± 5.9 cm (p = 0.004) in metastatic cases. Locations were extremities (n = 11), head/neck (n = 4), chest wall (n = 4), pelvis (n = 3), and retroperitoneum (n = 1). Skeletal MCS were aggressive mixed lytic and sclerotic (n = 8), purely lytic (n = 4), or juxtacortical (n = 1) lesions with cortical destruction and soft tissue extension. Chondroid calcifications were common (80%). On MRI, the presence of T2-hyperintense lobules was seen in 35%. A biphasic morphology on imaging was seen in 30%. Metastases were common (52%) with the most common site being the lungs (75%). All tumors were hypermetabolic with a mean SUVmax of 14.3 (5.6-34) on PET/CT.
    Conclusion: Skeletal MCS commonly present as aggressive lytic bone lesions with chondroid calcifications. A biphasic morphology was seen in one-third of cases. Metastases were common at initial presentation and more commonly seen with larger tumors.
    MeSH term(s) Adolescent ; Adult ; Bone Neoplasms/diagnostic imaging ; Chondrosarcoma ; Chondrosarcoma, Mesenchymal/diagnostic imaging ; Humans ; Magnetic Resonance Imaging ; Positron Emission Tomography Computed Tomography ; Retrospective Studies ; Young Adult
    Language English
    Publishing date 2020-07-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 527592-1
    ISSN 1432-2161 ; 0364-2348
    ISSN (online) 1432-2161
    ISSN 0364-2348
    DOI 10.1007/s00256-020-03558-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Publisher Correction: Integrating digital pathology into clinical practice.

    Hanna, Matthew G / Ardon, Orly / Reuter, Victor E / England, Christine / Klimstra, David S / Hameed, Meera R

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2021  Volume 35, Issue 2, Page(s) 287

    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1038/s41379-021-00948-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: RNA Sequencing for Solid Tumor Fusion Gene Detection: Proficiency Testing Practice and Performance Comparison.

    Bridge, Julia A / Halling, Kevin C / Moncur, Joel T / Souers, Rhona J / Hameed, Meera R / Fernandes, Helen / Roy, Angshumoy / Surrey, Lea / Tafe, Laura J / Vasalos, Patricia / Lopez-Terrada, Dolores H

    Archives of pathology & laboratory medicine

    2023  Volume 148, Issue 5, Page(s) 538–544

    Abstract: Context: Next-generation sequencing-based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, the College of American ... ...

    Abstract Context: Next-generation sequencing-based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, the College of American Pathologists (CAP) has advanced RNA sequencing proficiency testing (PT) to ensure optimal performance of these assays.
    Objective: To report on laboratory performance and practices of RNA sequencing for the detection of fusion genes, intragenic rearrangements, and exon-skipping events using CAP PT data from 8 mailings (2018-A through 2021-B).
    Design: CAP PT RNA sequencing program results from 153 laboratories across 24 proficiency test specimens, interrogating 22 distinct engineered fusion transcripts, were analyzed for correct identification of the fusion event, associated performance variables, and laboratory practices.
    Results: Overall, the 4-year program detection rate (sensitivity) was 95.5% (1486 of 1556 results). False-negative rates were 3.6% (53 of 1463) and 18.3% (17 of 93) for fusion gene and intragenic rearrangement/exon-skipping events, respectively. Only 19 false-positive results were reported among the 8 PT mailings, and most were likely the result of preanalytical or postanalytical errors. There were no practice characteristics (eg, instrumentation, sequencing method) significantly associated with the fusion detection results.
    Conclusions: These data reveal a high overall sensitivity and specificity for fusion gene detection by participating laboratories using clinical RNA sequencing. Performance was comparable across all laboratories, regardless of methodology. The fraction of false-negative results for intragenic rearrangement/exon-skipping events was greater than that for the chimeric fusion genes. False-negative results could not be attributed to any specific practice characteristics.
    MeSH term(s) Humans ; Laboratory Proficiency Testing ; High-Throughput Nucleotide Sequencing ; Oncogene Proteins, Fusion/genetics ; Sequence Analysis, RNA ; Neoplasms/genetics ; Neoplasms/diagnosis ; Gene Fusion ; Sensitivity and Specificity
    Chemical Substances Oncogene Proteins, Fusion
    Language English
    Publishing date 2023-08-04
    Publishing country United States
    Document type Journal Article ; Comparative Study
    ZDB-ID 194119-7
    ISSN 1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
    ISSN (online) 1543-2165
    ISSN 0363-0153 ; 0096-8528 ; 0003-9985
    DOI 10.5858/arpa.2023-0047-CP
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Quality Management System in Clinical Digital Pathology Operations at a Tertiary Cancer Center.

    Ardon, Orly / Labasin, Marc / Friedlander, Maria / Manzo, Allyne / Corsale, Lorraine / Ntiamoah, Peter / Wright, Jeninne / Elenitoba-Johnson, Kojo / Reuter, Victor E / Hameed, Meera R / Hanna, Matthew G

    Laboratory investigation; a journal of technical methods and pathology

    2023  Volume 103, Issue 11, Page(s) 100246

    Abstract: Digital pathology workflows can improve pathology operations by allowing reliable and fast retrieval of digital images, digitally reviewing pathology slides, enabling remote work and telepathology, use of computer-aided tools, and sharing of digital ... ...

    Abstract Digital pathology workflows can improve pathology operations by allowing reliable and fast retrieval of digital images, digitally reviewing pathology slides, enabling remote work and telepathology, use of computer-aided tools, and sharing of digital images for research and educational purposes. The need for quality systems is a prerequisite for successful clinical-grade digital pathology adoption and patient safety. In this article, we describe the development of a structured digital pathology laboratory quality management system (QMS) for clinical digital pathology operations at Memorial Sloan Kettering Cancer Center (MSK). This digital pathology-specific QMS development stemmed from the gaps that were identified when MSK integrated digital pathology into its clinical practice. The digital scan team in conjunction with the Department of Pathology and Laboratory Medicine quality team developed a QMS tailored to the scanning operation to support departmental and institutional needs. As a first step, systemic mapping of the digital pathology operations identified the prescan, scan, and postscan processes; instrumentation; and staffing involved in the digital pathology operation. Next, gaps identified in quality control and quality assurance measures led to the development of standard operating procedures and training material for the different roles and workflows in the process. All digital pathology-related documents were subject to regulatory review and approval by departmental leadership. The quality essentials were developed into an extensive Digital Pathology Quality Essentials framework to specifically address the needs of the growing clinical use of digital pathology technologies. Using the unique digital experience gained at MSK, we present our recommendations for QMS for large-scale digital pathology operations in clinical settings.
    MeSH term(s) Humans ; Laboratories ; Neoplasms/diagnosis ; Neoplasms/surgery ; Pathology, Clinical/methods ; Telepathology/methods ; Total Quality Management
    Language English
    Publishing date 2023-09-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80178-1
    ISSN 1530-0307 ; 0023-6837
    ISSN (online) 1530-0307
    ISSN 0023-6837
    DOI 10.1016/j.labinv.2023.100246
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  7. Article ; Online: Integrating digital pathology into clinical practice.

    Hanna, Matthew G / Ardon, Orly / Reuter, Victor E / Sirintrapun, Sahussapont Joseph / England, Christine / Klimstra, David S / Hameed, Meera R

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2021  Volume 35, Issue 2, Page(s) 152–164

    Abstract: The field of anatomic pathology has been evolving in the last few decades and the advancements have been largely fostered by innovative technology. Immunohistochemistry enabled a paradigm shift in discovery and diagnostic evaluation, followed by booming ... ...

    Abstract The field of anatomic pathology has been evolving in the last few decades and the advancements have been largely fostered by innovative technology. Immunohistochemistry enabled a paradigm shift in discovery and diagnostic evaluation, followed by booming genomic advancements which allowed for submicroscopic pathologic characterization, and now the field of digital pathology coupled with machine learning and big data acquisition is paving the way to revolutionize the pathology medical domain. Whole slide imaging (WSI) is a disruptive technology where glass slides are digitized to produce on-screen whole slide images. Specifically, in the past decade, there have been significant advances in digital pathology systems that have allowed this technology to promote integration into clinical practice. Whole slide images (WSI), or digital slides, can be viewed and navigated comparable to glass slides on a microscope, as digital files. Whole slide imaging has increased in adoption among pathologists, pathology departments, and scientists for clinical, educational, and research initiatives. Integration of digital pathology systems requires a coordinated effort with numerous stakeholders, not only within the pathology department, but across the entire enterprise. Each pathology department has distinct needs, use cases and blueprints, however the framework components and variables for successful clinical integration can be generalized across any organization seeking to undergo a digital transformation at any scale. This article will review those components and considerations for integrating digital pathology systems into clinical practice.
    MeSH term(s) Humans ; Microscopy/methods ; Pathologists ; Pathology, Clinical/methods
    Language English
    Publishing date 2021-10-01
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1038/s41379-021-00929-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Correction: Integrating digital pathology into clinical practice.

    Hanna, Matthew G / Ardon, Orly / Reuter, Victor E / Sirintrapun, Sahussapont Joseph / England, Christine / Klimstra, David S / Hameed, Meera R

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2021  Volume 35, Issue 2, Page(s) 286

    Language English
    Publishing date 2021-11-09
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1038/s41379-021-00968-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Digital pathology operations at a tertiary cancer center: Infrastructure requirements and operational cost.

    Ardon, Orly / Klein, Eric / Manzo, Allyne / Corsale, Lorraine / England, Christine / Mazzella, Allix / Geneslaw, Luke / Philip, John / Ntiamoah, Peter / Wright, Jeninne / Sirintrapun, Sahussapont Joseph / Lin, Oscar / Elenitoba-Johnson, Kojo / Reuter, Victor E / Hameed, Meera R / Hanna, Matthew G

    Journal of pathology informatics

    2023  Volume 14, Page(s) 100318

    Abstract: Whole slide imaging is revolutionizing the field of pathology and is currently being used for clinical, educational, and research initiatives by an increasing number of institutions. Pathology departments have distinct needs for digital pathology systems, ...

    Abstract Whole slide imaging is revolutionizing the field of pathology and is currently being used for clinical, educational, and research initiatives by an increasing number of institutions. Pathology departments have distinct needs for digital pathology systems, yet the cost of digital workflows is cited as a major barrier for widespread adoption by many organizations. Memorial Sloan Kettering Cancer Center (MSK) is an early adopter of whole slide imaging with incremental investments in resources that started more than 15 years ago. This experience and the large-scale scan operations led to the identification of required framework components of digital pathology operations. The cost of these components for the 2021 digital pathology operations at MSK were studied and calculated to enable an understanding of the operation and benchmark the accompanying costs. This paper describes the unique infrastructure cost and the costs associated with the digital pathology clinical operation use cases in a large, tertiary cancer center. These calculations can serve as a blueprint for other institutions to provide the necessary concepts and offer insights towards the financial requirements for digital pathology adoption by other institutions.
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2579241-6
    ISSN 2153-3539 ; 2229-5089
    ISSN (online) 2153-3539
    ISSN 2229-5089
    DOI 10.1016/j.jpi.2023.100318
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  10. Article ; Online: PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis.

    Hu, Jia / Hameed, Meera R / Agaram, Narasimhan P / Whiting, Karissa A / Qin, Li-Xuan / Villano, Anthony M / O'Connor, Rachael B / Rozenberg, Julian M / Cohen, Sonia / Prendergast, Katherine / Kryeziu, Sara / White, Richard L / Posner, Mitchell C / Socci, Nicholas D / Gounder, Mrinal M / Singer, Samuel / Crago, Aimee M

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2023  Volume 30, Issue 2, Page(s) 450–461

    Abstract: Purpose: This study sought to identify β-catenin targets that regulate desmoid oncogenesis and determine whether external signaling pathways, particularly those inhibited by sorafenib (e.g., PDGFRβ), affect these targets to alter natural history or ... ...

    Abstract Purpose: This study sought to identify β-catenin targets that regulate desmoid oncogenesis and determine whether external signaling pathways, particularly those inhibited by sorafenib (e.g., PDGFRβ), affect these targets to alter natural history or treatment response in patients.
    Experimental design: In vitro experiments utilized primary desmoid cell lines to examine regulation of β-catenin targets. Relevance of results was assessed in vivo using Alliance trial A091105 correlative biopsies.
    Results: CTNNB1 knockdown inhibited hypoxia-regulated gene expression in vitro and reduced levels of HIF1α protein. ChIP-seq identified ABL1 as a β-catenin transcriptional target that modulated HIF1α and desmoid cell proliferation. Abrogation of either CTNNB1 or HIF1A inhibited desmoid cell-induced VEGFR2 phosphorylation and tube formation in endothelial cell co-cultures. Sorafenib inhibited this activity directly but also reduced HIF1α protein expression and c-Abl activity while inhibiting PDGFRβ signaling in desmoid cells. Conversely, c-Abl activity and desmoid cell proliferation were positively regulated by PDGF-BB. Reduction in PDGFRβ and c-Abl phosphorylation was commonly observed in biopsy samples from patients after treatment with sorafenib; markers of PDGFRβ/c-Abl pathway activation in baseline samples were associated with tumor progression in patients on the placebo arm and response to sorafenib in patients receiving treatment.
    Conclusions: The β-catenin transcriptional target ABL1 is necessary for proliferation and maintenance of HIF1α in desmoid cells. Regulation of c-Abl activity by PDGF signaling and targeted therapies modulates desmoid cell proliferation, thereby suggesting a reason for variable biologic behavior between tumors, a mechanism for sorafenib activity in desmoids, and markers predictive of outcome in patients.
    MeSH term(s) Humans ; Fibromatosis, Aggressive/drug therapy ; Fibromatosis, Aggressive/genetics ; beta Catenin/genetics ; beta Catenin/metabolism ; Sorafenib/pharmacology ; Signal Transduction ; Biological Products
    Chemical Substances beta Catenin ; Sorafenib (9ZOQ3TZI87) ; Biological Products
    Language English
    Publishing date 2023-11-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-23-2313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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