A Chunking-for-Pooling Strategy for Cytometric Representation Learning for Automatic Hematologic Malignancy Classification.

Differentiating types of hematologic malignancies is vital to determine therapeutic strategies for the newly diagnosed patients. Flow cytometry (FC) can be used as diagnostic indicator by measuring the multi-parameter fluorescent markers on thousands of antibody-bound cells, but the manual interpretation of large scale flow cytometry data has long been a time-consuming and complicated task for hematologists and laboratory professionals. Past studies have led to the development of representation learning algorithms to perform sample-level automatic classification. In this work, we propose a chunking-for-pooling strategy to include large-scale FC data into a supervised deep representation learning procedure for automatic hematologic malignancy classification. The use of discriminatively-trained representation learning strategy and the fixed-size chunking and pooling design are key components of this framework. It improves the discriminative power of the FC sample-level embedding and simultaneously addresses the robustness issue due to an inevitable use of down-sampling in conventional distribution based approaches for deriving FC representation. We evaluated our framework on two datasets. Our framework outperformed other baseline methods and achieved 92.3% unweighted average recall (UAR) for four-class recognition on the UPMC dataset and 85.0% UAR for five-class recognition on the hema.to dataset. We further compared the robustness of our proposed framework with that of the traditional downsampling approach. Analysis of the effects of the chunk size and the error cases revealed further insights about different hematologic malignancy characteristics in the FC data.

Distinct pathologic feature of myeloid neoplasm with t(v;11p15); NUP98 rearrangement.

Chromosome rearrangements involving NUP98 at 11p15 are rare but recurring abnormalities in acute myeloid leukemia (AML). Here we described 12 cases of myeloid neoplasms with t(v; 11p15); NUP98 rearrangement and characterized their pathologic features. Our patient cohort included 10 adults and 2 children with a median age of 51 years. They were predominantly AML (n = 10) including de novo AML, therapy-related AML, chronic myeloid leukemia with myeloid blast crisis, and mixed phenotype acute leukemia, as well as therapy-related myelodysplastic syndrome (MDS) and MDS/myeloproliferative neoplasm with increased blasts. The blasts shared some common features including pink/red cytoplasmic granules, presence of a perinuclear hof, Auer rods, and occasional bilobed nuclei, mimicking acute promyelocytic leukemia (APML). Flow cytometric studies showed blasts positive for MPO, CD117, CD13 and CD33, with a subset of cases negative for CD34 and/or HLA-DR and a subset of cases expressing monocytic markers. The translocations of 11p15 included t(7; 11) (p15; p15), t(2; 11) (q31; p15), t(9; 11) (p22; p15), t(5; 11) (q32; p15), and t(11; 12) (p15; q13). Three cases showed cryptic NUP98 rearrangement. These patients showed incomplete response to therapy with median overall survival of 17.5 months, a complete remission rate of 25% following chemotherapy induction and primary refractory disease of 58%. It is clinically important to recognize this group of diseases because the blasts can be misclassified as promyelocytes, and NUP98 rearrangement may be cryptic requiring fluorescence in situ hybridization (FISH) study. This case series highlights that NUP98-rearranged myeloid neoplasms are clinically, morphologically, and cytogenetically distinct and could be considered as a separate entity in the WHO classification defined by cytogenetic abnormality.

A Machine Learning Approach to the Classification of Acute Leukemias and Distinction From Nonneoplastic Cytopenias Using Flow Cytometry Data.

OBJECTIVES: Flow cytometry (FC) is critical for the diagnosis and monitoring of hematologic malignancies. Machine learning (ML) methods rapidly classify multidimensional data and should dramatically improve the efficiency of FC data analysis. We aimed to build a model to classify acute leukemias, including acute promyelocytic leukemia (APL), and distinguish them from nonneoplastic cytopenias. We also sought to illustrate a method to identify key FC parameters that contribute to the model's performance. METHODS: Using data from 531 patients who underwent evaluation for cytopenias and/or acute leukemia, we developed an ML model to rapidly distinguish among APL, acute myeloid leukemia/not APL, acute lymphoblastic leukemia, and nonneoplastic cytopenias. Unsupervised learning using gaussian mixture model and Fisher kernel methods were applied to FC listmode data, followed by supervised support vector machine classification. RESULTS: High accuracy (ACC, 94.2%; area under the curve [AUC], 99.5%) was achieved based on the 37-parameter FC panel. Using only 3 parameters, however, yielded similar performance (ACC, 91.7%; AUC, 98.3%) and highlighted the significant contribution of light scatter properties. CONCLUSIONS: Our findings underscore the potential for ML to automatically identify and prioritize FC specimens that have critical results, including APL and other acute leukemias.

Harmonization of Training, Training Requirements, Board Certification, and Practice of Hematopathology.

OBJECTIVES: Hematopathology (HP) is a rapidly changing field with insufficient data to provide guidance to program directors (PDs), the Accreditation Council for Graduate Medical Education, or the American Board of Pathology. METHODS: Two surveys were performed-one for HP PDs and one, given twice, for HP diplomates doing Maintenance of Certification/Continuing Certification reporting in 2017 to 2018. RESULTS: Bone marrow (BM), lymph node (LN), and flow cytometry interpretations and peripheral blood/fluid reviews are performed by more than 80% of hematopathologists and are the areas with the greatest amount of training. A smaller proportion of hematopathologists is involved in other HP-related activities. Most PDs believed fellows should perform BM procedures. Interpretation of 400 or more LNs and 500 BMs was PDs' median expectations for fellows. PDs and HP diplomates considered coagulation and benign RBC disorders overemphasized on the certification examination. CONCLUSIONS: These results highlight how varied the practice of HP is and can provide guidance to HP PDs, those responsible for assessing HP programs, and the American Board of Pathology.

Immunomodulatory drugs downregulate IKZF1 leading to expansion of hematopoietic progenitors with concomitant block of megakaryocytic maturation.

The immunomodulatory drugs, lenalidomide and pomalidomide yield high response rates in multiple myeloma patients, but are associated with a high rate of thrombocytopenia and increased risk of secondary hematologic malignancies. Here, we demonstrate that the immunomodulatory drugs induce self-renewal of hematopoietic progenitors and upregulate megakaryocytic colonies by inhibiting apoptosis and increasing proliferation of early megakaryocytic progenitors via down-regulation of IKZF1. In this process, the immunomodulatory drugs degrade IKZF1 and subsequently down-regulate its binding partner, GATA1. This results in the decrease of GATA1 targets such as ZFPM1 and NFE2, leading to expansion of megakaryocytic progenitors with concomitant inhibition of maturation of megakaryocytes. The down-regulation of GATA1 further decreases CCND1 and increases CDKN2A expression. Overexpression of GATA1 abrogated the effects of the immunomodulatory drugs and restored maturation of megakaryocytic progenitors. Our data not only provide the mechanism for the immunomodulatory drugs induced thrombocytopenia but also help to explain the higher risk of secondary malignancies and long-term cytopenia induced by enhanced cell cycling and subsequent exhaustion of the stem cell pool.

Acute Myeloid Leukemia With a Rare t(7;14)(q21;q32) and Trisomy 4 With Poor Clinical Outcome: A Case Report.

OBJECTIVES: Recurrent cytogenetic abnormalities and/or molecular aberrations play an important role in the diagnosis and prognostification of acute myeloid leukemia (AML). We describe a case of a 40 year old woman diagnosed with de novo AML with a novel t(7;14)(q21,q32) and trisomy 4 with poor clinical outcome. Methods: Morphologic, flow cytometry and cytogenetic results of the patient's peripheral blood and bone marrow samples were analyzed. RESULTS: The diagnostic bone marrow was hypercellular for age (>95%) with increased blasts (62%) that by flow cytometry exhibited myeloid differentiation with a few T/NK lineage markers. Cytogenetics showed a t(7;14)(q21,q32) and trisomy 4. The patient had extremely poor response to two rounds of induction chemotherapy with persistent leukemia following therapy. CONCLUSION: To the best of our knowledge, the t(7;14) is a novel cytogenetic abnormality that has not been reported previously in acute myeloid leukemia, and is important to report as it appears to be associated with poor prognosis.

Cytogenetic and Cytogenomic Microarray Characterization of Chromothripsis in Chromosome 8 Affecting MOZ/NCOA2 (TIF2), FGFR1, RUNX1T1, and RUNX1 in a Pediatric Acute Myeloid Leukemia.

Concurrent perturbations in different driver genes have been reported primarily in lymphoma. In acute myeloid leukemia (AML), cases with concurrent alterations in 2 driver genes are infrequently reported. In contrast to pathogenetic pathways in lymphoma with concurrently perturbed genes, the initial gene alteration in AML arrests maturation and the alteration in the second gene promote self-renewal of the blasts. Here, we report a unique case of infantile leukemia in which chromothripsis in chromosome 8 completely altered the G-band structure and resulted in concurrent changes in MOZ/NCOA2, FGFR1, RUNX1T1, and RUNX1. These multiple-hit abnormalities in AML have not been reported previously.

Does Taking the Fellowship In-Service Hematopathology Examination and Performance Relate to Success on the American Board of Pathology Hematology Examination?

OBJECTIVES: The biannual Fellow In-Service Hematopathology Examination (FISHE) assesses knowledge in five content areas. We examined the relationship between taking the FISHE and performance on it with outcomes on the first attempted American Board of Pathology Hematology subspecialty certifying examination (ABP-HE). METHODS: The pass rate between the ABP-HE candidates who took the spring FISHE and those who did not were compared. The likelihood of fellows passing the ABP-HE based on their percentiles on the FISHE was also assessed. RESULTS: ABP-HE candidates who took the spring FISHE had a higher pass rate (96.4%) than those who did not (76.1%, P < .001). Spring FISHE performance, including total percentile and percentiles in four of five FISHE content areas, was only a weak predictor of passing the ABP-HE. CONCLUSIONS: Candidates who take the spring FISHE do better on the ABP-HE than those who do not. Most fellows passed the first attempted ABP-HE regardless of FISHE performance. Whether this is due to fellows making use of the FISHE as a self-evaluation tool to help identify and then correct their knowledge deficiencies remains to be determined.

Myeloid neoplasm with t(3;8)(q26;q24): report of six cases and review of the literature.

Balanced translocation between chromosomes 3q26 and 8q24 is a very rare event. Here we report six patients with t(3;8)(q26;q24) either as a sole or as a part of genetic abnormalities. Five of the six patients were men with ages ranging from 41 to 84 years old. One patient had a long history of granulocyte colony stimulating factor (G-CSF) treatment. Three of the patients were initially diagnosed with acute myeloid leukemia, two with myelodysplastic syndrome and one with chronic myelogenous leukemia with blast crisis. The peripheral blood in all patients showed severe to moderate anemia; one had absolute neutropenia, one with neutrophilia; four had thrombocytopenia, two with thrombocytosis. The bone marrows from all patients showed dysmegakaryopoiesis with additional erythroid (three patients) and granulocytic (two patients) dysplasia. Cytogenetics revealed t(3;8)(q26;q24) as the sole abnormality in three patients. The majority of patients (4/6) had a poor clinical course, with an average survival of 10 months.

Myelodysplastic syndrome (MDS)-associated cytogenetic abnormalities in pediatric chronic myelogenous leukemia.

Chronic myelogenous leukemia (CML) is very rare in the pediatric population. We report the case of a 2-year-old female with CML and concurrent myelodysplastic syndrome (MDS) associated cytogenetic abnormalities. The co-existence of t(9;22) and chromosomal deletions that are associated with MDS poses a unique diagnostic challenge. Given the reported association of t(9;22) and genomic instability, we hypothesize that the chromosomal deletions represent clonal evolution of the CML.

Longitudinal bone marrow evaluations for myelodysplasia in patients with myeloma before and after treatment with lenalidomide.

Lenalidomide (LEN) treatment in multiple myeloma (MM) results in a superior outcome. However, there is concern for increased myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) associated with LEN. Thus, bone marrow morphology and cytogenetics studies from 40 patients were evaluated for early signs of MDS prior to therapy, during therapy and at follow-up. Newly diagnosed patients with MM treated with LEN and dexamethasone (LD) alone or followed by autologous stem cell transplant (LD/ASCT), or patients with relapsed/refractory MM treated with LEN, bendamustine and dexamethasone (BLD) were included. One patient developed MDS. Baseline prevalence of mild morphologic myelodysplasia was highest in pretreated patients with MM (BLD, 71%), but was also seen in newly diagnosed patients (LD and LD/ASCT, 17%). The prevalence of myelodysplasia did not increase over time. Thus, this study did not reveal rapidly emerging MDS in 39 of 40 patients with MM treated with LEN. The development of MDS in one patient suggests that longer follow-up is needed for all.

Altered neutrophil maturation patterns that limit identification of myelodysplastic syndromes.

BACKGROUND: Altered neutrophil maturation patterns have been reported useful for identification of myelodysplastic syndromes (MDS). METHODS: Neutrophil maturation patterns based on CD11b, CD13, and CD16 were visually and numerically evaluated in 19 control, 23 MDS, 37 nondiagnostic for MDS (NDM) specimens, and 19 also processed 1 and 2 days subsequently. RESULTS: In contrast to maturation patterns illustrated previously by others as "normal," 84% of controls displayed diminished acquisition of CD16, imparting a contracted appearance. Such divergence from published "normal" patterns was usually mild-moderate, considered nonspecific, and associated with delayed processing: longer intervals between collection and processing (median 20.5 vs. 5.2 h), and following 1 and 2 days delay. Findings restricted to nonspecific contraction were found in 56% MDS and 78% NDM specimens. Evaluation for aberrant patterns was still performed with mild-moderate contraction present, but concern for over interpretation led to use of an equivocal-aberrant category. Nine cases had aberrant or equivocal-aberrant patterns (seven MDS, two NDM) with distinct visual alterations that differed from nonspecific contraction and had numerical evidence for a left shift: myeloblasts increased (67%) and least mature neutrophils (CD11b-/low, CD16-/low) increased (78%). Although evidence for a left shift was associated with MDS, it was also seen in NDM specimens with a synchronous left shift. CONCLUSIONS: Neutrophil maturation patterns that diverge from previously illustrated "normal" patterns, not specific for MDS, may be common in some settings. Laboratories seeking to implement FC evaluation for MDS must determine which findings have sufficient specificity for MDS within their own practice and patient population.

Toxoplasmosis in a post-transplant bronchoalveolar lavage: a case report.

Toxoplasma gondii usually causes an asymptomatic and then latent infection in human adults; however, a potentially fatal disseminated form can occur in immunocompromised patients. Given that the diagnosis of acute Toxoplasma infection, as opposed to latent disease, relies on finding direct evidence of T. gondii infection in tissue, pathologic examination is critical. There have only been a few reports describing the cytomorphology of Toxoplasma in exfoliative cytology, and no reports of the findings in Thin Prep. In this report, we describe a fatal case of toxoplasmosis in a cardiac transplant patient that was diagnosed by respiratory cytopathology. Although the extracellular organisms were well visualized on the Wright-Giemsa stained cytospin, they were only faintly seen on the Pap-stained cytospin trapped within mucin and were not easily appreciated on the ThinPrep slides nor the H&E stained cell block sections. An immunohistochemical stain for Toxoplasma performed on the cell block was strongly positive, and an autopsy performed on the patient confirmed disseminated infection. Our case illustrates that the diagnosis of Toxoplasma in exfoliative cytology specimens can be challenging since organisms are not well visualized on ThinPrep or Pap-stained material; therefore, Wright-Giemsa stained material can be particularly helpful.

ZAP-70 and Bcl-2 expression in B lymphoblastic leukemia cells and hematogones.

BACKGROUND: Flow cytometric immunophenotyping has an established role in the diagnosis and monitoring of B-lymphoblastic leukemia (B-LL). However, the search continues for an optimal reagent set that can identify leukemic blasts with specificity, reproducibility, and sensitivity, at any point during the course of the disease and in every specimen type. METHODS: This study evaluated the diagnostic utility of detecting the intracytoplasmic antigens zeta-associated protein (ZAP-70) and Bcl-2 in the distinction between the leukemic blasts of B-LL and hematogones. RESULTS: In comparison with hematogones in reference specimens, significantly higher levels of Bcl-2 were identified in 21 of 23 (91%) B-LL. In particular, Bcl-2 expression was consistently higher in leukemic blasts with bright intensity CD10 expression than the equivalent most immature (CD10 bright intensity) hematogones. As previously reported, Bcl-2 expression was lower in B-LL with BCR-ABL1 gene rearrangement, but the fluorescence intensity of this group of specimens was still significantly higher than that seen for hematogones. In contrast, ZAP-70 was expressed at significantly higher levels in only 7 of 23 (30%) B-LL and demonstrated other findings that might limit clinical utility, including differences in the level of ZAP-70 expression during therapy and between blasts in the peripheral blood and bone marrow. CONCLUSIONS: Bcl-2 over-expression provides a useful tool for the distinction between B-LL and hematogones. In contrast, although further optimization of the ZAP-70 assay might increase the sensitivity of detection, over-expression of ZAP-70 was identified in only a minority of B-LL.

IMiD immunomodulatory compounds block C/EBP{beta} translation through eIF4E down-regulation resulting in inhibition of MM.

Immunomodulatory derivatives of thalidomide (IMiD compounds), such as pomalidomide and lenalidomide, are highly active in multiple myeloma (MM) treatment. However, the precise mechanisms of action and resistance in MM are unresolved. Here we show that IMiD compounds down-regulate CCAAT/enhancer-binding protein-ß (C/EBPß) resulting in abrogation of cell proliferation. Overexpression of C/EBPß rescued MM cells from IMiD-induced inhibition of proliferation, indicating that C/EBPß is critical in mediating antiproliferative effects. IMiD-induced decrease of C/EBPß protein led to impaired transcription of interferon regulatory factor 4 (IRF4). Down-regulation of IRF4 by lenalidomide was confirmed by longitudinal studies of bone marrow samples from 23 patients obtained before and during lenalidomide treatment using CD138⁺/IRF4⁺ double labeling. In contrast to down-regulation of C/EBPß protein, IMiD compounds did not alter C/EBPß mRNA levels or protein stability, suggesting translational regulation of C/EBPß. We could demonstrate that C/EBPß protein expression is under eIF4E-translational control in MM. Furthermore, inhibition of the eIF4E-C/EBPß axis by IMiD compounds was not observed in IMiD-resistant MM cells. However, targeting translation at a different level by inhibiting eukaryotic translation initiation factor 4E-binding protein 1 phosphorylation overcame resistance, suggesting that this pathway is critical and might be a target to overcome drug resistance.

Immunomodulatory derivatives induce PU.1 down-regulation, myeloid maturation arrest, and neutropenia.

The immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide yield high response rates in patients with multiple myeloma, but the use of IMiDs in multiple myeloma is associated with neutropenia and increased risk for venous thromboembolism (VTE) by mechanisms that are unknown. We show that IMiDs down-regulate PU.1, a key transcription factor involved in granulocyte differentiation in vitro and in patients treated with lenalidomide. Loss of PU.1 results in transient maturation arrest with medullary accumulation of immature myeloid precursors and subsequent neutropenia. Accumulation of promyelocytes leads to high levels of the platelet aggregation agonist, cathepsin G stored in the azurophilic granules of promyelocytes. High levels of cathepsin G subsequently may increase the risk of VTE. To our knowledge, this is the first report investigating the underlying mechanism of IMiD-induced neutropenia and increased risk of VTE in multiple myeloma.

Zinc-induced copper deficiency: a report of three cases initially recognized on bone marrow examination.

Copper deficiency is a rare cause of sideroblastic anemia and neutropenia that often is not suspected clinically. The morphologic findings in bone marrow, while not pathognomonic, are sufficiently characteristic to suggest the diagnosis, leading to further testing to establish the correct diagnosis. Excess zinc ingestion is among the causes of copper deficiency. We present 3 cases of zinc-induced copper deficiency in which the diagnosis first was suggested on the basis of bone marrow examination. The first patient was a 47-year-old man with a debilitating peripheral neuropathy that had progressed during the previous 18 months, mild anemia, and severe neutropenia. The second was a 21-year-old man receiving zinc supplementation for acrodermatitis enteropathica in whom moderate normocytic anemia and neutropenia developed. The third patient was a 42-year-old man with anemia, severe neutropenia, and a peripheral neuropathy that had progressed during 8 months. The bone marrow findings in all cases suggested copper deficiency, which was confirmed by further laboratory testing and determined to be due to zinc excess. The morphologic features, clinical manifestations, differential diagnosis, and pathogenetic mechanisms are discussed.