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Article ; Online: Superficial dedifferentiated liposarcoma: A clinicopathologic study.

Bourgeau, Melanie / Gandhi, Jatin S / Deeb, Kristin K / Bahrami, Armita

2024 Volume 145, Page(s) 63–70

Abstract: Introduction: Dedifferentiation occurs in approximately 10% of atypical lipomatous tumors/well-differentiated liposarcomas (ALT/WDLPS), primarily in retroperitoneal or deep-seated tumors, conferring metastatic potential. Superficial dedifferentiated ... ...

Abstract	Introduction: Dedifferentiation occurs in approximately 10% of atypical lipomatous tumors/well-differentiated liposarcomas (ALT/WDLPS), primarily in retroperitoneal or deep-seated tumors, conferring metastatic potential. Superficial dedifferentiated liposarcoma (sDDLPS) is rare, and its progression and natural history are poorly documented. Methods: We performed a 15-year retrospective review of our pathology database to identify cases of DDLPS in the skin or subcutaneous tissue. Diagnosis of primary sDDLPS required evidence of non-lipogenic sarcoma in the skin or subcutis, with concurrent ALT/WDLPS and/or MDM2 amplification. Results: We identified 14 cases of DDLPS involving skin or subcutis: 7 primary sDDLPS and 7 secondary lesions (3 from recurrent deep DDLPS and 4 from metastasis). Primary sDDLPS cases (4 females, 3 males; median age: 74) mainly presented as undifferentiated spindle cell or pleomorphic sarcoma. Tumor grades were grade 2 (5 cases) and grade 3 (2 cases), with three cases also showing grade 1 areas. MDM2 amplification was confirmed in 6 sDDLPSs for which FISH was successfully performed. Follow-up available for 6 sDDLPS patients showed 2 local recurrences, treated with re-excision and radiation therapy, with all disease-free at last follow-up (5-126 months). Of the 7 secondary cases, 2 had ongoing disease after multiple recurrences, 1 was disease-free, and all 4 with cutaneous metastasis died of disease (follow-up range: 24-263 months). Conclusion: These findings emphasize the importance of distinguishing between primary sDDLPS and secondary lesions due to their distinct prognoses. Metastasis or superficial extensions from deep DDLP correlate with a considerably worse prognosis than those originating in superficial tissues.
MeSH term(s)	Female ; Male ; Humans ; Aged ; Skin ; Lipoma ; Sarcoma ; Skin Neoplasms/genetics ; Skin Neoplasms/therapy ; Liposarcoma/genetics ; Proto-Oncogene Proteins c-mdm2/genetics
Chemical Substances	Proto-Oncogene Proteins c-mdm2 (EC 2.3.2.27)
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	207657-3
ISSN	1532-8392 ; 0046-8177
ISSN (online)	1532-8392
ISSN	0046-8177
DOI	10.1016/j.humpath.2024.02.008
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Zs.A 722: Show issues

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Article: Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives.

Zhang, Linsheng / Deeb, George / Deeb, Kristin K / Vale, Colin / Peker Barclift, Deniz / Papadantonakis, Nikolaos

Cancers

2024 Volume 16, Issue 8

Abstract: Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable ( ... ...

Abstract	Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
Language	English
Publishing date	2024-04-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers16081503
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Article ; Online: Comment on "A Novel

Deeb, Kristin K / Li, Shiyong / Zhang, Linsheng

International journal of surgical pathology

2021 Volume 30, Issue 7, Page(s) 839–840

MeSH term(s)	Calcium-Binding Proteins ; Fasciitis/diagnosis ; Fasciitis/genetics ; Hemangioendothelioma, Epithelioid ; Humans ; Trans-Activators ; Transcription Factors
Chemical Substances	CAMTA1 protein, human ; Calcium-Binding Proteins ; Trans-Activators ; Transcription Factors
Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	1336393-1
ISSN	1940-2465 ; 1066-8969
ISSN (online)	1940-2465
ISSN	1066-8969
DOI	10.1177/10668969211065113
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Zs.A 4500: Show issues

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Article ; Online: Loss of heterozygosity leading to incorrect HLA typing for platelet-transfusion refractory patient.

Horwath, Michael / Tvrdik, Tatiana / Saxe, Debra / Deeb, Kristin K / Roback, John D / Gebel, Howard M / Bray, Robert A / Sullivan, Harold Clifford

Transfusion

2022 Volume 63, Issue 1, Page(s) 263–268

Abstract: Background: Management of platelet-transfusion refractory (PR) patients due to anti-HLA antibodies includes the provision of HLA-matched (HLAm) platelets (PLT) or PLTs that are negative for HLA antigens corresponding to the recipient antibodies. ... ...

Abstract	Background: Management of platelet-transfusion refractory (PR) patients due to anti-HLA antibodies includes the provision of HLA-matched (HLAm) platelets (PLT) or PLTs that are negative for HLA antigens corresponding to the recipient antibodies. Obtaining HLAm PLTs is predicated on accurate HLA antigen typing of the recipient and donor. Here, we present the clinical implications of a case involving loss of heterozygosity (LOH) in a patient presented for PR workup. Study design and methods: HLA typing was performed by three methods: (1) Real-time PCR; (2) Sequence-specific oligonucleotide (SSO) typing test; and (3) Next-Generation Sequencing (NGS). Cytogenomic SNP microarray was utilized to assess LOH. Results: A 30-year-old female with newly diagnosed acute myelogenous leukemia was found to be PR secondary to HLA sensitization. A peripheral blood (PB) sample, containing 93% myeloid blast cells, was sent for HLA typing for the provision of HLAm PLTs. HLA typing revealed homozygosity at the HLA-A locus but was heterozygous at the -B and -C loci. After chemotherapy, HLA typing on a new PB sample, devoid of blast cells, identified HLA-A locus heterozygosity, which was subsequently confirmed by real-time PCR and NGS. Cytogenomic SNP microarray analysis demonstrated LOH of the HLA-A locus on chromosome 6p in the pretreatment sample but not in the posttreatment sample. Conclusion: In hematologic patients with high tumor burden, HLA homozygosity should be viewed with suspicion for potential LOH. Therefore, HLA testing should be repeated, preferably with a non-hematological source (e.g., buccal swab) or following successful reduction of the tumor burden.
MeSH term(s)	Adult ; Female ; Humans ; Histocompatibility Testing ; HLA-A Antigens/genetics ; Leukemia, Myeloid, Acute/genetics ; Leukemia, Myeloid, Acute/therapy ; Leukemia, Myeloid, Acute/diagnosis ; Loss of Heterozygosity ; Platelet Transfusion
Chemical Substances	HLA-A Antigens
Language	English
Publishing date	2022-11-25
Publishing country	United States
Document type	Case Reports
ZDB-ID	208417-x
ISSN	1537-2995 ; 0041-1132
ISSN (online)	1537-2995
ISSN	0041-1132
DOI	10.1111/trf.17189
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Zs.A 284: Show issues

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Article ; Online: Genetic Profiling of African American Patients With Prostatic Adenocarcinoma Metastatic to the Lymph Nodes: A Pilot Study.

Bidot, Samuel / Yin, Jun / Zhou, Pengbo / Zhang, Linsheng / Deeb, Kristin K / Smith, Geoffrey / Hill, Charles E / Xiu, Joanne / Bilen, Mehmet A / Case, Katherine B / Tinsley, Mazie / Carthon, Bradley / Harik, Lara R

Archives of pathology & laboratory medicine

2023 Volume 148, Issue 3, Page(s) 310–317

Abstract: Context.—: Genetic profiling data of prostatic adenocarcinoma are derived from predominantly White patients. In African Americans, prostatic adenocarcinoma has a poorer prognosis, raising the possibility of distinct genetic alterations.: Objective.—: ...

Abstract	Context.—: Genetic profiling data of prostatic adenocarcinoma are derived from predominantly White patients. In African Americans, prostatic adenocarcinoma has a poorer prognosis, raising the possibility of distinct genetic alterations. Objective.—: To investigate the genomic alterations of prostatic adenocarcinoma metastatic to regional lymph nodes in African American patients, with an emphasis on SPOP mutation. Design.—: We retrospectively reviewed African American patients with pN1 prostatic adenocarcinoma managed with radical prostatectomy and lymph node dissection. Comprehensive molecular profiling was performed, and androgen receptor signaling scores were calculated. Results.—: Nineteen patients were included. The most frequent genetic alteration was SPOP mutations (5 of 17; 29.4% [95% CI: 10.3-56.0]). While most alterations were associated with a high androgen receptor signaling score, mutant SPOP was exclusively associated with a low median and interquartile range (IQR) androgen receptor signaling score (0.788 [IQR 0.765-0.791] versus 0.835 [IQR 0.828-0.842], P = .003). In mutant SPOP, mRNA expression of SPOP inhibitor G3BP1 and SPOP substrates showed a significantly decreased expression of AR (33.40 [IQR 28.45-36.30] versus 59.53 [IQR 53.10-72.83], P = .01), TRIM24 (3.95 [IQR 3.28-5.03] versus 9.80 [IQR 7.39-11.70], P = .008), and NCOA3 (15.19 [IQR 10.59-15.93] versus 21.88 [IQR 18.41-28.33], P = .046). Conclusions.—: African American patients with metastatic prostate adenocarcinoma might have a higher prevalence of mutant SPOP (30%), compared to ∼10% in unselected cohorts with lower expressions of SPOP substrates. In our study, in patients with mutant SPOP, the mutation was associated with decreased SPOP substrate expression and androgen receptor signaling, raising concern for suboptimal efficacy of androgen deprivation therapy in this subset of patients.
MeSH term(s)	Humans ; Male ; Adenocarcinoma/genetics ; Adenocarcinoma/pathology ; Androgen Antagonists ; Black or African American/genetics ; Carrier Proteins ; DNA Helicases ; Lymph Nodes/pathology ; Nuclear Proteins/genetics ; Pilot Projects ; Poly-ADP-Ribose Binding Proteins ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology ; Receptors, Androgen/genetics ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Retrospective Studies ; RNA Helicases/metabolism ; RNA Recognition Motif Proteins
Chemical Substances	Androgen Antagonists ; Carrier Proteins ; DNA Helicases (EC 3.6.4.-) ; G3BP1 protein, human (EC 3.6.4.12) ; Nuclear Proteins ; Poly-ADP-Ribose Binding Proteins ; Receptors, Androgen ; Repressor Proteins ; RNA Helicases (EC 3.6.4.13) ; RNA Recognition Motif Proteins ; SPOP protein, human ; TRIM24 protein, human
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article
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.2022-0274-OA
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Article ; Online: Cytologic features of hepatic YAP1-TFE3 rearranged epithelioid hemangioendothelioma.

Bourgeau, Melanie / Martinez, Anthony / Deeb, Kristin K / Reid, Michelle D / Lewis, Melinda / Point du Jour, Kimberly S / Lai, Jinping / Shi, Qiuying

Diagnostic cytopathology

2021 Volume 49, Issue 12, Page(s) E447–E452

Abstract: Epithelioid hemangioendothelioma (EHE) is a rare vascular tumor of intermediate malignancy, often with indolent behavior. Though most cases have a characteristic WWTR1-CAMTA1 gene fusion, a subtype of EHE with YAP1-TFE3 fusions and a distinct morphology ... ...

Abstract	Epithelioid hemangioendothelioma (EHE) is a rare vascular tumor of intermediate malignancy, often with indolent behavior. Though most cases have a characteristic WWTR1-CAMTA1 gene fusion, a subtype of EHE with YAP1-TFE3 fusions and a distinct morphology has recently been described histologically, but no cases of YAP1-TFE3 EHE have been described in the cytology literature. We herein report on a case of YAP1-TFE3 fusion associated EHE diagnosed on fine-needle aspiration and core biopsy of a liver mass in an 18-year-old male patient who presented with synchronous lung and liver involvement. We also discuss the differential diagnosis of EHE on cytology specimens.
MeSH term(s)	Adolescent ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Biopsy, Fine-Needle ; Hemangioendothelioma, Epithelioid/diagnostic imaging ; Hemangioendothelioma, Epithelioid/pathology ; Humans ; Liver/diagnostic imaging ; Liver/pathology ; Magnetic Resonance Imaging ; Male ; Oncogene Proteins, Fusion/genetics ; YAP-Signaling Proteins/metabolism
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Oncogene Proteins, Fusion ; TFE3 protein, human ; YAP-Signaling Proteins ; YAP1 protein, human
Language	English
Publishing date	2021-08-19
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	632710-2
ISSN	1097-0339 ; 8755-1039
ISSN (online)	1097-0339
ISSN	8755-1039
DOI	10.1002/dc.24853
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Zs.A 2117: Show issues

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Article ; Online: Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms.

Sahajpal, Nikhil S / Mondal, Ashis K / Tvrdik, Tatiana / Hauenstein, Jennifer / Shi, Huidong / Deeb, Kristin K / Saxe, Debra / Hastie, Alex R / Chaubey, Alka / Savage, Natasha M / Kota, Vamsi / Kolhe, Ravindra

The Journal of molecular diagnostics : JMD

2022 Volume 24, Issue 12, Page(s) 1279–1291

Abstract: The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive and time and cost prohibitive, and they ... ...

Abstract	The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive and time and cost prohibitive, and they often do not reveal the genetic complexity of the tumor, demonstrating the need for alternative technology for better characterization of these tumors. Herein, we report the results from our clinical validation study and demonstrate the utility of optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 hematological neoplasms and 10 controls). The technical performance (quality control metrics) resulted in 100% first-pass rate, with analytical performance (concordance) showing a sensitivity of 98.7%, a specificity of 100%, and an accuracy of 99.2%. OGM demonstrated robust technical, analytical performance, and interrun, intrarun, and interinstrument reproducibility. The limit of detection was determined to be at 5% allele fraction for aneuploidy, translocation, interstitial deletion, and duplication. OGM identified several additional structural variations, revealing the genomic architecture in these neoplasms that provides an opportunity for better tumor classification, prognostication, risk stratification, and therapy selection. Overall, OGM has outperformed the standard-of-care tests in this study and demonstrated its potential as a first-tier cytogenomic test for hematologic malignancies.
MeSH term(s)	Humans ; In Situ Hybridization, Fluorescence ; Reproducibility of Results ; Karyotyping ; Hematologic Neoplasms/diagnosis ; Hematologic Neoplasms/genetics ; Chromosome Mapping ; Chromosome Aberrations
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2022.09.009
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Zs.A 5146: Show issues

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Article ; Online: The Value of Comprehensive Thyroid Function Testing and Family History for Early Diagnosis of MCT8 Deficiency.

Bedoyan, Jirair K / Tim-Aroon, Thipwimol / Deeb, Kristin K / Ganganna, Sreenath Thati / Bass, Nancy E

Clinical pediatrics

2016 Volume 55, Issue 3, Page(s) 286–289

MeSH term(s)	Child ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Mental Retardation, X-Linked/diagnosis ; Mental Retardation, X-Linked/drug therapy ; Mental Retardation, X-Linked/genetics ; Muscle Hypotonia/diagnosis ; Muscle Hypotonia/drug therapy ; Muscle Hypotonia/genetics ; Muscular Atrophy/diagnosis ; Muscular Atrophy/drug therapy ; Muscular Atrophy/genetics ; Neonatal Screening ; Thyroid Function Tests
Language	English
Publishing date	2016-03
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	207678-0
ISSN	1938-2707 ; 0009-9228
ISSN (online)	1938-2707
ISSN	0009-9228
DOI	10.1177/0009922815584219
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Article ; Online: Multigene assays in metastatic colorectal cancer.

Deeb, Kristin K / Sram, Jakub P / Gao, Hanlin / Fakih, Marwan G

Journal of the National Comprehensive Cancer Network : JNCCN

2013 Volume 11 Suppl 4, Page(s) S9–17

Abstract: Specific genomic colorectal cancer alterations are increasingly linked to prognosis and/or response to specific anticancer agents. The identification of KRAS mutations as markers of resistance to epidermal growth factor receptor (EGFR) inhibitors has ... ...

Abstract	Specific genomic colorectal cancer alterations are increasingly linked to prognosis and/or response to specific anticancer agents. The identification of KRAS mutations as markers of resistance to epidermal growth factor receptor (EGFR) inhibitors has paved the way to the interrogation of numerous other markers of resistance to anti-EGFR therapy, such as NRAS, BRAF, and PI3KCA mutations. Other genomic and protein expression alterations have recently been identified as potential targets of treatment or as markers of chemotherapy or targeted-therapy resistance, including ERCC1 expression, c-Met expression, PTEN expression, HER2 amplification, HER3 expression, and rare KRAS mutations. As the number of distinct validated intratumor genomic assays increases, numerous molecular assays will need to be compiled into one multigene panel assay. Several companies and academic centers are now offering multigene assays to patients with metastatic colorectal cancer and other solid tumors. This article discusses the technology behind multigene assays, its limitations, its current advantages, and its potential in the clinical care of metastatic colorectal cancer.
MeSH term(s)	Biomarkers, Tumor/genetics ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; Neoplasm Metastasis
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2013-10-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2250759-0
ISSN	1540-1413 ; 1540-1405
ISSN (online)	1540-1413
ISSN	1540-1405
DOI	10.6004/jnccn.2013.0221
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Article ; Online: Routine Clinical Mutation Profiling of Non-Small Cell Lung Cancer Using Next-Generation Sequencing.

Deeb, Kristin K / Hohman, Colleen M / Risch, Nicholas F / Metzger, Daniel J / Starostik, Petr

Archives of pathology & laboratory medicine

2015 Volume 139, Issue 7, Page(s) 913–921

Abstract: Context: The availability of massive, parallel-sequencing technologies makes possible efficient, simultaneous detection of driver and druggable mutations in cancer.: Objective: To develop an amplicon-based, next-generation sequencing, mutation- ... ...

Abstract	Context: The availability of massive, parallel-sequencing technologies makes possible efficient, simultaneous detection of driver and druggable mutations in cancer. Objective: To develop an amplicon-based, next-generation sequencing, mutation-detection assay for lung cancer using the 454 GS Junior (Roche Applied Science, Indianapolis, Indiana) platform. Design: Fusion primers incorporating target sequence, 454 adaptors, and multiplex identifiers were designed to generate 35 amplicons (median length 246 base pairs) covering 8.9 kilobases of mutational hotspots in AKT1, BRAF, EGFR, ERBB2, HRAS, KRAS, NRAS, PIK3CA, and MAP2K1 genes and all exons of the PTEN gene. Results: The assay was validated on 23 formalin-fixed, paraffin-embedded lung cancer specimens. A minimum number of reads was consistently achieved with overall median read depth of 529× per amplicon. In total, 25 point mutations and 4 insertions/deletions (indels) with a frequency of 5.5% to 93.1% mutant alleles were detected. All EGFR, ERBB2, KRAS, PIK3CA, KRAS, and PTEN mutations, as detected by next-generation sequencing, were confirmed by pyrosequencing, with the exception of 3 point mutations in a tumor sample with low mutant-allele burden (below the pyrosequencing limit of detection). Conclusions: The GS Junior-based, targeted, resequencing assay for a focused set of non-small cell lung cancer driver genes allows for quick and sensitive detection of point mutations and indels for the most relevant therapeutic genes in this type of cancer.
MeSH term(s)	Biomarkers, Tumor/genetics ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/pathology ; DNA Mutational Analysis/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Mutation ; Sequence Analysis, DNA/methods
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2015-07
Publishing country	United States
Document type	Journal Article
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.2014-0095-OA
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