Quality Management System in Clinical Digital Pathology Operations at a Tertiary Cancer Center

Digital pathology workflows can improve pathology operations by allowing reliable and fast retrieval of digital images, digitally reviewing pathology slides, enabling remote work and telepathology, use of computer-aided tools, and sharing of digital images for research and educational purposes. The need for quality systems is a prerequisite for successful clinical-grade digital pathology adoption and patient safety. In this article, we describe the development of a structured digital pathology laboratory quality management system (QMS) for clinical digital pathology operations at Memorial Sloan Kettering Cancer Center (MSK). This digital pathology-specific QMS development stemmed from the gaps that were identified when MSK integrated digital pathology into its clinical practice. The digital scan team in conjunction with the Department of Pathology and Laboratory Medicine quality team developed a QMS tailored to the scanning operation to support departmental and institutional needs. As a first step, systemic mapping of the digital pathology operations identified the prescan, scan, and postscan processes; instrumentation; and staffing involved in the digital pathology operation. Next, gaps identified in quality control and quality assurance measures led to the development of standard operating procedures and training material for the different roles and workflows in the process. All digital pathology-related documents were subject to regulatory review and approval by departmental leadership. The quality essentials were developed into an extensive Digital Pathology Quality Essentials framework to specifically address the needs of the growing clinical use of digital pathology technologies. Using the unique digital experience gained at MSK, we present our recommendations for QMS for large-scale digital pathology operations in clinical settings.

MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia

Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT, and the loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.

Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia

In chronic lymphocytic leukemia (CLL), epigenetic alterations are considered to centrally shape the transcriptional signatures that drive disease evolution and underlie its biological and clinical subsets. Characterizations of epigenetic regulators, particularly histone-modifying enzymes, are very rudimentary in CLL. In efforts to establish effectors of the CLL-associated oncogene T-cell leukemia 1A (TCL1A), we identified here the lysine-specific histone demethylase KDM1A to interact with the TCL1A protein in B cells in conjunction with an increased catalytic activity of KDM1A. We demonstrate that KDM1A is upregulated in malignant B cells. Elevated KDM1A and associated gene expression signatures correlated with aggressive disease features and adverse clinical outcomes in a large prospective CLL trial cohort. Genetic Kdm1a knockdown in Eμ-TCL1A mice reduced leukemic burden and prolonged animal survival, accompanied by upregulated p53 and proapoptotic pathways. Genetic KDM1A depletion also affected milieu components (T, stromal, and monocytic cells), resulting in significant reductions in their capacity to support CLL-cell survival and proliferation. Integrated analyses of differential global transcriptomes (RNA sequencing) and H3K4me3 marks (chromatin immunoprecipitation sequencing) in Eμ-TCL1A vs iKdm1aKD;Eμ-TCL1A mice (confirmed in human CLL) implicate KDM1A as an oncogenic transcriptional repressor in CLL which alters histone methylation patterns with pronounced effects on defined cell death and motility pathways. Finally, pharmacologic KDM1A inhibition altered H3K4/9 target methylation and revealed marked anti-B-cell leukemic synergisms. Overall, we established the pathogenic role and effector networks of KDM1A in CLL via tumor-cell intrinsic mechanisms and its impacts in cells of the microenvironment. Our data also provide rationales to further investigate therapeutic KDM1A targeting in CLL.

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

Whole slide imaging is revolutionizing the field of pathology and is currently being used for clinical, educational, and research initiatives by an increasing number of institutions. Pathology departments have distinct needs for digital pathology systems, yet the cost of digital workflows is cited as a major barrier for widespread adoption by many organizations. Memorial Sloan Kettering Cancer Center (MSK) is an early adopter of whole slide imaging with incremental investments in resources that started more than 15 years ago. This experience and the large-scale scan operations led to the identification of required framework components of digital pathology operations. The cost of these components for the 2021 digital pathology operations at MSK were studied and calculated to enable an understanding of the operation and benchmark the accompanying costs. This paper describes the unique infrastructure cost and the costs associated with the digital pathology clinical operation use cases in a large, tertiary cancer center. These calculations can serve as a blueprint for other institutions to provide the necessary concepts and offer insights towards the financial requirements for digital pathology adoption by other institutions.

Abstract A28: BCL10 mutations define distinct dependencies guiding precision therapy for DLBCL

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy and the activated B cell-like subtype (ABC-DLBCL) is the most aggressive form and harbors frequent mutations of immune signaling pathways that culminate in constitutive activation of CARD11-MALT1-BCL10 (CBM) complex and downstream NF-κB pathway. CBM complexes form large macromolecular structures due to signal-induced polymerization of the BCL10 subunit, which is affected by recurrent somatic mutations in ABC-DLBCLs. Through biochemical, structural and functional dissection of these mutations, we find that BCL10 mutations fall into two functionally distinct classes: missense mutations of the BCL10 CARD domain (hotspot R58Q) and truncation of its C-terminal tail (hotspot E140X). To explore the functional consequences of BCL10 mutations, we established reporter systems to evaluate their impact on MALT1 and NF-𝜅B activities which are BCL10 downstream signaling cascades. We found that almost all mutants induced aberrantly strong NF-𝜅B and MALT1 activities in lymphoma cells as compared to WT BCL10, indicating the gain-of-function effect of BCL10 mutations. By performing immunohistochemistry staining of p65 in a set of tumor tissue microarray from DLBCL patients (n=298), we revealed that BCL10 mutant tumors have significantly (Mann-Whitney p<0.0001) increased p65 nuclear staining score compared to BCL10 WT tumors, suggesting enhanced NF-𝜅B activity. To investigate the biochemical impact of BCL10 mutants on CBM complex formation, we performed fluorescence polarization and filamentation formation assays with purified WT and mutant BCL10 proteins and found that both BCL10R58Q and BCL10E140X manifested faster and more spontaneous polarization compared to BCL10WT. Surprisingly, through mapping the BCL10-MALT1 interaction, we found that truncating mutation (E140X) abrogated a novel protein interaction motif through which MALT1 inhibits BCL10 polymerization, thus unleashing spontaneous CBM filament formation and inducing addiction to MALT1 activity. In marked contrast, the CARD missense mutation (R58Q) on BCL10 filament interface not only does not disrupt but enhances filament formation and it also alters CBM complex kinetics forming glutamine network structures that stabilize BCL10 filaments, but this still may require the upstream signal to activate MALT1. Importantly, we found that BCL10 mutant cells were less dependent on upstream CARD11 activation in MALT1 activation, NF-𝜅B signaling and cell growth assays performed in ABC-DLBCL lines. Furthermore, in vitro and in vivo xenograft studies revealed that BCL10 mutant lymphomas are resistant to BTK inhibitors, whereas BCL10 truncating (E140X) but not missense CARD (R58Q) mutants were hypersensitive to MALT1 protease inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL and further precision can be achieved by tailoring therapy (e.g. MALT1 inhibitors that are currently being tested in clinical trials) according to specific biochemical effects of distinct mutation classes.

Citation Format: Min Xia, Liron David, Matthew R Teater, Johana Gutierrez, Xiang Wang, Cem Meydan, Andrew Lytle, Graham Slack, David Scott, Ozlem Onder, Kojo Elenitoba-Johnson, Nahuel Zamponi, Leandro Cerchietti, Tianbao Lu, Ulrike Philippar, Lorena Fontan, Hao Wu, Ari Melnick. BCL10 mutations define distinct dependencies guiding precision therapy for DLBCL [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A28.

ACCELERATE: A Patient-Powered Natural History Study Design Enabling Clinical and Therapeutic Discoveries in a Rare Disorder

Geographically dispersed patients, inconsistent treatment tracking, and limited infrastructure slow research for many orphan diseases. We assess the feasibility of a patient-powered study design to overcome these challenges for Castleman disease, a rare hematologic disorder. Here, we report initial results from the ACCELERATE natural history registry. ACCELERATE includes a traditional physician-reported arm and a patient-powered arm, which enables patients to directly contribute medical data and biospecimens. This study design enables successful enrollment, with the 5-year minimum enrollment goal being met in 2 years. A median of 683 clinical, laboratory, and imaging data elements are captured per patient in the patient-powered arm compared with 37 in the physician-reported arm. These data reveal subgrouping characteristics, identify off-label treatments, support treatment guidelines, and are used in 17 clinical and translational studies. This feasibility study demonstrates that the direct-to-patient design is effective for collecting natural history data and biospecimens, tracking therapies, and providing critical research infrastructure.

Pyrimidine tract-binding protein 1 mediates pyruvate kinase M2-dependent phosphorylation of signal transducer and activator of transcription 3 and oncogenesis in anaplastic large cell lymphoma

PKM2 (pyruvate kinase M2), a critical regulator of glycolysis, is phosphorylated by numerous growth factor receptors and oncogenic tyrosine kinases including NPM-ALK which is expressed in a subset of aggressive T-cell non-Hodgkin lymphomas known as anaplastic large cell lymphoma, ALK-positive. Our previous work demonstrated that phosphorylation of Y105-PKM2 by NPM-ALK regulates a major metabolic shift to promote lymphomagenesis. In addition to its role in metabolism, recent studies have shown that PKM2 promotes oncogenesis by phosphorylating nuclear STAT3 (signal transducer and activator of transcription 3) and regulating transcription of genes involved in cell survival and proliferation. We hypothesized that identification of novel PKM2 interactors could provide additional insights into its expanding functional role in cancer. To this end, immunocomplexes of FLAG-tagged PKM2 were isolated from NPM-ALK-positive ALCL (anaplastic large cell lymphoma) cells and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) which led to the identification of polypyrimidine tract-binding protein (PTBP1) as a novel interactor of PKM2. The interaction between PTBP1 and PKM2 was restricted to the nucleus and was dependent on NPM-ALK mediated Y105 phosphorylation of PKM2. Stable shRNA-mediated silencing of PTBP1 resulted in a marked decrease in pY105-PKM2 and pY705-STAT3 which led to decreased ALCL cell proliferation and colony formation. Overall, our data demonstrate that PTBP1 interacts with PKM2 and promotes ALCL oncogenesis by facilitating PKM2-dependent activation of STAT3 within the nucleus.

Loss of the Ubiquitin-conjugating Enzyme UBE2W Results in Susceptibility to Early Postnatal Lethality and Defects in Skin, Immune, and Male Reproductive Systems

UBE2W ubiquitinates N termini of proteins rather than internal lysine residues, showing a preference for substrates with intrinsically disordered N termini. The in vivo functions of this intriguing E2, however, remain unknown. We generated Ube2w germ line KO mice that proved to be susceptible to early postnatal lethality without obvious developmental abnormalities. Although the basis of early death is uncertain, several organ systems manifest changes in Ube2w KO mice. Newborn Ube2w KO mice often show altered epidermal maturation with reduced expression of differentiation markers. Mirroring higher UBE2W expression levels in testis and thymus, Ube2w KO mice showed a disproportionate decrease in weight of these two organs (~50%), suggesting a functional role for UBE2W in the immune and male reproductive systems. Indeed, Ube2w KO mice displayed sustained neutrophilia accompanied by increased G-CSF signaling and testicular vacuolation associated with decreased fertility. Proteomic analysis of a vulnerable organ, presymptomatic testis, showed a preferential accumulation of disordered proteins in the absence of UBE2W, consistent with the view that UBE2W preferentially targets disordered polypeptides. These mice further allowed us to establish that UBE2W is ubiquitously expressed as a single isoform localized to the cytoplasm and that the absence of UBE2W does not alter cell viability in response to various stressors. Our results establish that UBE2W is an important, albeit not essential, protein for early postnatal survival and normal functioning of multiple organ systems.

Pharmacoproteomics identifies combinatorial therapy targets for diffuse large B cell lymphoma

Rationally designed combinations of targeted therapies for refractory cancers, such as activated B cell-like diffuse large B cell lymphoma (ABC DLBCL), are likely required to achieve potent, durable responses. Here, we used a pharmacoproteomics approach to map the interactome of a tumor-enriched isoform of HSP90 (teHSP90). Specifically, we chemically precipitated teHSP90-client complexes from DLBCL cell lines with the small molecule PU-H71 and found that components of the proximal B cell receptor (BCR) signalosome were enriched within teHSP90 complexes. Functional assays revealed that teHSP90 facilitates BCR signaling dynamics by enabling phosphorylation of key BCR signalosome components, including the kinases SYK and BTK. Consequently, treatment of BCR-dependent ABC DLBCL cells with PU-H71 attenuated BCR signaling, calcium flux, and NF-κB signaling, ultimately leading to growth arrest. Combined exposure of ABC DLBCL cell lines to PU-H71 and ibrutinib, a BCR pathway inhibitor, more potently suppressed BCR signaling than either drug alone. Correspondingly, PU-H71 combined with ibrutinib induced synergistic killing of lymphoma cell lines, primary human lymphoma specimens ex vivo, and lymphoma xenografts in vivo, without notable toxicity. Together, our results demonstrate that a pharmacoproteome-driven rational combination therapy has potential to provide more potent BCR-directed therapy for ABC DLCBL patients.

Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma

BACKGROUND

Burkitt lymphoma (BL) is the most common non-Hodgkin lymphoma in children worldwide and the most common paediatric malignancy in sub-Saharan Africa. The endemic (eBL) and sporadic (sBL) variants have distinct epidemiologic and virologic characteristics. Although gene expression studies have defined the transcriptional profiles of both, their proteomic signatures have not been studied.

METHODS

We compared the proteomic expression profiles using differential mass spectrometry-based isotope tag for relative and absolute quantitation (iTRAQ) analysis of a cell line representing Epstein-Barr virus (EBV)+ eBL, EBV+ and EBV- sBL, and EBV+/- normal B cells from healthy donors.

RESULTS

In total, there were 144 differentially expressed proteins with a statistically significant false discovery rate (FDR) of ⩽0.2. Results revealed over-expression of specific proteins with well-established links to lymphomagenesis such as TUBB2C (FDR 0.05), UCHL1 (FDR 0.05) and HSP90AB1 (FDR 0.1). Distinct characteristics based upon the epidemiologic and virologic subtypes of BL were also identified. In sBL, PCNA (FDR 0.05) and SLC3A2 (FDR 0.1) were significantly over-expressed. In eBL, C1QBP (FDR 0.1) and ENO1 (FDR 0.25) were significantly over-expressed. Comparison of EBV+ to EBV- BL cell lines and B cells revealed significant over-expression of DDX3X (FDR 0.1). Proteins were validated using Western blot analysis.

CONCLUSION

Our results suggest unique signal transduction pathways associated with EBV infection and epidemiological subtype of BL that may contribute to lymphomagenesis. These proteomic findings provide potential diagnostic, prognostic and therapeutic links to BL.

CGG repeat-associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome

Fragile X-associated tremor ataxia syndrome (FXTAS) results from a CGG repeat expansion in the 5' UTR of FMR1. This repeat is thought to elicit toxicity as RNA, yet disease brains contain ubiquitin-positive neuronal inclusions, a pathologic hallmark of protein-mediated neurodegeneration. We explain this paradox by demonstrating that CGG repeats trigger repeat-associated non-AUG-initiated (RAN) translation of a cryptic polyglycine-containing protein, FMRpolyG. FMRpolyG accumulates in ubiquitin-positive inclusions in Drosophila, cell culture, mouse disease models, and FXTAS patient brains. CGG RAN translation occurs in at least two of three possible reading frames at repeat sizes ranging from normal (25) to pathogenic (90), but inclusion formation only occurs with expanded repeats. In Drosophila, CGG repeat toxicity is suppressed by eliminating RAN translation and enhanced by increased polyglycine protein production. These studies expand the growing list of nucleotide repeat disorders in which RAN translation occurs and provide evidence that RAN translation contributes to neurodegeneration.

Abstract 953: Mechanistic rationale for inhibition of Poly(ADP-Ribose) Polymerase in ETS gene fusion positive prostate cancer

Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers including Ewing's sarcoma, acute myeloid leukemia, and epithelial tumors such as prostate cancer. However, transcription factors like the ETS genes have been notoriously difficult to target therapeutically. In fact, while approximately 50% of all prostate cancers harbor ETS gene fusions, the most common variant fuses an androgen regulated promoter and the 5’-UTR of TMPRSS2 to the second exon of ERG resulting in the pathogenic overexpression of a slightly truncated ERG transcription factor. Here, we use IP-mass spectrometry to characterize the ETS protein interactome in prostate cancer. We show that the TMPRSS2:ERG gene fusion product interacts with the enzymes poly(ADP-ribose)polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs) in a DNA-independent manner in both prostate cancer cells and tissues. ETS gene fusion-mediated transcription of several target genes including the invasion associated gene EZH2 requires both PARP1 and DNA-PKcs expression and activity. Likewise, cell invasion driven by ETS gene overexpression is inhibited by small molecule inhibitors or siRNA against these enzymes in matrigel coated transwell invasion assays (in vitro) as well as chicken chorioallantoic membrane intravasation and metastasis assays (in vivo). Importantly, pharmacological inhibition of PARP1 selectively inhibited the growth of 4 ETS positive, but not 5 ETS negative, prostate cancer cell xenografts. This analysis includes several prostate cancer cell lines, an isogenic model of hormone refractory prostate cancer and primary human tumors that were serially grown in mice. Finally, we find that TMPRSS2:ERG gene fusion overexpression leads to increased DNA double strand breaks as assessed by gamma-H2A.X staining and COMET assays. This DNA damage is then potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2-deficiency.Thus, we propose that the ETS:PARP1 interaction axis may represent a novel target for therapeutic intervention in cancers with ETS gene fusions and that future clinical trials will help determine if this subgroup of patients preferentially benefits from the addition of PARP inhibitor therapy. Moreover, our study suggests that inhibition of co-factors necessary for function may represent a new paradigm of treatment for malignancies driven by oncogenic transcription factors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 953. doi:10.1158/1538-7445.AM2011-953

Activity and cellular functions of the deubiquitinating enzyme and polyglutamine disease protein ataxin-3 are regulated by ubiquitination at lysine 117

Deubiquitinating enzymes (DUbs) play important roles in many ubiquitin-dependent pathways, yet how DUbs themselves are regulated is not well understood. Here, we provide insight into the mechanism by which ubiquitination directly enhances the activity of ataxin-3, a DUb implicated in protein quality control and the disease protein in the polyglutamine neurodegenerative disorder, Spinocerebellar Ataxia Type 3. We identify Lys-117, which resides near the catalytic triad, as the primary site of ubiquitination in wild type and pathogenic ataxin-3. Further studies indicate that ubiquitin-dependent activation of ataxin-3 at Lys-117 is important for its ability to reduce high molecular weight ubiquitinated species in cells. Ubiquitination at Lys-117 also facilitates the ability of ataxin-3 to induce aggresome formation in cells. Finally, structure-function studies support a model of activation whereby ubiquitination at Lys-117 enhances ataxin-3 activity independent of the known ubiquitin-binding sites in ataxin-3, most likely through a direct conformational change in or near the catalytic domain.

Abstract 1199: Global proteomic evaluation of the relationship between Epstein-Barr virus (EBV) and c-myc deregulation in endemic versus sporadic Burkitt lymphoma (BL)

Endemic BL (eBL) is characteristically positive(100%) for EBV, contrasting with sporadic(sBL) BL(∼30% EBV+). eBL vs sBL have different breakpoint regions within c-myc. The different mechanisms of lymphomagenesis however, remain unknown. Global analysis of proteins expressed in the different subtypes may provide insights into biologic, pathogenetic, and molecular differences.

Objectives: To compare the proteomic expression profile and signal transduction pathways of EBV+ eBL with EBV+/- sBL and EBV+/- normal B-cells.

Normal B-cells (EBV+/-) were isolated from leukopacks obtained from the NY Blood Center using Magnetic Cell Sorting CD20 MicroBeads (Miltenyi biotec, CA). Whole cell lysates obtained from EBV+ eBL Raji, EBV+ sBL NC37, EBV- sBL Ramos, and EBV± B-cells were digested and labeled with iTRAQ reagents. The peptides were resolved by 2D-LC technique. MS/MS spectra were acquired using an Orbitrap XL Tandem Mass Spectrometer (ThermoFisher). MS/MS data was searched using X! Tandem TPP software against human IPI database (v3.50) appended with decoy sequences. iTRAQ ratios of proteins (ProteinProphet probability of >0.9) were normalized and differentially expressed proteins were selected for further analysis. Over 400 proteins were identified; 827 binary differential protein expressions were established with a False Discovery Rate (FDR) of <0.4. Hierarchical clustering of the expression profiles grouped the 3 lymphoma cell lines and the 2 normal B-cell specimens. Specific cellular functions were implicated by differential protein expressions (with associated proteins in parentheses) including apoptotic signaling (AK2, C1QBP, DIABLO, PCNA, PPIF, SERPIN8&9, SET), viral pathogenesis (DDX3X, SYNCRIP, EIF5A), cell proliferation pathways and oncogenes (ANXA6, DDX5, DEK, GNB2L1, NME2, RAP1A&B, RIPK4, STMN1), c-myc expression regulation (ENO1, FUBP1), heat shock and ubiquitination (HSP90AB1, HSP90B1, HSPA5, UCHL1). There are several proteins with established links to malignancy (RPL15, PSMA4, SLC3A2, TLX2, VIM) including TUBB2C, whose overexpression is found in pediatric BL and potential biomarkers for disease (IGHM, IGSF3, LDHA, LDHB, PPBP, LSP1, LYZ, DEFA1, DEFA3). We identified 41 proteins within the c-myc network, 21 of which are c-myc targets.

Our results suggest that there are potentially different mechanisms driving cell proliferation and resistance to apoptosis in the different BL subtypes. Confirmatory studies will be required to establish the correlation between EBV, c-myc, and geographical subtype and how they may be involved in promoting lymphomagenesis. Ultimately, identification of proteins unique to the distinct disease subtypes will serve to establish tumor markers that may enable development of new diagnostic, prognostic, and therapeutic strategies.

* Drs. Lim and Cairo are equal senior authors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1199.

Laboratory practice guidelines for detecting and reporting BCR-ABL drug resistance mutations in chronic myelogenous leukemia and acute lymphoblastic leukemia: a report of the Association for Molecular Pathology

The BCR-ABL tyrosine kinase produced by the t(9;22)(q34;q11) translocation, also known as the Philadelphia chromosome, is the initiating event in chronic myeloid leukemia (CML) and Ph+ acute lymphoblastic leukemia (ALL). Targeting of BCR-ABL with tyrosine kinase inhibitors (TKIs) has resulted in rapid clinical responses in the vast majority of patients with CML and Philadelphia chromosome+ ALL. However, long-term use of TKIs occasionally results in emergence of therapy resistance, in part through the selection of clones with mutations in the BCR-ABL kinase domain. We present here an overview of the current practice in monitoring for such mutations, including the methods used, the clinical and laboratory criteria for triggering mutational analysis, and the guidelines for reporting BCR-ABL mutations. We also present a proposal for a public database for correlating mutational status with in vitro and in vivo responses to different TKIs to aid in the interpretation of mutation studies.

Lymphoepithelioma-like carcinoma of the colon in a patient with hereditary nonpolyposis colorectal cancer

Tumors with features similar to those of nasopharyngeal carcinoma, so-called lymphoepithelioma-like carcinomas, have been described in several organs but are extremely rare in the colon. We describe a patient with a family history consistent with hereditary nonpolyposis colorectal cancer who had 3 malignant lesions in the right colon, namely, a mucinous cancer, a lymphoepithelioma-like carcinoma, and a well-differentiated adenocarcinoma with prominent lymphoid stroma. To the best of our knowledge, lymphoepithelioma-like carcinoma has not been described previously in hereditary nonpolyposis colorectal cancer.

Lymphoepithelioma-like carcinoma of the colon in a patient with hereditary nonpolyposis colorectal cancer

Tumors with features similar to those of nasopharyngeal carcinoma, so-called lymphoepithelioma-like carcinomas, have been described in several organs but are extremely rare in the colon. We describe a patient with a family history consistent with hereditary nonpolyposis colorectal cancer who had 3 malignant lesions in the right colon, namely, a mucinous cancer, a lymphoepithelioma-like carcinoma, and a well-differentiated adenocarcinoma with prominent lymphoid stroma. To the best of our knowledge, lymphoepithelioma-like carcinoma has not been described previously in hereditary nonpolyposis colorectal cancer.

Extramedullary myeloid cell tumors arising in the setting of chronic myelomonocytic leukemia. A report of two cases

We report two cases of extramedullary myeloid cell tumor that arose in patients with chronic myelomonocytic leukemia. In both cases, the tumors were difficult to recognize histologically because the neoplasms lacked cytological evidence of granulocyte maturation, such as cytoplasmic granulation or eosinophilic myelocytes, and the Leder stains for chloroacetate esterase were negative. Immunohistochemical studies were necessary to establish the correct diagnosis. The neoplastic cells in both tumors expressed myeloperoxidase, lysozyme, and CD43 and were negative for B-cell, T-cell, and other nonhematopoietic antigens tested. We report these cases to emphasize that extramedullary myeloid cell tumors may rarely precede transformation to acute myeloid leukemia in patients with chronic myelomonocytic leukemia. Extramedullary myeloid cell tumors of monocytic lineage may be difficult to recognize in routine and Leder-stained sections, and immunohistochemical studies may be essential for establishing the diagnosis.

Extramedullary myeloid cell tumors. An immunohistochemical study of 29 cases using routinely fixed and processed paraffin-embedded tissue sections

OBJECTIVE

Extramedullary myeloid cell tumors (EMCTs) may be unsuspected clinically and difficult to recognize histologically. Fresh or frozen tissue is often not available for analysis. We studied 29 cases of EMCT using routinely fixed and processed paraffin-embedded tissue, an immunohistochemical method, and a panel of antibodies.

PATIENTS

We studied 29 patients with EMCTs: 22 males and 7 females, with a median age of 48 years (range, 5 to 80 years). Histologically, 9 tumors were well differentiated, 16 were poorly differentiated, and 4 were blastic.

RESULTS

The Leder stain (napthol-ASD-chloroacetate esterase) was positive in 21 (77.7%) of 27 tumors. Immunohistochemically, the following antibodies reacted with the greatest number of cases: Leu-22 or MT1 (CD43) in 28 (96.6%) of 29, antilysozyme in 27 (96.4%) of 28, and antimyeloperoxidase (MP07) in 21 (91.3%) of 23 cases. Other myeloid lineage-associated antibodies were positive in a subset of cases: antineutrophil elastase (NP57) in 10 (62.5%) of 16, Leu-M1 (CD15) in 7 (46.6%) of 15, and Mac-387 in 6 (40.0%) of 15 cases. The well-differentiated EMCTs reacted with most myeloid-associated antibodies; poorly differentiated and blastic tumors were more often negative. The pan-leukocyte antibody LCA (CD45RB) reacted with 15 (60%) of 25 neoplasms. Three (16.6%) of 18 tumors contained numerous p53-positive cells, ranging from 10% to 50% of the tumor cell population. In 10 cases, exons 5 through 8 of the p53 gene were analyzed using the polymerase chain reaction and single-stranded conformational polymorphism analysis. Gel shifts consistent with mutations were identified in exon 8 of one tumor (10%) that exhibited abundant p53 immunostaining.

CONCLUSIONS

Immunohistochemical studies using fixed, paraffin-embedded sections are very useful in the diagnosis of EMCTs. The most sensitive antibodies are anti-CD43, antilysozyme, and antimyeloperoxidase. Immunohistochemical methods are more sensitive than the Leder stain. We found p53 staining in a small subset of cases, in which we were able to confirm evidence of p53 gene mutation using the polymerase chain reaction and single-stranded conformational polymorphism analysis in one case; p53 gene mutations appear to be uncommon in EMCTs.

Lymphoma of the mucosa-associated lymphoid tissue of the lung. A multifocal case of common clonal origin

Low-grade B-cell lymphomas of the mucosa-associated lymphoid tissue (MALT) are extranodal tumors that tend to be localized. In this case report, the authors describe an unusual multifocal pulmonary MALT lymphoma, which presented radiologically as three discrete lesions involving two separate lobes of the lung, in addition to numerous separate macroscopic and microscopic foci of disease. The lesions were composed of centrocyte-like cells and cytologically bland plasma cells surrounding reactive lymphoid follicles with focal areas resembling lymphoid interstitial pneumonia (LIP). Immunohistochemical studies demonstrated a predominance of immunoglobulin kappa light chain positive plasma cells in the largest lesion. A polymerase chain reaction (PCR) assay demonstrated conserved immunoglobulin heavy chain gene rearrangements in the large tumor nodules as well as microscopic foci resembling LIP. This case illustrates the utility of PCR for identifying the clonal nature of lymphoid lesions that are too small or heterogeneous to unequivocally assess by other means.