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1.
Cell ; 169(2): 258-272.e17, 2017 Apr 06.
Article in English | MEDLINE | ID: mdl-28388410

ABSTRACT

A complex interplay of environmental factors impacts the metabolism of human cells, but neither traditional culture media nor mouse plasma mimic the metabolite composition of human plasma. Here, we developed a culture medium with polar metabolite concentrations comparable to those of human plasma (human plasma-like medium [HPLM]). Culture in HPLM, relative to that in traditional media, had widespread effects on cellular metabolism, including on the metabolome, redox state, and glucose utilization. Among the most prominent was an inhibition of de novo pyrimidine synthesis-an effect traced to uric acid, which is 10-fold higher in the blood of humans than of mice and other non-primates. We find that uric acid directly inhibits uridine monophosphate synthase (UMPS) and consequently reduces the sensitivity of cancer cells to the chemotherapeutic agent 5-fluorouracil. Thus, media that better recapitulates the composition of human plasma reveals unforeseen metabolic wiring and regulation, suggesting that HPLM should be of broad utility.


Subject(s)
Culture Media/chemistry , Multienzyme Complexes/antagonists & inhibitors , Orotate Phosphoribosyltransferase/antagonists & inhibitors , Orotidine-5'-Phosphate Decarboxylase/antagonists & inhibitors , Uric Acid/metabolism , Aged , Animals , Cell Culture Techniques , Cell Line, Tumor , Fluorouracil/pharmacology , Glucose/metabolism , Humans , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/pathology , Male , Mice , Middle Aged , Multienzyme Complexes/chemistry , Orotate Phosphoribosyltransferase/chemistry , Orotidine-5'-Phosphate Decarboxylase/chemistry , Protein Domains , Pyrimidines/biosynthesis
2.
Oncologist ; 29(6): 473-483, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38520743

ABSTRACT

Thymic epithelial tumors (TETs) are rare tumors for which treatment options are limited. The ongoing need for improved systemic therapies reflects a limited understanding of tumor biology as well as the normal thymus. The essential role of the thymus in adaptive immunity is largely effected by its epithelial compartment, which directs thymocyte (T-cell) differentiation and immunologic self-tolerance. With aging, the thymus undergoes involution whereby epithelial tissue is replaced by adipose and other connective tissue, decreasing immature T-cell production. Against this natural drive toward involution, a fraction of thymuses will instead undergo oncologic transformation, leading to the formation of TETs, including thymoma and thymic carcinoma. The rarity of these tumors restricts investigation of the mechanisms of tumorigenesis and development of rational treatment options. To this end, the development of technologies which allow deep molecular profiling of individual tumor cells permits a new window through which to view normal thymic development and contrast the malignant changes that result in oncogenic transformation. In this review, we describe the findings of recent illuminating studies on the diversity of cell types within the epithelial compartment through thymic differentiation and aging. We contextualize these findings around important unanswered questions regarding the spectrum of known somatic tumor alterations, cell of origin, and tumor heterogeneity. The perspectives informed by single-cell molecular profiling offer new approaches to clinical and basic investigation of thymic epithelial tumors, with the potential to accelerate development of improved therapeutic strategies to address ongoing unmet needs in these rare tumors.


Subject(s)
Neoplasms, Glandular and Epithelial , Thymus Gland , Thymus Neoplasms , Humans , Thymus Neoplasms/pathology , Thymus Gland/pathology , Thymus Gland/immunology , Neoplasms, Glandular and Epithelial/pathology , Single-Cell Analysis/methods , Cell Differentiation
3.
Blood ; 138(14): 1225-1236, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34115827

ABSTRACT

Cutaneous T-cell lymphomas (CTCLs) are a clinically heterogeneous collection of lymphomas of the skin-homing T cell. To identify molecular drivers of disease phenotypes, we assembled representative samples of CTCLs from patients with diverse disease subtypes and stages. Via DNA/RNA-sequencing, immunophenotyping, and ex vivo functional assays, we identified the landscape of putative driver genes, elucidated genetic relationships between CTCLs across disease stages, and inferred molecular subtypes in patients with stage-matched leukemic disease. Collectively, our analysis identified 86 putative driver genes, including 19 genes not previously implicated in this disease. Two mutations have never been described in any cancer. Functionally, multiple mutations augment T-cell receptor-dependent proliferation, highlighting the importance of this pathway in lymphomagenesis. To identify putative genetic causes of disease heterogeneity, we examined the distribution of driver genes across clinical cohorts. There are broad similarities across disease stages. Many driver genes are shared by mycosis fungoides (MF) and Sezary syndrome (SS). However, there are significantly more structural variants in leukemic disease, leading to highly recurrent deletions of putative tumor suppressors that are uncommon in early-stage skin-centered MF. For example, TP53 is deleted in 7% and 87% of MF and SS, respectively. In both human and mouse samples, PD1 mutations drive aggressive behavior. PD1 wild-type lymphomas show features of T-cell exhaustion. PD1 deletions are sufficient to reverse the exhaustion phenotype, promote a FOXM1-driven transcriptional signature, and predict significantly worse survival. Collectively, our findings clarify CTCL genetics and provide novel insights into pathways that drive diverse disease phenotypes.


Subject(s)
Lymphoma, T-Cell, Cutaneous/genetics , Transcriptome , Animals , Cells, Cultured , Forkhead Box Protein M1/genetics , Gene Expression Regulation, Neoplastic , Genes, Tumor Suppressor , Humans , Mice , Mutation , Oncogenes , Tumor Suppressor Protein p53/genetics
4.
Br J Haematol ; 196(6): 1381-1387, 2022 03.
Article in English | MEDLINE | ID: mdl-34967008

ABSTRACT

Relapsed follicular lymphoma (FL) can arise from common progenitor cells (CPCs). Conceptually, CPC-defining mutations are somatic alterations shared by the initial and relapsed tumours, mostly B-cell leukaemia/lymphoma 2 (BCL2)/immunoglobulin heavy locus (IGH) translocations and other recurrent gene mutations. Through complementary approaches for highly sensitive mutation detection, we do not find CPC-defining mutations in highly purified BCL2/IGH-negative haematopoietic progenitor cells in clinical remission samples from three patients with relapsed FL. Instead, we find cells harbouring the same BCL2/IGH translocation but lacking CREB binding protein (CREBBP), lysine methyltransferase 2D (KMT2D) and other recurrent gene mutations. Thus, (i) the BCL2/IGH translocation can precede CPC-defining mutations in human FL, and (ii) BCL2/IGH-translocated cells can persist in clinical remission.


Subject(s)
Lymphoma, B-Cell , Lymphoma, Follicular , Hematopoietic Stem Cells/metabolism , Humans , Immunoglobulin Heavy Chains/genetics , Lymphoma, B-Cell/genetics , Lymphoma, Follicular/pathology , Mutation , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/metabolism , Translocation, Genetic
5.
Oncologist ; 26(7): e1263-e1272, 2021 07.
Article in English | MEDLINE | ID: mdl-33904632

ABSTRACT

BACKGROUND: Histiocytic and dendritic cell neoplasms are a diverse group of tumors arising from monocytic or dendritic cell lineage. Whereas the genomic features for Langerhans cell histiocytosis and Erdheim-Chester disease have been well described, other less common and often aggressive tumors in this broad category remain poorly characterized, and comparison studies across the World Health Organization diagnostic categories are lacking. METHODS: Tumor samples from a total of 102 patient cases within four major subtypes of malignant histiocytic and dendritic cell neoplasms, including 44 follicular dendritic cell sarcomas (FDCSs), 41 histiocytic sarcomas (HSs), 7 interdigitating dendritic cell sarcomas (IDCSs), and 10 Langerhans cell sarcomas (LCSs), underwent hybridization capture with analysis of up to 406 cancer-related genes. RESULTS: Among the entire cohort of 102 patients, CDKN2A mutations were most frequent across subtypes and made up 32% of cases, followed by TP53 mutations (22%). Mitogen-activated protein kinase (MAPK) pathway mutations were present and enriched among the malignant histiocytosis (M) group (HS, IDCS, and LCS) but absent in FDCS (72% vs. 0%; p < .0001). In contrast, NF-κB pathway mutations were frequent in FDCSs but rare in M group histiocytoses (61% vs. 12%; p < .0001). Tumor mutational burden was significantly higher in M group histiocytoses as compared with FDCSs (median 4.0/Mb vs. 2.4/Mb; p = .012). We also describe a pediatric patient with recurrent secondary histiocytic sarcoma treated with targeted therapy and interrogated by molecular analysis to identify mechanisms of therapeutic resistance. CONCLUSION: A total of 42 patient tumors (41%) harbored pathogenic mutations that were potentially targetable by approved and/or investigative therapies. Our findings highlight the potential value of molecular testing to enable precise tumor classification, identify candidate oncogenic drivers, and define personalized therapeutic options for patients with these aggressive tumors. IMPLICATIONS FOR PRACTICE: This study presents comprehensive genomic profiling results on 102 patient cases within four major subtypes of malignant histiocytic and dendritic cell neoplasms, including 44 follicular dendritic cell sarcomas (FDCSs), 41 histiocytic sarcomas (HSs), 7 interdigitating dendritic cell sarcomas (IDCSs), and 10 Langerhans cell sarcomas (LCSs). MAPK pathway mutations were present and enriched among the malignant histiocytosis (M) group (HS, IDCS, and LCS) but absent in FDCSs. In contrast, NF-κB pathway mutations were frequent in FDCSs but rare in M group histiocytosis. A total of 42 patient tumors (41%) harbored pathogenic mutations that were potentially targetable by approved and/or investigative therapies.


Subject(s)
Dendritic Cell Sarcoma, Follicular , Hematopoietic Stem Cell Transplantation , Sarcoma , Child , Dendritic Cell Sarcoma, Follicular/genetics , Dendritic Cells , Genomics , Humans , Mutation , Neoplasm Recurrence, Local , Sarcoma/genetics
6.
Blood ; 134(17): 1430-1440, 2019 10 24.
Article in English | MEDLINE | ID: mdl-31383641

ABSTRACT

Antibodies that bind CD47 on tumor cells and prevent interaction with SIRPα on phagocytes are active against multiple cancer types including T-cell lymphoma (TCL). Here we demonstrate that surface CD47 is heterogeneously expressed across primary TCLs, whereas major histocompatibility complex (MHC) class I, which can also suppress phagocytosis, is ubiquitous. Multiple monoclonal antibodies (mAbs) that block CD47-SIRPα interaction promoted phagocytosis of TCL cells, which was enhanced by cotreatment with antibodies targeting MHC class I. Expression levels of surface CD47 and genes that modulate CD47 pyroglutamation did not correlate with the extent of phagocytosis induced by CD47 blockade in TCL lines. In vivo treatment of multiple human TCL patient-derived xenografts or an immunocompetent murine TCL model with a short course of anti-CD47 mAb markedly reduced lymphoma burden and extended survival. Depletion of macrophages reduced efficacy in vivo, whereas depletion of neutrophils had no effect. F(ab')2-only fragments of anti-CD47 antibodies failed to induce phagocytosis by human macrophages, indicating a requirement for Fc-Fcγ receptor interactions. In contrast, F(ab')2-only fragments increased phagocytosis by murine macrophages independent of SLAMF7-Mac-1 interaction. Full-length anti-CD47 mAbs also induced phagocytosis by Fcγ receptor-deficient murine macrophages. An immunoglobulin G1 anti-CD47 mAb induced phagocytosis and natural killer cell-mediated cytotoxicity of TCL cells that was augmented by cotreatment with mogamulizumab, an anti-CCR4 mAb, or a mAb blocking MHC class I. These studies help explain the disparate activity of monotherapy with agents that block CD47 in murine models compared with patients. They also have direct translational implications for the deployment of anti-CD47 mAbs alone or in combination.


Subject(s)
Antigens, Differentiation/immunology , Antineoplastic Agents, Immunological/pharmacology , CD47 Antigen/immunology , Lymphoma, T-Cell/drug therapy , Receptors, IgG/immunology , Receptors, Immunologic/immunology , Animals , Antineoplastic Agents, Immunological/therapeutic use , CD47 Antigen/antagonists & inhibitors , Cell Line, Tumor , Humans , Lymphoma, T-Cell/immunology , Lymphoma, T-Cell/pathology , Mice , Receptors, Fc/immunology
7.
Blood ; 134(8): 678-687, 2019 08 22.
Article in English | MEDLINE | ID: mdl-31243042

ABSTRACT

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an uncommon hematologic malignancy with poor outcomes. Existing data on the clinical behavior of BPDCN are limited because reported outcomes are from small retrospective series, and standardized treatment guidelines are lacking. The interleukin-3 cytotoxin conjugate tagraxofusp was recently tested in phase 1/2 trials that led to US Food and Drug Administration approval, the first ever for BPDCN. However, because there was no matched internal comparator in this or any clinical study to date, results of BPDCN trials testing new drugs are difficult to compare with alternative therapies. We therefore sought to define the clinical characteristics and outcomes of a group of patients with BPDCN treated at 3 US cancer centers in the modern era but before tagraxofusp was available. In 59 studied patients with BPDCN, the median overall survival from diagnosis was 24 months, and outcomes were similar in patients with "skin only" or with systemic disease at presentation. Intensive first-line therapy and "lymphoid-type" chemotherapy regimens were associated with better outcomes. Only 55% of patients received intensive chemotherapy, and 42% of patients underwent stem cell transplantation. Clinical characteristics at diagnosis associated with poorer outcomes included age >60 years, abnormal karyotype, and terminal deoxynucleotidyltransferase (TdT) negativity in the BPDCN cells. We also identified disease responses to pralatrexate and enasidenib in some patients. This study highlights poor outcomes for patients with BPDCN in the modern era and the need for new treatments. Outcomes from ongoing clinical trials for BPDCN can be evaluated relative to this contemporary cohort.


Subject(s)
Dendritic Cells/pathology , Hematologic Neoplasms/therapy , Skin Neoplasms/therapy , Adolescent , Adult , Aged , Aged, 80 and over , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Benchmarking , Child , Cohort Studies , Female , Hematologic Neoplasms/complications , Hematologic Neoplasms/diagnosis , Hematopoietic Stem Cell Transplantation , Humans , Male , Middle Aged , Multicenter Studies as Topic , Skin Neoplasms/complications , Skin Neoplasms/diagnosis , Treatment Outcome , Young Adult
8.
Mod Pathol ; 33(11): 2307-2317, 2020 11.
Article in English | MEDLINE | ID: mdl-32461620

ABSTRACT

Sarcomas are driven by diverse pathogenic mechanisms, including gene rearrangements in a subset of cases. Rare soft tissue sarcomas containing KMT2A fusions have recently been reported, characterized by a predilection for young adults, sclerosing epithelioid fibrosarcoma-like morphology, and an often aggressive course. Nonetheless, clinicopathologic and molecular descriptions of KMT2A-rearranged sarcomas remain limited. In this study, we identified by targeted next-generation RNA sequencing an index patient with KMT2A fusion-positive soft tissue sarcoma. In addition, we systematically searched for KMT2A structural variants in a comprehensive genomic profiling database of 14,680 sarcomas interrogated by targeted next-generation DNA and/or RNA sequencing. We characterized the clinicopathologic and molecular features of KMT2A fusion-positive sarcomas, including KMT2A breakpoints, rearrangement partners, and concurrent genetic alterations. Collectively, we identified a cohort of 34 sarcomas with KMT2A fusions (0.2%), and YAP1 was the predominant partner (n = 16 [47%]). Notably, a complex rearrangement with YAP1 consistent with YAP1-KMT2A-YAP1 fusion was detected in most cases, with preservation of KMT2A CxxC-binding domain in the YAP1-KMT2A-YAP1 fusion and concurrent deletions of corresponding exons in KMT2A. The tumors often affected younger adults (age 20-66 [median 40] years) and histologically showed variably monomorphic epithelioid-to-spindle shaped cells embedded in a dense collagenous stroma. Ultrastructural evidence of fibroblastic differentiation was noted in one tumor examined. Our cohort also included two sarcomas with VIM-KMT2A fusions, each harboring concurrent mutations in CTNNB1, SMARCB1, and ARID1A and characterized histologically by sheets of spindle-to-round blue cells. The remaining 16 KMT2A-rearranged sarcomas in our cohort exhibited diverse histologic subtypes, each with unique novel fusion partners. In summary, KMT2A-fusion-positive sarcomas most commonly exhibit sclerosing epithelioid fibrosarcoma-like morphology and complex YAP1-KMT2A-YAP1 fusions. Cases also include rare spindle-to-round cell sarcomas with VIM-KMT2A fusions and tumors of diverse histologic subtypes with unique KMT2A fusions to non-YAP1 non-VIM partners.


Subject(s)
Histone-Lysine N-Methyltransferase/genetics , Myeloid-Lymphoid Leukemia Protein/genetics , Oncogene Fusion/genetics , Sarcoma/genetics , Soft Tissue Neoplasms/genetics , Adult , Aged , Biomarkers, Tumor , Epithelioid Cells/pathology , Female , Gene Rearrangement , Humans , Male , Middle Aged , Sarcoma/pathology , Soft Tissue Neoplasms/pathology , Young Adult
9.
Blood ; 132(9): 935-947, 2018 08 30.
Article in English | MEDLINE | ID: mdl-29769264

ABSTRACT

Patients with angioimmunoblastic T-cell lymphoma (AITL) and other peripheral T-cell lymphomas that harbor features of follicular helper T (TFH) cells have a very poor prognosis. These lymphomas commonly present with paraneoplastic autoimmunity and lymphopenia. RhoA G17V mutation is present in 60% of TFH-like lymphomas, but its role in tumorigenesis is poorly understood. We generated transgenic mice that express RhoA G17V under the control of murine CD4 regulatory elements at levels comparable to a heterozygous mutation (tgRhoA mice). These mice had markedly reduced naive T cells but relatively increased TFH-cell populations. Surprisingly, naive CD4 T cells expressing RhoA G17V were hyperreactive to T-cell receptor stimulation. All tgRhoA mice developed autoimmunity that included a cellular infiltrate within ears and tails that was recapitulated in wild-type (WT) recipients after bone marrow transplantation. Older tgRhoA mice developed elevated serum titers of anti-double-stranded DNA antibodies and renal immune complex deposition. RhoA G17V mice crossed with Tet2fl/fl; Vav-Cre+ mice, which delete Tet2 throughout the hematopoietic compartment, developed T-cell lymphomas that retained histologic and immunophenotypic features of AITL and had transcriptional signatures enriched for mechanistic target of rapamycin (mTOR)-associated genes. Transplanted tumors were responsive to the mTOR inhibitor everolimus, providing a possible strategy for targeting RhoA G17V. Taken together, these data indicate that RhoA G17V contributes to both neoplastic and paraneoplastic phenotypes similar to those observed in patients with TFH lymphomas.


Subject(s)
Lymphoma, T-Cell , Mutation, Missense , Neoplasm Proteins , T-Lymphocytes, Helper-Inducer , rho GTP-Binding Proteins , Amino Acid Substitution , Animals , Antibodies, Antinuclear/immunology , Autoimmune Diseases , Lymphoma, Follicular/genetics , Lymphoma, Follicular/immunology , Lymphoma, Follicular/pathology , Lymphoma, T-Cell/genetics , Lymphoma, T-Cell/immunology , Lymphoma, T-Cell/pathology , Mice , Mice, Transgenic , Neoplasm Proteins/genetics , Neoplasm Proteins/immunology , T-Lymphocytes, Helper-Inducer/immunology , T-Lymphocytes, Helper-Inducer/pathology , rho GTP-Binding Proteins/genetics , rho GTP-Binding Proteins/immunology , rhoA GTP-Binding Protein
10.
Blood ; 132(16): 1695-1702, 2018 10 18.
Article in English | MEDLINE | ID: mdl-30126979

ABSTRACT

Duodenal-type follicular lymphoma (DTFL) is a rare and highly indolent follicular lymphoma (FL) variant. It is morphologically and immunophenotypically indistinguishable from typical FL, characterized by restricted involvement of intestinal mucosa, and lacks extraintestinal manifestations. The molecular determinants of this distinct clinical behavior are largely unknown. Thirty-eight diagnostic biopsies from patients with DTFL were evaluated. The 10-year overall survival rate was 100% in clinically evaluable patients (n = 19). We compared the targeted mutation profile of DTFL (n = 31), limited-stage typical FL (LSTFL; n = 17), and advanced-stage typical FL (ASTFL; n = 241). The mutation frequencies of recurrently mutated genes, including CREBBP, TNFRSF14/HVEM, and EZH2 were not significantly different. However, KMT2D was less commonly mutated in DTFL (52%) and LSTFL (24%) as compared with ASTFL (79%). In ASTFL, 41% of KMT2D-mutated cases harbored multiple mutations in KMT2D, as compared with only 12% in LSTFL (P = .019) and 0% in DTFL (P < .0001). Whole exome and targeted sequencing of DTFL revealed high mutation frequencies of EEF1A1 (35%) and HVCN1 (22%). We compared the immune microenvironment gene expression signatures of DTFL (n = 8) and LSTFL (n = 7). DTFL clearly separated from LSTFL by unsupervised, hierarchical clustering of 147 chemokines and cytokines and was enriched for a chronic inflammation signature. In conclusion, the mutational landscape of DTFL is highly related to typical FL. The lower frequency of multiple mutations in KMT2D in DTFL and LSTFL indicates an increasing selection pressure for complete KMT2D loss in ASTFL pathogenesis. The highly dissimilar immune microenvironment of DTFL suggests a central role in the biology of this disease.


Subject(s)
Biomarkers, Tumor/genetics , DNA-Binding Proteins/genetics , Duodenal Neoplasms/immunology , Inflammation/immunology , Lymphoma, Follicular/immunology , Mutation , Neoplasm Proteins/genetics , Adult , Aged , Aged, 80 and over , Cytokines/metabolism , DNA Mutational Analysis , Duodenal Neoplasms/genetics , Duodenal Neoplasms/pathology , Exome , Female , Follow-Up Studies , Gene Expression Regulation, Neoplastic , Humans , Inflammation/genetics , Inflammation/pathology , Lymphoma, Follicular/genetics , Lymphoma, Follicular/pathology , Male , Middle Aged , Prognosis , Survival Rate , Tumor Microenvironment , Young Adult
13.
Orbit ; 38(2): 154-157, 2019 Apr.
Article in English | MEDLINE | ID: mdl-29557698

ABSTRACT

We report a case of myeloid sarcoma with multifocal skeletal involvement, including the greater wing of the sphenoid bone. A 23-month-old boy presented with left-sided proptosis and fevers, and was found to have an infiltrative mass involving the left sphenoid bone on orbital imaging. Full body imaging further demonstrated multiple bony lesions in the pelvis, thoracic and lumbar vertebrae, bilateral femura, and left humerus, and biopsies of the humerus were consistent with myeloid sarcoma. The patient was started on a standard chemotherapy regimen and is responding well. Myeloid sarcoma presenting with proptosis due to sphenoid bone involvement with simultaneous multifocal skeletal involvement is very uncommon and highlights the importance of biopsy for establishing a definitive diagnosis.


Subject(s)
Bone Neoplasms/diagnosis , Exophthalmos/diagnosis , Fever/diagnosis , Neoplasms, Multiple Primary/diagnosis , Sarcoma, Myeloid/diagnosis , Skull Neoplasms/diagnosis , Sphenoid Bone/pathology , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Biomarkers, Tumor/metabolism , Bone Neoplasms/drug therapy , Bone Neoplasms/metabolism , Humans , Infant , Magnetic Resonance Imaging , Male , Neoplasm Proteins/metabolism , Neoplasms, Multiple Primary/drug therapy , Neoplasms, Multiple Primary/metabolism , Sarcoma, Myeloid/drug therapy , Sarcoma, Myeloid/metabolism , Skull Neoplasms/drug therapy , Skull Neoplasms/metabolism , Tomography, X-Ray Computed
15.
Blood ; 128(8): 1093-100, 2016 08 25.
Article in English | MEDLINE | ID: mdl-27325104

ABSTRACT

Pediatric-type nodal follicular lymphoma (PTNFL) is a variant of follicular lymphoma (FL) characterized by limited-stage presentation and invariably benign behavior despite often high-grade histological appearance. It is important to distinguish PTNFL from typical FL in order to avoid unnecessary treatment; however, this distinction relies solely on clinical and pathological criteria, which may be variably applied. To define the genetic landscape of PTNFL, we performed copy number analysis and exome and/or targeted sequencing of 26 PTNFLs (16 pediatric and 10 adult). The most commonly mutated gene in PTNFL was MAP2K1, encoding MEK1, with a mutation frequency of 43%. All MAP2K1 mutations were activating missense mutations localized to exons 2 and 3, which encode negative regulatory and catalytic domains, respectively. Missense mutations in MAPK1 (2/22) and RRAS (1/22) were identified in cases that lacked MAP2K1 mutations. The second most commonly mutated gene in PTNFL was TNFRSF14, with a mutation frequency of 29%, similar to that seen in limited-stage typical FL (P = .35). PTNFL was otherwise genomically bland and specifically lacked recurrent mutations in epigenetic modifiers (eg, CREBBP, KMT2D). Copy number aberrations affected a mean of only 0.5% of PTNFL genomes, compared with 10% of limited-stage typical FL genomes (P < .02). Importantly, the mutational profiles of PTNFLs in children and adults were highly similar. Together, these findings define PTNFL as a biologically and clinically distinct indolent lymphoma of children and adults characterized by a high prevalence of MAPK pathway mutations and a near absence of mutations in epigenetic modifiers.


Subject(s)
Lymphoma, Follicular/enzymology , Lymphoma, Follicular/genetics , MAP Kinase Signaling System/genetics , Mutation/genetics , Adolescent , Age Factors , Cell Shape , Child , Child, Preschool , DNA Copy Number Variations/genetics , Epigenesis, Genetic , Female , Humans , Immunophenotyping , Infant , Lymphoma, Follicular/pathology , Male
16.
Mod Pathol ; 30(9): 1321-1334, 2017 09.
Article in English | MEDLINE | ID: mdl-28621320

ABSTRACT

Follicular dendritic cell sarcoma is a rare malignant neoplasm of dendritic cell origin that is currently poorly characterized by genetic studies. To investigate whether recurrent genomic alterations may underlie the biology of follicular dendritic cell sarcoma and to identify potential contributory regions and genes, molecular inversion probe array analysis was performed on 14 independent formalin-fixed, paraffin-embedded samples. Abnormal genomic profiles were observed in 11 out of 14 (79%) cases. The majority showed extensive genomic complexity that was predominantly represented by hemizygous losses affecting multiple chromosomes. Alterations of chromosomal regions 1p (55%), 2p (55%), 3p (82%), 3q (45%), 6q (55%), 7q (73%), 8p (45%), 9p (64%), 11q (64%), 13q (91%), 14q (82%), 15q (64%), 17p (55%), 18q (64%), and 22q (55%) were recurrent across the 11 samples showing abnormal genomic profiles. Many recurrent genomic alterations in follicular dendritic cell sarcoma overlap deletions that are frequently observed across human cancers, suggesting selection, or an active role for these alterations in follicular dendritic cell sarcoma pathogenesis. In support of a tumor suppressor-driven biology, homozygous deletions involving tumor suppressor genes CDKN2A, RB1, BIRC3, and CYLD were also observed. Neither recurrent gains nor amplifications were observed. This genomic characterization provides new information regarding follicular dendritic cell sarcoma biology that may improve understanding about the underlying pathophysiology, provide better prognostication, and identify potential therapeutic markers for this rare disease.


Subject(s)
Biomarkers, Tumor/genetics , Chromosomes, Human , Dendritic Cell Sarcoma, Follicular/genetics , Gene Expression Profiling , Genes, Tumor Suppressor , Genomics/methods , Oligonucleotide Array Sequence Analysis , Adult , Aged , Dendritic Cell Sarcoma, Follicular/pathology , Female , Gene Deletion , Gene Expression Regulation, Neoplastic , Genetic Predisposition to Disease , Homozygote , Humans , Loss of Heterozygosity , Male , Middle Aged , Phenotype , Young Adult
17.
Cytometry A ; 91(6): 609-621, 2017 06.
Article in English | MEDLINE | ID: mdl-28110507

ABSTRACT

The advance of high resolution digital scans of pathology slides allowed development of computer based image analysis algorithms that may help pathologists in IHC stains quantification. While very promising, these methods require further refinement before they are implemented in routine clinical setting. Particularly critical is to evaluate algorithm performance in a setting similar to current clinical practice. In this article, we present a pilot study that evaluates the use of a computerized cell quantification method in the clinical estimation of CD3 positive (CD3+) T cells in follicular lymphoma (FL). Our goal is to demonstrate the degree to which computerized quantification is comparable to the practice of estimation by a panel of expert pathologists. The computerized quantification method uses entropy based histogram thresholding to separate brown (CD3+) and blue (CD3-) regions after a color space transformation. A panel of four board-certified hematopathologists evaluated a database of 20 FL images using two different reading methods: visual estimation and manual marking of each CD3+ cell in the images. These image data and the readings provided a reference standard and the range of variability among readers. Sensitivity and specificity measures of the computer's segmentation of CD3+ and CD- T cell are recorded. For all four pathologists, mean sensitivity and specificity measures are 90.97 and 88.38%, respectively. The computerized quantification method agrees more with the manual cell marking as compared to the visual estimations. Statistical comparison between the computerized quantification method and the pathologist readings demonstrated good agreement with correlation coefficient values of 0.81 and 0.96 in terms of Lin's concordance correlation and Spearman's correlation coefficient, respectively. These values are higher than most of those calculated among the pathologists. In the future, the computerized quantification method may be used to investigate the relationship between the overall architectural pattern (i.e., interfollicular vs. follicular) and outcome measures (e.g., overall survival, and time to treatment). © 2017 International Society for Advancement of Cytometry.


Subject(s)
Algorithms , Image Processing, Computer-Assisted/statistics & numerical data , Lymphoma, Follicular/diagnosis , T-Lymphocytes/pathology , Automation, Laboratory , CD3 Complex/genetics , Entropy , Gene Expression , Humans , Image Processing, Computer-Assisted/methods , Immunohistochemistry/methods , Lymphoma, Follicular/genetics , Lymphoma, Follicular/pathology , Lymphoma, Follicular/ultrastructure , Pilot Projects , Reproducibility of Results , Sensitivity and Specificity , Staining and Labeling/methods , T-Lymphocytes/ultrastructure
19.
Blood ; 123(9): 1293-6, 2014 Feb 27.
Article in English | MEDLINE | ID: mdl-24345752

ABSTRACT

The genetics of angioimmunoblastic T-cell lymphoma (AITL) are very poorly understood. We defined the mutational landscape of AITL across 219 genes in 85 cases from the United States and Europe. We identified ≥2 mutations in 34 genes, nearly all of which were not previously implicated in AITL. These included loss-of-function mutations in TP53 (n = 4), ETV6 (n = 3), CCND3 (n = 2), and EP300 (n = 5), as well as gain-of-function mutations in JAK2 (n = 2) and STAT3 (n = 4). TET2 was mutated in 65 (76%) AITLs, including 43 that harbored 2 or 3 TET2 mutations. DNMT3A mutations occurred in 28 (33%) AITLs; 100% of these also harbored TET2 mutations (P < .0001). Seventeen AITLs harbored IDH2 R172 substitutions, including 15 with TET2 mutations. In summary, AITL is characterized by high frequencies of overlapping mutations in epigenetic modifiers and targetable mutations in a subset of cases.


Subject(s)
Immunoblastic Lymphadenopathy/genetics , Lymphoma, T-Cell/genetics , Mutation , Adult , Aged , Aged, 80 and over , Cohort Studies , DNA Mutational Analysis , Female , Gene Frequency , Humans , Immunoblastic Lymphadenopathy/epidemiology , Lymphoma, T-Cell/epidemiology , Male , Middle Aged
20.
Forensic Sci Med Pathol ; 12(2): 139-45, 2016 06.
Article in English | MEDLINE | ID: mdl-27020890

ABSTRACT

Purpose Assessment of body size at autopsy is important for interpreting organ weight measurements and in some cases body identification. The reliability of post-mortem body size measurements, the causes for perturbations in these measurements from their corresponding pre-mortem values, and the impact of such perturbations on heart weight interpretation have not been fully explored. Methods Autopsy body length and weight measurements and pre-mortem height and body weight measurements were compared in 132 autopsies. Clinical records were evaluated for peripheral edema and serum albumin levels. Causes of death, body cavity fluid collections, and heart weights were obtained from the autopsy reports. A subset of patients underwent quantitative post-mortem computed tomography assessment of anasarca. Results At autopsy, body weight differed from the pre-mortem value by 11 ± 1 %, compared with -0.2 ± 0.3 % for body length (P < 0.0001). The percent change in body weight at autopsy correlated with the presence of peripheral edema (14 ± 2 % vs. 7 ± 2 %, P = 0.01), serum albumin < 3.0 g/dL (16 ± 2 % vs. 7 ± 2 %, P = 0.001), and the degree of anasarca (P = 0.01). In 4 % of autopsies, heart weights were abnormal based on the pre-mortem body weight, but would be classified as normal based on the elevated post-mortem body weight. Conclusions At autopsy, body weight is a less reliable parameter than body length in correlating with the corresponding pre-mortem measurement. Autopsy body weights are elevated in part due to peripheral edema/anasarca. Alterations in body weight at autopsy can confound the interpretation of organ weight measurements.


Subject(s)
Autopsy , Body Height , Body Weight , Myocardium/pathology , Edema/pathology , Female , Forensic Pathology , Humans , Male , Middle Aged , Organ Size , Postmortem Changes , Reproducibility of Results , Serum Albumin
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