Publications by authors named "Govind Bhagat"

286 Publications

induces NF-κB signaling-driven peripheral T cell lymphoma.

Nat Cancer 2021 Jan 13;2(1):98-113. Epub 2021 Jan 13.

Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA.

Angioimmunoblastic T cell lymphoma (AITL) and peripheral T cell lymphoma not-otherwise-specified (PTCL, NOS) have poor prognosis and lack driver actionable targets for directed therapies in most cases. Here we identify as a recurrent oncogenic gene fusion in AITL and PTCL, NOS tumors. Mechanistically, we show that FYN-TRAF3IP2 leads to aberrant NF-κB signaling downstream of T cell receptor activation. Consistent with a driver oncogenic role, FYN-TRAF3IP2 expression in hematopoietic progenitors induces NF-κB-driven T cell transformation in mice and cooperates with loss of the tumor suppressor in PTCL development. Moreover, abrogation of NF-κB signaling in -induced tumors with IκB kinase inhibitors delivers strong anti-lymphoma effects and . These results demonstrate an oncogenic and pharmacologically targetable role for FYN-TRAF3IP2 in PTCLs and call for the clinical testing of anti-NF-κB targeted therapies in these diseases.
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http://dx.doi.org/10.1038/s43018-020-00161-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081346PMC
January 2021

Automated interpretation of biopsy images for the detection of celiac disease using a machine learning approach.

Comput Methods Programs Biomed 2021 May 27;203:106010. Epub 2021 Feb 27.

Department of Electronics and Computer Engineering, Ngee Ann Polytechnic, Singapore; School of Science and Technology, Singapore University of Social Sciences, Singapore; School of Business, University of Southern Queensland Springfield, Australia; Department of Bioinformatics and Medical Engineering, Asia University, Taiwan; International Research Organization for Advanced Science and Technology (IROAST) Kumamoto University, Kumamoto, Japan. Electronic address:

Background And Objectives: Celiac disease is an autoimmune disease occurring in about 1 in 100 people worldwide. Early diagnosis and efficient treatment are crucial in mitigating the complications that are associated with untreated celiac disease, such as intestinal lymphoma and malignancy, and the subsequent high morbidity. The current diagnostic methods using small intestinal biopsy histopathology, endoscopy, and video capsule endoscopy (VCE) involve manual interpretation of photomicrographs or images, which can be time-consuming and difficult, with inter-observer variability. In this paper, a machine learning technique was developed for the automation of biopsy image analysis to detect and classify villous atrophy based on modified Marsh scores. This is one of the first studies to employ conventional machine learning to automate the use of biopsy images for celiac disease detection and classification.

Methods: The Steerable Pyramid Transform (SPT) method was used to obtain sub bands from which various types of entropy and nonlinear features were computed. All extracted features were automatically classified into two-class and multi-class, using six classifiers.

Results: An accuracy of 88.89%, was achieved for the classification of two-class villous abnormalities based on analysis of Hematoxylin and Eosin (H&E) stained biopsy images. Similarly, an accuracy of 82.92% was achieved for the two-class classification of red-green-blue (RGB) biopsy images. Also, an accuracy of 72% was achieved in the classification of multi-class biopsy images.

Conclusion: The results obtained are promising, and demonstrate the possibility of automating biopsy image interpretation using machine learning. This can assist pathologists in accelerating the diagnostic process without bias, resulting in greater accuracy, and ultimately, earlier access to treatment.
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http://dx.doi.org/10.1016/j.cmpb.2021.106010DOI Listing
May 2021

Interphase fluorescence in situ hybridization analysis of CD19-selected cells: Utility in detecting disease in post-therapy samples of B-cell neoplasms.

Cancer Med 2021 Apr 15;10(8):2680-2689. Epub 2021 Mar 15.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA.

Context: The detection of low-level persistent or relapsed B-cell neoplasms, particularly post-therapy, can be challenging, often requiring multiple testing modalities.

Objective: Here we investigate the utility of CD19-based selection of neoplastic B-cells (CD19S) as an enrichment strategy to improve the detection rate of cytogenetic abnormalities in post-therapy samples of B-cell neoplasms, especially those with low-level disease.

Design: In a cohort largely comprised of post-therapy B-ALL and CLL samples, we performed fluorescence in situ hybridization (FISH) analysis on CD19-selected cells (CD19S FISH) in 128 specimens from 88 patients, and on non-selected cells (NS FISH) in a subset of cases. The FISH findings were compared with the concurrent flow cytometry (FC) results in all samples and molecular analysis in a subset.

Results: CD19S FISH was able to detect cytogenetic aberrations in 86.0% of post-therapy samples with evidence of disease as determined by routine or MRD FC, compared to 59.1% of samples by NS FISH. CD19S FISH detected significantly higher percentages of positive cells compared to NS FISH (p < 0.001). Importantly, CD19S FISH enabled the detection of emergent subclones (clonal evolution) associated with poor prognosis.

Conclusions: CD19S FISH can be useful in daily diagnostic practice. Compared to NS FISH, CD19S FISH is quantitatively and qualitatively superior for the detection of cytogenetic aberrations in B-cell neoplasms, which are important for risk stratification and optimal management of patients with B-cell neoplasms, especially in the relapsed setting. Although CD19S FISH has a diagnostic sensitivity inferior to that of MRD FC, the sensitivity of this modality is comparable to routine FC for the evaluation of low-level disease in the post-therapy setting. Moreover, CD19S samples are invaluable for additional molecular and genetic analyses.
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http://dx.doi.org/10.1002/cam4.3853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026942PMC
April 2021

Cellular and molecular bases of refractory celiac disease.

Int Rev Cell Mol Biol 2021 13;358:207-240. Epub 2021 Feb 13.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States. Electronic address:

Refractory celiac disease (RCD) encompasses biologically heterogeneous disorders that develop in a small proportion (0.3%) of individuals with celiac disease that are associated with high morbidity. Two broad categories are currently recognized, type I (RCD I) and type II (RCD II), based on immunophenotypic and molecular features of the intraepithelial lymphocytes (IELs). RCD I is characterized by a polyclonal expansion of IELs displaying a normal immunophenotype, while RCD II represents a clonal proliferation of immunophenotypically "aberrant" IELs, and is considered a low-grade lymphoproliferative disorder. The pathogenesis of RCD I has not been clarified, but limited studies suggest multifactorial etiology. On the other hand, recent immunologic, molecular and immunophenotypic analyses have proposed lineage-negative innate IELs to be the cell of origin of a proportion of RCD II cases. Furthermore, sequencing studies have identified frequent, recurrent, activating mutations in members of the JAK-STAT pathway in RCD II. This finding, in conjunction with prior in vitro experimental observations, suggests roles of deregulated cytokine signaling in disease pathogenesis. In this review, we describe current understanding of environmental, immune and genetic factors associated with the development of RCD and briefly discuss diagnostic and therapeutic considerations.
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http://dx.doi.org/10.1016/bs.ircmb.2020.12.001DOI Listing
February 2021

Immunophenotypic Spectrum and Genomic Landscape of Refractory Celiac Disease Type II.

Am J Surg Pathol 2021 Feb 2. Epub 2021 Feb 2.

*Department of Pathology and Cell Biology, Columbia University Irving Medical Center †Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, NY ‡Department of Pathology, University of Virginia, Charlottesville, VA §Bacchi Laboratory, Pathology Reference Laboratory, Botucatu, Brazil.

Refractory celiac disease type II (RCD II), also referred to as "cryptic" enteropathy-associated T-cell lymphoma (EATL) or "intraepithelial T-cell lymphoma," is a rare clonal lymphoproliferative disorder that arises from innate intraepithelial lymphocytes. RCD II has a poor prognosis and frequently evolves to EATL. The pathogenesis of RCD II is not well understood and data regarding the immunophenotypic spectrum of this disease and underlying genetic alterations are limited. To gain further biological insights, we performed comprehensive immunophenotypic, targeted next-generation sequencing, and chromosome microarray analyses of 11 RCD II cases: CD4/CD8 (n=6), CD8 (n=4), and CD4 (n=1), and 2 of 3 ensuing EATLs. Genetic alterations were identified in 9/11 (82%) of the RCD II cases. All 9 displayed mutations in members of the JAK-STAT signaling pathway, including frequent, recurrent STAT3 (7/9, 78%) and JAK1 (4/9, 44%) mutations, and 9/10 evaluable cases expressed phospho-STAT3. The mutated cases also harbored recurrent alterations in epigenetic regulators (TET2, n=5 and KMT2D, n=5), nuclear factor-κB (TNFAIP3, n=4), DNA damage repair (POT1, n=3), and immune evasion (CD58, n=2) pathway genes. The CD4/CD8 and other immunophenotypic subtypes of RCD II exhibited similar molecular features. Longitudinal genetic analyses of 4 RCD II cases revealed stable mutation profiles, however, additional mutations were detected in the EATLs, which occurred at extraintestinal sites and were clonally related to antecedent RCD II. Chromosome microarray analysis demonstrated copy number changes in 3/6 RCD II cases, and 1 transformed EATL with sufficient neoplastic burden for informative analysis. Our findings provide novel information about the immunophenotypic and genomic characteristics of RCD II, elucidate early genetic events in EATL pathogenesis, and reveal potential therapeutic targets.
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http://dx.doi.org/10.1097/PAS.0000000000001658DOI Listing
February 2021

Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific translation in epithelial cells.

Gut 2021 Feb 1. Epub 2021 Feb 1.

Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain

Objectives: Coeliac disease (CD) is a complex autoimmune disorder that develops in genetically susceptible individuals. Dietary gluten triggers an immune response for which the only available treatment so far is a strict, lifelong gluten free diet. Human leucocyte antigen (HLA) genes and several non-HLA regions have been associated with the genetic susceptibility to CD, but their role in the pathogenesis of the disease is still essentially unknown, making it complicated to develop much needed non-dietary treatments. Here, we describe the functional involvement of a CD-associated single-nucleotide polymorphism (SNP) located in the 5'UTR of in the inflammatory environment characteristic of the coeliac intestinal epithelium.

Design: The function of the CD-associated SNP was investigated using an intestinal cell line heterozygous for the SNP, N6-methyladenosine (mA)-related knock-out and HLA-DQ2 mice, and human samples from patients with CD.

Results: Individuals harbouring the risk allele had higher mA methylation in the 5'UTR of RNA, rendering greater XPO1 protein amounts that led to downstream nuclear factor kappa B (NFkB) activity and subsequent inflammation. Furthermore, gluten exposure increased overall mA methylation in humans as well as in in vitro and in vivo models.

Conclusion: We identify a novel mA-XPO1-NFkB pathway that is activated in CD patients. The findings will prompt the development of new therapeutic approaches directed at mA proteins and XPO1, a target under evaluation for the treatment of intestinal disorders.
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http://dx.doi.org/10.1136/gutjnl-2020-322566DOI Listing
February 2021

Innate Lymphoid Cells and Celiac Disease: Current Perspective.

Cell Mol Gastroenterol Hepatol 2021 10;11(3):803-814. Epub 2020 Dec 10.

Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York. Electronic address:

Celiac disease (CD) is a common autoimmune disorder triggered by the ingestion of gluten in genetically susceptible individuals. Although the mechanisms underlying gliadin-mediated activation of adaptive immunity in CD have been well-characterized, regulation of innate immune responses and the functions of certain immune cell populations within the epithelium and lamina propria are not well-understood at present. Innate lymphoid cells (ILCs) are types of innate immune cells that have lymphoid morphology, lack antigen-specific receptors, and play important roles in tissue homeostasis, inflammation, and protective immune responses against pathogens. Information regarding the diversity and functions of ILCs in lymphoid organs and at mucosal sites has grown over the past decade, and roles of different ILC subsets in the pathogenesis of some inflammatory intestinal diseases have been proposed. However, our understanding of the contribution of ILCs toward the initiation and progression of CD is still limited. In this review, we discuss current pathophysiological aspects of ILCs within the gastrointestinal tract, findings of recent investigations characterizing ILC alterations in CD and refractory CD, and suggest avenues for future research.
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http://dx.doi.org/10.1016/j.jcmgh.2020.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851184PMC
December 2020

Phenogenomic heterogeneity of post-transplant plasmablastic lymphomas.

Haematologica 2020 12 3;Online ahead of print. Epub 2020 Dec 3.

Division of Hematopathology.

Plasmablastic lymphoma (PBL) is a rare and clinically aggressive neoplasm that typically occurs in immunocompromised individuals, including those with HIV infection and solid organ allograft recipients. Most prior studies have focused on delineating the clinicopathologic features and genetic attributes of HIV-related PBLs, where MYC deregulation and EBV infection, and more recently, mutations in JAK/STAT, MAP kinase, and NOTCH pathway genes have been implicated in disease pathogenesis. The phenotypic spectrum of post-transplant (PT)-PBLs is not well characterized and data on underlying genetic alterations are limited. Hence, we performed comprehensive histopathologic and immunophenotypic evaluation and targeted sequencing of 18 samples from 11 patients (8 males, 3 females, age range 12-76 years) with PT-PBL; 8 de novo and 3 preceded by other types of PTLDs. PT-PBLs displayed morphologic and immunophenotypic heterogeneity and some features overlapped those of plasmablastic myeloma. Six (55%) cases were EBV+ and 5 (45%) showed MYC rearrangement by fluorescence in situ hybridization. Recurrent mutations in epigenetic regulators (KMT2/MLL family, TET2) and DNA damage repair and response (TP53, mismatch repair genes, FANCA, ATRX), MAP kinase (KRAS, NRAS, HRAS, BRAF), JAK/STAT (STAT3, STAT6, SOCS1), NOTCH (NOTCH1, NOTCH3, SPEN), and immune surveillance (FAS, CD58) pathway genes were observed, with EBV+ and EBV- cases exhibiting similarities and differences in their mutational profiles. Clinical outcomes also varied, with survival ranging from 0-15.9 years postdiagnosis. Besides uncovering the biological heterogeneity of PT-PBL, our study highlights similarities and distinctions between PT-PBLs and PBLs occurring in other settings and reveals potentially targetable oncogenic pathways in disease subsets.
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http://dx.doi.org/10.3324/haematol.2020.267294DOI Listing
December 2020

Spindle-cell (Sarcomatoid) Variant of Cutaneous Anaplastic Large-cell Lymphoma (C-ALCL): An Unusual Mimicker of Cutaneous Malignant Mesenchymal Tumors-A Series of 11 Cases.

Am J Surg Pathol 2020 Nov 23. Epub 2020 Nov 23.

Department of Pathology & Dermatology, The Ohio State University Wexner Medical Center, Columbus, OH.

Cutaneous anaplastic large-cell lymphoma (C-ALCL) represents one of the entities within the group of CD30-positive lymphoproliferative disorders of the skin. Most cases are ALK-negative, though isolated cases of ALK-positive C-ALCL have also been reported. By definition, the diagnosis of C-ALCL requires the expression of CD30 in >75% of the cells. Histopathologically, C-ALCL shows a dermal-based nodular and circumscribed proliferation of large pleomorphic cells with vesicular nuclei, prominent nucleoli, and eosinophilic cytoplasm, including hallmark cells. Since 1990, isolated case reports of a so-called "sarcomatoid" variant have been published in the literature. Herein, we present a series of 11 cases of spindle (sarcomatoid) C-ALCL, with comprehensive histopathologic, immunophenotypic, and molecular data. Spindle C-ALCL represents a potential mimicker of malignant mesenchymal or hematopoietic tumors in the skin and should always be considered in the differential diagnosis when assessing cutaneous pleomorphic spindle cell neoplasms.
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http://dx.doi.org/10.1097/PAS.0000000000001623DOI Listing
November 2020

Combined oral 5-azacytidine and romidepsin are highly effective in patients with PTCL: a multicenter phase 2 study.

Blood 2021 Apr;137(16):2161-2170

Division of Hematology and Oncology, Program for T-Cell Lymphoma Research, University of Virginia Cancer Center, Charlottesville, VA.

Peripheral T-cell lymphomas (PTCLs) are uniquely vulnerable to epigenetic modifiers. We demonstrated in vitro synergism between histone deacetylase inhibitors and DNA methyltransferase inhibitors in preclinical models of T-cell lymphoma. In a phase 1 trial, we found oral 5-azacytidine and romidepsin to be safe and effective, with lineage-selective activity among patients with relapsed/refractory (R/R) PTCL. Patients who were treatment naïve or who had R/R PTCL received azacytidine 300 mg once per day on days 1 to 14, and romidepsin 14 mg/m2 on days 8, 15, and 22 every 35 days. The primary objective was overall response rate (ORR). Targeted next-generation sequencing was performed on tumor samples to correlate mutational profiles and response. Among 25 enrolled patients, the ORR and complete response rates were 61% and 48%, respectively. However, patients with T-follicular helper cell (tTFH) phenotype exhibited higher ORR (80%) and complete remission rate (67%). The most frequent grade 3 to 4 adverse events were thrombocytopenia (48%), neutropenia (40%), lymphopenia (32%), and anemia (16%). At a median follow-up of 13.5 months, the median progression-free survival, duration of response, and overall survival were 8.0 months, 20.3 months, and not reached, respectively. The median progression-free survival and overall survival were 8.0 months and 20.6 months, respectively, in patients with R/R disease. Patients with tTFH enjoyed a particularly long median survival (median not reached). Responders harbored a higher average number of mutations in genes involved in DNA methylation and histone deacetylation. Combined azacytidine and romidepsin are highly active in PTCL patients and could serve as a platform for novel regimens in this disease. This trial was registered at www.clinicaltrials.gov as #NCT01998035.
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http://dx.doi.org/10.1182/blood.2020009004DOI Listing
April 2021

Aggressive B-cell Lymphoma with MYC/TP53 Dual Alterations Displays Distinct Clinicopathobiological Features and Response to Novel Targeted Agents.

Mol Cancer Res 2021 02 5;19(2):249-260. Epub 2020 Nov 5.

Duke University Medical Center, Division of Hematopathology and Department of Pathology, Durham, North Carolina.

Diffuse large B-cell lymphoma (DLBCL) is the major type of aggressive B-cell lymphoma. High-grade B-cell lymphoma (HGBCL) with / double-hit (DH) represents a distinct entity with dismal prognosis after standard immunochemotherapy in the current WHO lymphoma classification. However, whether mutation synergizes with MYC abnormalities ( rearrangement and/or Myc protein overexpression) contributing to HGBCL-like biology and prognosis is not well investigated. In this study, patients with DLBCL with MYC/TP53 abnormalities demonstrated poor clinical outcome, high-grade morphology, and distinct gene expression signatures. To identify more effective therapies for this distinctive DLBCL subset, novel MYC/TP53/BCL-2-targeted agents were investigated in DLBCL cells with MYC/TP53 dual alterations or HGBCL-/-DH. A BET inhibitor INCB057643 effectively inhibited cell viability and induced apoptosis in DLBCL/HGBCL cells regardless of // status. Combining INCB057643 with a MDM2-p53 inhibitor DS3032b significantly enhanced the cytotoxic effects in HGBCL-DH without mutation, while combining with the BCL-2 inhibitor venetoclax displayed potent therapeutic synergy in DLBCL/HGBCL cells with and without concurrent mutation. Reverse-phase protein arrays revealed the synergistic molecular actions by INCB057643, DS3032b and venetoclax to induce cell-cycle arrest and apoptosis and to inhibit AKT/MEK/ERK/mTOR pathways, as well as potential drug resistance mechanisms mediated by upregulation of Mcl-1 and RAS/RAF/MEK/ERK pathways. In summary, these findings support subclassification of DLBCL/HGBCL with dual MYC/TP53 alterations, which demonstrates distinct pathobiologic features and dismal survival with standard therapy, therefore requiring additional targeted therapies. IMPLICATIONS: The clinical and pharmacologic studies suggest recognizing DLBCL with concomitant mutation and MYC abnormalities as a distinctive entity necessary for precision oncology practice. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/2/249/F1.large.jpg.
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http://dx.doi.org/10.1158/1541-7786.MCR-20-0466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092941PMC
February 2021

XPO1 expression worsens the prognosis of unfavorable DLBCL that can be effectively targeted by selinexor in the absence of mutant p53.

J Hematol Oncol 2020 11 4;13(1):148. Epub 2020 Nov 4.

Division of Hematopathology, Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.

The XPO1 inhibitor selinexor was recently approved in relapsed/refractory DLBCL patients but only demonstrated modest anti-DLBCL efficacy, prompting us to investigate the prognostic effect of XPO1 in DLBCL patients and the rational combination therapies in high-risk DLBCL. High XPO1 expression (XPO1) showed significant adverse prognostic impact in 544 studied DLBCL patients, especially in those with BCL2 overexpression. Therapeutic study in 30 DLBCL cell lines with various molecular and genetic background found robust cytotoxicity of selinexor, especially in cells with BCL2-rearranged (BCL2-R) DLBCL or high-grade B-cell lymphoma with MYC/BCL2 double-hit (HGBCL-DH). However, expression of mutant (Mut) p53 significantly reduced the cytotoxicity of selinexor in overall cell lines and the BCL2-R and HGBCL-DH subsets, consistent with the favorable impact of XPO1 observed in Mut-p53-expressing patients. The therapeutic effect of selinexor in HGBCL-DH cells was significantly enhanced when combined with a BET inhibitor INCB057643, overcoming the drug resistance in Mut-p53-expressing cells. Collectively, these data suggest that XPO1 worsens the survival of DLBCL patients with unfavorable prognostic factors such as BCL2 overexpression and double-hit, in line with the higher efficacy of selinexor demonstrated in BCL2-R DLBCL and HGBCL-DH cell lines. Expression of Mut-p53 confers resistance to selinexor treatment, which can be overcome by combined INCB057643 treatment in HGBCL-DH cells. This study provides insight into the XPO1 significance and selinexor efficacy in DLBCL, important for developing combination therapy for relapsed/refractory DLBCL and HGBCL-DH.
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http://dx.doi.org/10.1186/s13045-020-00982-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641823PMC
November 2020

Exosomes and extracellular vesicles as liquid biopsy biomarkers in diffuse large B-cell lymphoma: Current state of the art and unmet clinical needs.

Br J Clin Pharmacol 2021 Feb 18;87(2):284-294. Epub 2020 Nov 18.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY, 10032.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma, and it constitutes biologically heterogeneous entities. Standard first-line therapies cure ~60% of patients, the rest being either refractory or experiencing relapse. Currently, there are no robust predictive biomarkers of therapeutic response. Heterogeneity of DLBCL is partly explained by the cell of origin (COO), ie, germinal centre B cell or activated B cell, with the latter exhibiting worse prognosis. While gene expression profiling (GEP) is the gold standard for determining COO, surrogate immunohistochemical algorithms are used clinically, but show significant discordance with GEP. Recently, additional genetic subgroups with different prognoses have been reported. However, the tools/expertise required for analysis prohibit widespread deployment. Liquid biopsy-based assays show promise in providing clinically actionable information, are noninvasive and facilitate serial sampling to assess mechanisms of therapy resistance. Circulating, cell-free DNA analysis has shown enhanced sensitivity for detecting molecular alterations, but this modality cannot determine alterations of the tumor proteome or on signalling pathways. Exosomes are endosomally derived vesicles, are found in high abundance in body fluids and are readily isolated using a variety of methods. Tumour-derived exosomes can yield data regarding genetic, transcriptional, and proteomic changes useful for diagnosis, prognosis, and therapy of DLBCL. At present, standardized techniques for isolating exosomes are lacking and discriminating between exosomes from neoplastic and normal B cells is challenging. Refinements in isolation procedures are required to realize their full potential as precision medicine tools to provide comprehensive information on disease subtypes, identify prognostic factors, allow real-time monitoring of therapy response and delineate novel drug targets.
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http://dx.doi.org/10.1111/bcp.14611DOI Listing
February 2021

Masson Trichrome and Sulfated Alcian Blue Stains Distinguish Light Chain Deposition Disease From Amyloidosis in the Lung.

Am J Surg Pathol 2021 03;45(3):405-413

Department of Pathology and Cell Biology, Columbia University Irving Medical Center and New York-Presbyterian Hospital, New York, NY.

Light chain deposition disease, characterized by nonamyloidogenic deposits of immunoglobulin light chains, is rare in the lung and possibly underdiagnosed due to low clinical suspicion and lack of readily accessible tests. We encountered a case of pulmonary light chain deposition disease (PLCDD) in which light chain deposits appeared crimson red with a Masson trichrome (MT) stain and salmon pink with a sulfated Alcian blue (SAB) stain. This prompted us to characterize a series of PLCDD cases and assess the utility of MT and SAB stains to distinguish them from amyloidosis. From the pathology archives of 2 institutions spanning 10 years, we identified 11 cases of PLCDD, including 7 diagnosed as such and 4 determined retrospectively. The deposits in all cases of PLCDD stained crimson red with MT and salmon pink with SAB, while the cases of pulmonary amyloid (n=10) stained blue-gray and blue-green, respectively. The immunoglobulin light chain nature of the deposits was confirmed in 10 of 11 cases by either immunofluorescence microscopy (n=5) or mass spectrometry (n=5). Transmission electron microscopy revealed osmiophilic, electron-dense deposits in all cases analyzed (n=3). An extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue type was diagnosed in 10 cases and 1 represented a plasma cell neoplasm. Our study highlights the importance of considering PLCDD in the differential diagnosis of amyloid-like deposits in the lung and the value of performing MT and SAB stains to distinguish between PLCDD and amyloidosis.
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http://dx.doi.org/10.1097/PAS.0000000000001593DOI Listing
March 2021

The clinical and pathological features of plasma cell myeloma post solid organ transplantation.

Am J Hematol 2020 12 17;95(12):1531-1541. Epub 2020 Sep 17.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, US.

Plasma cell neoplasms (PCNs), comprising plasma cell myelomas (PCMs) and plasmacytomas, which occur after solid organ transplantation, represent rare subtypes of monomorphic post-transplant lymphoproliferative disorders (M-PTLDs). Data regarding the clinical and pathological features of post-transplant (PT)-PCMs are limited. To gain a better understanding of disease biology, we performed comprehensive immunophenotypic analysis, reviewed cytogenetic analysis results and evaluated clinical outcomes of PT-PCMs diagnosed and treated at our institution. Fifteen PT-PCM (M: F - 4:1) and two PT-MGUS (two males) cases were identified. The median age of PT-PCM patients was 68 years (29-79 years) and PCMs presented at a median of 9.7 years (0.5-24.7 years) after transplantation. The PT-PCMs accounted for 11.6% of all M-PTLDs and the period prevalence was 9/3108 (0.29%), 3/1071 (0.28%), 2/1345 (0.15%) and 1/878 (0.11%) post kidney, heart, liver and lung transplantation. Lytic bone disease was observed in 1/11 (9%) patients. Marrow plasma cell infiltration ranged from 10%-70% (median 20%), with 10/15 (67%) and 5/15 (33%) cases manifesting immature and plasmablastic morphology. The immunophenotype of all cases and cytogenetic abnormalities, identified in 60% of cases, were similar to multiple myeloma (MM) of immunocompetent individuals. All PT-PCMs were EBER negative. Ten of 11 (91%) patients with active MM were treated, all with proteasome inhibitor-based therapy. Treatment response and 5-year overall survival (54.5%) was comparable to MM of immunocompetent individuals. However, the survival of patients with plasmablastic PCMs was inferior to those with immature PCMs. 0ur findings indicate PT-PCMs to be predominantly late onset PTLDs that have similar clinicopathologic characteristics as conventional MM.
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http://dx.doi.org/10.1002/ajh.25988DOI Listing
December 2020

Cancer testis antigen expression across T-cell lymphoma subtypes.

Hematol Oncol 2020 Dec 14;38(5):827-830. Epub 2020 Aug 14.

Divison of Hematology and Oncology, University of Virginia Cancer Center, University of Virginia, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1002/hon.2785DOI Listing
December 2020

A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL.

Blood Adv 2020 07;4(14):3391-3404

Division of Hematopathology and Department of Pathology, Duke University Medical Center, Durham, NC.

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous entity of B-cell lymphoma. Cell-of-origin (COO) classification of DLBCL is required in routine practice by the World Health Organization classification for biological and therapeutic insights. Genetic subtypes uncovered recently are based on distinct genetic alterations in DLBCL, which are different from the COO subtypes defined by gene expression signatures of normal B cells retained in DLBCL. We hypothesize that classifiers incorporating both genome-wide gene-expression and pathogenetic variables can improve the therapeutic significance of DLBCL classification. To develop such refined classifiers, we performed targeted RNA sequencing (RNA-Seq) with a commercially available next-generation sequencing (NGS) platform in a large cohort of 418 DLBCLs. Genetic and transcriptional data obtained by RNA-Seq in a single run were explored by state-of-the-art artificial intelligence (AI) to develop a NGS-COO classifier for COO assignment and NGS survival models for clinical outcome prediction. The NGS-COO model built through applying AI in the training set was robust, showing high concordance with COO classification by either Affymetrix GeneChip microarray or the NanoString Lymph2Cx assay in 2 validation sets. Although the NGS-COO model was not trained for clinical outcome, the activated B-cell-like compared with the germinal-center B-cell-like subtype had significantly poorer survival. The NGS survival models stratified 30% high-risk patients in the validation set with poor survival as in the training set. These results demonstrate that targeted RNA-Seq coupled with AI deep learning techniques provides reproducible, efficient, and affordable assays for clinical application. The clinical grade assays and NGS models integrating both genetic and transcriptional factors developed in this study may eventually support precision medicine in DLBCL.
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http://dx.doi.org/10.1182/bloodadvances.2020001949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391158PMC
July 2020

Henoch-Schönlein Purpura Associated With Diffuse Large B-cell Lymphoma of the Orbit.

Ophthalmic Plast Reconstr Surg 2021 Mar-Apr 01;37(2):e47-e50

Department of Ophthalmology, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York.

The association between Henoch-Schönlein purpura (HSP) and neoplasia is rare and has been more commonly reported in cases of solid tumors rather than hemotological malignancies. To the authors' knowledge, HSP in association with orbital lymphoma has not been previously reported. An 84-year-old man underwent anterior orbitotomy with biopsy for a rapidly growing orbital mass. Immediately following this procedure, he developed petechial rash, flash pulmonary edema, and kidney dysfunction with hematuria and proteinuria. Orbital biopsy revealed diffuse large B-cell lymphoma while skin and kidney biopsies showed features consistent with HSP. Multidisciplinary team involvement and treatment with chemotherapy and corticosteroid resulted in an excellent clinical response. Clinicians should be aware that HSP and orbital diffuse large B-cell lymphoma can co-occur, potentially leading to life-threatening rapid fluid shifts and metabolic derangements.
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http://dx.doi.org/10.1097/IOP.0000000000001739DOI Listing
April 2021

Primary large B-cell lymphoma of the central nervous system with cyclin D1 expression and t(11;14) (IGH-CCND1): Diffuse large B-cell lymphoma with CCND1 rearrangement or mantle cell lymphoma?

Hematol Oncol 2020 Dec 13;38(5):817-822. Epub 2020 Aug 13.

Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York, USA.

Mantle cell lymphomas (MCLs) are the prototypic B-cell non-Hodgkin lymphomas defined by cyclin D1 gene (CCND1; or other cyclin D family gene) rearrangements. However, extremely rare cases of diffuse large B-cell lymphomas (DLBCLs) harboring CCND1 rearrangements, resulting in cyclin D1 protein expression, have also been reported. In this report, we describe an unusual primary large B-cell lymphoma of non-germinal center immunophenotype of the central nervous system (CNS) in an elderly male patient, which was negative for CD5 and SOX11, and exhibited cyclin D1 expression. Fluorescence in situ hybridization analysis detected IGH-CCND1 and BCL6 rearrangements. This case may represent the first report of a primary CNS DLBCL with IGH-CCND1 rearrangement. The clinico-pathologic features that can help differentiate primary CNS MCL from primary DLBCL of the CNS with IGH-CCND1 rearrangement are discussed.
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http://dx.doi.org/10.1002/hon.2779DOI Listing
December 2020

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs.

Genome Biol 2020 06 29;21(1):153. Epub 2020 Jun 29.

Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.

Background: Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified.

Results: We perform whole genome methyl-seq on diverse normal cells and tissues and three cancer types. After excluding imprinting, the data pinpoint 15,112 high-confidence ASM differentially methylated regions, of which 1838 contain SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies are increased in cancers versus matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancer cells show increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor binding motifs are similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes track with de novo ASM. Allele-specific transcription factor binding from ChIP-seq is enriched among ASM loci, but most ASM differentially methylated regions lack such annotations, and some are found in otherwise uninformative "chromatin deserts."

Conclusions: ASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and transcription factor binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, cardiometabolic, neuropsychiatric, and neoplastic diseases.
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http://dx.doi.org/10.1186/s13059-020-02059-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322865PMC
June 2020

DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis.

Nature 2020 03 26;579(7798):291-296. Epub 2020 Feb 26.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

The DNA-dependent protein kinase (DNA-PK), which comprises the KU heterodimer and a catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor. KU binds to DNA ends, initiates cNHEJ, and recruits and activates DNA-PKcs. KU also binds to RNA, but the relevance of this interaction in mammals is unclear. Here we use mouse models to show that DNA-PK has an unexpected role in the biogenesis of ribosomal RNA (rRNA) and in haematopoiesis. The expression of kinase-dead DNA-PKcs abrogates cNHEJ. However, most mice that both expressed kinase-dead DNA-PKcs and lacked the tumour suppressor TP53 developed myeloid disease, whereas all other previously characterized mice deficient in both cNHEJ and TP53 expression succumbed to pro-B cell lymphoma. DNA-PK autophosphorylates DNA-PKcs, which is its best characterized substrate. Blocking the phosphorylation of DNA-PKcs at the T2609 cluster, but not the S2056 cluster, led to KU-dependent defects in 18S rRNA processing, compromised global protein synthesis in haematopoietic cells and caused bone marrow failure in mice. KU drives the assembly of DNA-PKcs on a wide range of cellular RNAs, including the U3 small nucleolar RNA, which is essential for processing of 18S rRNA. U3 activates purified DNA-PK and triggers phosphorylation of DNA-PKcs at T2609. DNA-PK, but not other cNHEJ factors, resides in nucleoli in an rRNA-dependent manner and is co-purified with the small subunit processome. Together our data show that DNA-PK has RNA-dependent, cNHEJ-independent functions during ribosome biogenesis that require the kinase activity of DNA-PKcs and its phosphorylation at the T2609 cluster.
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http://dx.doi.org/10.1038/s41586-020-2041-2DOI Listing
March 2020

Reversal of CYLD phosphorylation as a novel therapeutic approach for adult T-cell leukemia/lymphoma (ATLL).

Cell Death Dis 2020 02 5;11(2):94. Epub 2020 Feb 5.

Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

Adult T-cell leukemia/lymphoma (ATLL) is a malignancy of mature T cells associated with chronic infection by human T-cell lymphotropic virus type-1 (HTLV-1). ATLL patients with aggressive subtypes have dismal outcomes. We demonstrate that ATLL cells co-opt an early checkpoint within the tumor necrosis factor receptor 1 (TNFR1) pathway, resulting in survival advantage. This early checkpoint revolves around an interaction between the deubiquitinase CYLD and its target RIPK1. The status of RIPK1 K63-ubiquitination determines cell fate by creating either a prosurvival signal (ubiquitinated RIPK1) or a death signal (deubiquitinated RIPK1). In primary ATLL samples and in cell line models, an increased baseline level of CYLD phosphorylation was observed. We therefore tested the hypothesis that this modification of CYLD, which has been reported to inhibit its deubiquitinating function, leads to increased RIPK1 ubiquitination and thus provides a prosurvival signal to ATLL cells. CYLD phosphorylation can be pharmacologically reversed by IKK inhibitors, specifically by TBK1/IKKε and IKKβ inhibitors (MRT67307 and TPCA). Both of the IKK sub-families can phosphorylate CYLD, and the combination of MRT67307 and TPCA have a marked effect in reducing CYLD phosphorylation and triggering cell death. ATLL cells overexpressing a kinase-inactive TBK1 (TBK1-K38A) demonstrate lower CYLD phosphorylation and subsequently reduced proliferation. IKK blockade reactivates CYLD, as evidenced by the reduction in RIPK1 ubiquitination, which leads to the association of RIPK1 with the death-inducing signaling complex (DISC) to trigger cell death. In the absence of CYLD, RIPK1 ubiquitination remains elevated following IKK blockade and it does not associate with the DISC. SMAC mimetics can similarly disrupt CYLD phosphorylation and lead to ATLL cell death through reduction of RIPK1 ubiquitination, which is CYLD dependent. These results identify CYLD as a crucial regulator of ATLL survival and point to its role as a potential novel target for pharmacologic modification in this disease.
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http://dx.doi.org/10.1038/s41419-020-2294-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002447PMC
February 2020

Refractory celiac disease type II: An atypical case highlighting limitations of the current classification system.

Hematol Oncol 2020 Aug 19;38(3):399-405. Epub 2020 Feb 19.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA.

Refractory celiac disease (RCD) is a rare condition associated with high morbidity that develops in individuals with celiac disease. It is known to be biologically heterogeneous, and currently two types are recognized based on immunophenotypic and molecular features, type I (RCD I) and type II (RCD II). Differentiating between RCD I and RCD II is critical, as patients with RCD II have substantially worse outcomes and a high risk of developing enteropathy-associated T-cell lymphoma. However, the current RCD classification is limited in scope, and atypical presentations and immunophenotypes are not recognized at present. Herein, we describe a unique case of RCD II with atypical clinical (primarily neurologic manifestations and lack of significant gastrointestinal symptoms), histopathologic (no villous atrophy), immunophenotypic (virtual absence of cytoplasmic CD3 expression), and molecular features (absence of clonal TR rearrangement and identification of pathogenic STAT3 and KMT2D mutations). This case highlights limitations of the current RCD classification system and the utility of next generation sequencing (NGS) studies in the diagnostic workup of RCD. Future algorithms need to recognize extraintestinal manifestations and incorporate atypical histopathologic and immunophenotypic features, as well as results of NGS analysis for RCD II classification.
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http://dx.doi.org/10.1002/hon.2720DOI Listing
August 2020

Survival benefit in patients with peripheral T-cell lymphomas after treatments with novel therapies and clinical trials.

Hematol Oncol 2020 Feb 29;38(1):51-58. Epub 2019 Dec 29.

Center for Lymphoid Malignancies, Columbia University Irving Medical Center, New York, New York.

The peripheral T-cell lymphomas (PTCL) are rare and heterogeneous diseases characterized by an unfavorable prognosis. Chemotherapy is standard upfront treatment in most patients, but responses are short-lived with few FDA-approved "novel" agents available. We sought to define the impact of these novel agents as single agents or in clinical trials on the outcomes of patients with PTCL. From January 1994 to May 2019, adult patients with PTCL who were managed at our institution were included in this analysis. In addition to patients with incomplete data, those diagnosed with large granular lymphocytic leukemia and cutaneous T-cell lymphoma (CTCL) except for transformed mycosis fungoides were excluded. Statistical analyses were performed using SAS version 9.4. There were 219 patients included in the analysis. The median age at diagnosis was 56 years (range, 18-90 years). First line therapies mostly consisted of combination chemotherapy (75%). There was a statistical difference among patients who received chemotherapy, novel agents alone and in chemotherapy-free combinations, other, and no treatment (P < .0001). In patients who were treated with second line chemotherapy, novel agents alone and in combination without chemotherapy, or other, there was a still a survival benefit favoring novel agents (P = .0417). In the third line, there was no statistical difference among the three groups (P = .569). All patients who received novel therapies and underwent autologous stem cell transplant (autoSCT) achieved a complete response (CR) and had a better survival compared with patients who underwent chemotherapy who had a 70% CR rate prior to autoSCT (P = .046). Exposure to FDA-approved novel agents, immunoepigenetic trials, and clinical trials in general was associated with an overall survival (OS) benefit (P = .003, P = .04, and P = .006, respectively). These data suggest that patients who receive novel agents have superior outcomes compared with patients without exposure to novel therapies who receive chemotherapy-predicated treatments.
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http://dx.doi.org/10.1002/hon.2705DOI Listing
February 2020

Celiac disease diagnosis from videocapsule endoscopy images with residual learning and deep feature extraction.

Comput Methods Programs Biomed 2020 Apr 20;187:105236. Epub 2019 Nov 20.

School of Instrument Science and Opto-electronic Engineering, Hefei University of Technology, Hefei 230009, China. Electronic address:

Background And Objective: Videocapsule endoscopy (VCE) is a relatively new technique for evaluating the presence of villous atrophy in celiac disease patients. The diagnostic analysis of video frames is currently time-consuming and tedious. Recently, computer-aided diagnosis (CAD) systems have become an attractive research area for diagnosing celiac disease. However, the images captured from VCE are susceptible to alterations in light illumination, rotation direction, and intestinal secretions. Moreover, textural features of the mucosal villi obtained by VCE are difficult to characterize and extract. This work aims to find a novel deep learning feature learning module to assist in the diagnosis of celiac disease.

Methods: In this manuscript, we propose a novel deep learning recalibration module which shows significant gain in diagnosing celiac disease. In this recalibration module, the block-wise recalibration component is newly employed to capture the most salient feature in the local channel feature map. This learning module was embedded into ResNet50, Inception-v3 to diagnose celiac disease using a 10-time 10-fold cross-validation based upon analysis of VCE images. In addition, we employed model weights to extract feature points from training and test samples before the last fully connected layer, and then input to a support vector machine (SVM), k-nearest neighbor (KNN), and linear discriminant analysis (LDA) for differentiating celiac disease images from heathy controls.

Results: Overall, the accuracy, sensitivity and specificity of the 10-time 10-fold cross-validation were 95.94%, 97.20% and 95.63%, respectively.

Conclusions: A novel deep learning recalibration module, with global response and local salient factors is proposed, and it has a high potential for utilizing deep learning networks to diagnose celiac disease using VCE images.
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http://dx.doi.org/10.1016/j.cmpb.2019.105236DOI Listing
April 2020

Immunoglobulin somatic hypermutation has clinical impact in DLBCL and potential implications for immune checkpoint blockade and neoantigen-based immunotherapies.

J Immunother Cancer 2019 10 22;7(1):272. Epub 2019 Oct 22.

Hematopathology Division, Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.

Background: Diffuse large B-cell lymphoma (DLBCL) harbors somatic hypermutation (SHM) in the immunoglobulin heavy chain and light chain variable region genes, IGHV and IGK/LV. Recent studies have revealed that IGV SHM creates neoantigens that activate T-cell responses against B-cell lymphoma.

Methods: To determine the clinical relevance of IGV SHM in DLBCL treated with standard immunochemotherapy, we performed next-generation sequencing of the immunoglobulin variable regions and complementarity determining region 3 (CDR3) for 378 patients with de novo DLBCL. The prognostic effects of IGV SHM and ongoing SHM or intra-clonal heterogeneity were analyzed in the training (192 patients), validation (186 patients), and overall DLBCL cohorts. To gain mechanistic insight, we analyzed the predicted IG-derived neoantigens' immunogenicity potential, determined by the major histocompatibility complex-binding affinity and the frequency-of-occurrence of T cell-exposed motifs (TCEMs) in a TCEM repertoire derived from human proteome, microbiome, and pathogen databases. Furthermore, IGV SHM was correlated with molecular characteristics of DLBCL and PD-1/L1 expression in the tumor microenvironment assessed by fluorescent multiplex immunohistochemistry.

Results: SHM was commonly found in IGHV and less frequently in IGK/LV. High levels of clonal IGHV SHM (SHM) were associated with prolonged overall survival in DLBCL patients, particularly those without BCL2 or MYC translocation. In contrast, long heavy chain CDR3 length, the presence of IGHV ongoing SHM in DLBCL, and high clonal IGK/LV SHM in germinal center B-cell-like (GCB)-DLBCL were associated with poor prognosis. These prognostic effects were significant in both the training and validation sets. By prediction, the SHM groups harbored more potentially immune-stimulatory neoantigens with high binding affinity and rare TCEMs. PD-1/L1 expression in CD8 T cells was significantly lower in IGHV SHM than in SHM patients with activated B-cell-like DLBCL, whereas PD-1 expression in CD4 T cells and PD-L1 expression in natural killer cells were higher in IGK/LV SHM than in SHM patients with GCB-DLBCL. PD-L1/L2 (9p24.1) amplification was associated with high IGHV SHM and ongoing SHM.

Conclusions: These results show for the first time that IGV SHM and ongoing SHM have prognostic effects in DLBCL and potential implications for PD-1/PD-L1 blockade and neoantigen-based immunotherapies.
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http://dx.doi.org/10.1186/s40425-019-0730-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6806565PMC
October 2019

Detection of Nonhematologic Neoplasms by Routine Flow Cytometry Analysis.

Am J Clin Pathol 2020 01;153(1):99-104

Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY.

Objectives: We investigated the ability of routine flow cytometry (FC) to detect nonhematologic neoplasms (non-HN) using antibody panels routinely used for the diagnosis of hematologic neoplasms.

Methods: FC analyses of 4,000 various diagnostic samples were retrospectively reviewed to identify cases in which an aberrant, viable CD45-negative, nonhematologic neoplastic population was detected by FC panels designed to evaluate hematologic neoplasms.

Results: A total of 57 (1.4%) diverse non-HNs were identified, representing neuroendocrine tumors (33/57) and carcinomas (9/57), as well as other malignancies (15/57) such as sarcoma and melanoma. The majority of neoplasms were positive for at least one antibody, typically CD56 (43/51, 84.3%), followed by CD117 (15/34, 44.1%) and CD138 (6/33, 18.2%).

Conclusions: Our findings highlight the importance of carefully inspecting CD45-negative events to identify non-HNs by routine FC analysis. This can help expedite further downstream immunophenotypic analysis of specimens and triage samples for appropriate genetic and molecular studies.
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http://dx.doi.org/10.1093/ajcp/aqz138DOI Listing
January 2020

Genetic and phenotypic characterization of indolent T-cell lymphoproliferative disorders of the gastrointestinal tract.

Haematologica 2020 07 26;105(7):1895-1906. Epub 2019 Sep 26.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA

Indolent T-cell lymphoproliferative disorders of the gastrointestinal tract are rare clonal T-cell diseases that more commonly occur in the intestines and have a protracted clinical course. Different immunophenotypic subsets have been described, but the molecular pathogenesis and cell of origin of these lymphocytic proliferations is poorly understood. Hence, we performed targeted next-generation sequencing and comprehensive immunophenotypic analysis of ten indolent T-cell lymphoproliferative disorders of the gastrointestinal tract, which comprised CD4 (n=4), CD8 (n=4), CD4/CD8 (n=1) and CD4/CD8 (n=1) cases. Genetic alterations, including recurrent mutations and novel rearrangements, were identified in 8/10 (80%) of these lymphoproliferative disorders. The CD4, CD4/CD8, and CD4/CD8 cases harbored frequent alterations of JAK-STAT pathway genes (5/6, 82%); mutations (n=3), deletion (n=1) and rearrangement (n=1), and 4/6 (67%) had concomitant mutations in epigenetic modifier genes (, , ). Conversely, 2/4 (50%) of the CD8 cases exhibited structural alterations involving the 3' untranslated region of the gene. Longitudinal genetic analysis revealed stable mutational profiles in 4/5 (80%) cases and acquisition of mutations in one case was a harbinger of disease transformation. The CD4 and CD4/CD8 lymphoproliferative disorders displayed heterogeneous Th1 (T-bet), Th2 (GATA3) or hybrid Th1/Th2 (T-bet/GATA3) profiles, while the majority of CD8 disorders and the CD4/CD8 disease showed a type-2 polarized (GATA3) effector T-cell (Tc2) phenotype. Additionally, CD103 expression was noted in 2/4 CD8 cases. Our findings provide insights into the pathogenetic bases of indolent T-cell lymphoproliferative disorders of the gastrointestinal tract and confirm the heterogeneous nature of these diseases. Detection of shared and distinct genetic alterations of the JAK-STAT pathway in certain immunophenotypic subsets warrants further mechanistic studies to determine whether therapeutic targeting of this signaling cascade is efficacious for a proportion of patients with these recalcitrant diseases.
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http://dx.doi.org/10.3324/haematol.2019.230961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327650PMC
July 2020

The whole-genome landscape of Burkitt lymphoma subtypes.

Blood 2019 11;134(19):1598-1607

Department of Immunology and.

Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in the setting of HIV. In this study, we comprehensively delineated the genomic basis of BL through whole-genome sequencing (WGS) of 101 tumors representing all 3 subtypes of BL to identify 72 driver genes. These data were additionally informed by CRISPR screens in BL cell lines to functionally annotate the role of oncogenic drivers. Nearly every driver gene was found to have both coding and non-coding mutations, highlighting the importance of WGS for identifying driver events. Our data implicate coding and non-coding mutations in IGLL5, BACH2, SIN3A, and DNMT1. Epstein-Barr virus (EBV) infection was associated with higher mutation load, with type 1 EBV showing a higher mutational burden than type 2 EBV. Although sporadic and immunodeficiency-associated BLs had similar genetic profiles, endemic BLs manifested more frequent mutations in BCL7A and BCL6 and fewer genetic alterations in DNMT1, SNTB2, and CTCF. Silencing mutations in ID3 were a common feature of all 3 subtypes of BL. In vitro, mass spectrometry-based proteomics demonstrated that the ID3 protein binds primarily to TCF3 and TCF4. In vivo knockout of ID3 potentiated the effects of MYC, leading to rapid tumorigenesis and tumor phenotypes consistent with those observed in the human disease.
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http://dx.doi.org/10.1182/blood.2019001880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6871305PMC
November 2019

Posttransplant lymphoproliferative disorder: EBV plasma cell myeloma with large multinucleated plasma cells.

Blood 2019 09;134(12):992

New York-Presbyterian Hospital/Columbia University Irving Medical Center.

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http://dx.doi.org/10.1182/blood.2019001939DOI Listing
September 2019