Publications by authors named "Mohamed E Salama"

88 Publications

COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation.

J Med Internet Res 2021 09 28;23(9):e30157. Epub 2021 Sep 28.

Mayo Clinic, Rochester, MN, United States.

Background: COVID-19 is caused by the SARS-CoV-2 virus and has strikingly heterogeneous clinical manifestations, with most individuals contracting mild disease but a substantial minority experiencing fulminant cardiopulmonary symptoms or death. The clinical covariates and the laboratory tests performed on a patient provide robust statistics to guide clinical treatment. Deep learning approaches on a data set of this nature enable patient stratification and provide methods to guide clinical treatment.

Objective: Here, we report on the development and prospective validation of a state-of-the-art machine learning model to provide mortality prediction shortly after confirmation of SARS-CoV-2 infection in the Mayo Clinic patient population.

Methods: We retrospectively constructed one of the largest reported and most geographically diverse laboratory information system and electronic health record of COVID-19 data sets in the published literature, which included 11,807 patients residing in 41 states of the United States of America and treated at medical sites across 5 states in 3 time zones. Traditional machine learning models were evaluated independently as well as in a stacked learner approach by using AutoGluon, and various recurrent neural network architectures were considered. The traditional machine learning models were implemented using the AutoGluon-Tabular framework, whereas the recurrent neural networks utilized the TensorFlow Keras framework. We trained these models to operate solely using routine laboratory measurements and clinical covariates available within 72 hours of a patient's first positive COVID-19 nucleic acid test result.

Results: The GRU-D recurrent neural network achieved peak cross-validation performance with 0.938 (SE 0.004) as the area under the receiver operating characteristic (AUROC) curve. This model retained strong performance by reducing the follow-up time to 12 hours (0.916 [SE 0.005] AUROC), and the leave-one-out feature importance analysis indicated that the most independently valuable features were age, Charlson comorbidity index, minimum oxygen saturation, fibrinogen level, and serum iron level. In the prospective testing cohort, this model provided an AUROC of 0.901 and a statistically significant difference in survival (P<.001, hazard ratio for those predicted to survive, 95% CI 0.043-0.106).

Conclusions: Our deep learning approach using GRU-D provides an alert system to flag mortality for COVID-19-positive patients by using clinical covariates and laboratory values within a 72-hour window after the first positive nucleic acid test result.
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http://dx.doi.org/10.2196/30157DOI Listing
September 2021

Interleukin 1 receptor antagonism abrogates acute pressure-overload induced murine heart failure.

Ann Thorac Surg 2021 Aug 19. Epub 2021 Aug 19.

Division of Cardiothoracic Surgery and Cardiovascular Research Training Institute, University of Utah, Salt Lake City, UT. Electronic address:

Background: Recent clinical trials have suggested that blockade of interleukin-1 can favorably impact patients with myocardial infarction and heart failure. However, the mechanism of how antagonism of this specific cytokine in mediating cardiac disease remains unclear. Hence, we sought to determine the influence of IL-1 blockade on acute hypertensive remodeling.

Methods: Transverse aortic constriction (TAC) was performed in C57BL mice with or without intraperitoneal administration of interleukin 1 receptor antagonism (IL-1ra). Function, structure, and molecular diagnostics were subsequently performed and analyzed.

Results: Six weeks after TAC, a progressive decline of ejection fraction and increases in LV mass and dimensions was effectively mitigated with IL-1ra. TAC resulted in an expected profile of hypertrophic markers including myosin heavy chain, atrial natriuretic peptide, and skeletal muscle actin which were all significantly lower in IL-1ra treated mice. While trichrome staining 2-weeks post TAC demonstrated similar levels of fibrosis, IL-1ra reduced expression of collagen-1, TIMP1, and periostin. Investigating the angiogenic response to pressure overload, similar levels of VEGF were observed, but IL-1ra was associated with more SDF-1. Immune cell infiltration (macrophages and lymphocytes) was also decreased in IL-1ra treated mice. Similarly, cytokine concentrations of IL-1, IL-18, and IL-6 were all reduced in IL-1ra-treated animals.

Conclusions: IL-1ra prevents the progression towards heart failure associated with acute pressure overload. This functional response was associated with reductions in mediators of fibrosis, cellular infiltration, and cytokine production. These results provide mechanistic insight into recent clinical trials and could springboard future investigations in patients with pressure-overload based cardiomyopathies.
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http://dx.doi.org/10.1016/j.athoracsur.2021.07.044DOI Listing
August 2021

Classification of Monocytes, Promonocytes and Monoblasts Using Deep Neural Network Models: An Area of Unmet Need in Diagnostic Hematopathology.

J Clin Med 2021 May 24;10(11). Epub 2021 May 24.

Division of Hematopathology, Mayo Clinic, Rochester, MN 55905, USA.

The accurate diagnosis of chronic myelomonocytic leukemia (CMML) and acute myeloid leukemia (AML) subtypes with monocytic differentiation relies on the proper identification and quantitation of blast cells and blast-equivalent cells, including promonocytes. This distinction can be quite challenging given the cytomorphologic and immunophenotypic similarities among the monocytic cell precursors. The aim of this study was to assess the performance of convolutional neural networks (CNN) in separating monocytes from their precursors (i.e., promonocytes and monoblasts). We collected digital images of 935 monocytic cells that were blindly reviewed by five experienced morphologists and assigned into three subtypes: monocyte, promonocyte, and blast. The consensus between reviewers was considered as a ground truth reference label for each cell. In order to assess the performance of CNN models, we divided our data into training (70%), validation (10%), and test (20%) datasets, as well as applied fivefold cross validation. The CNN models did not perform well for predicting three monocytic subtypes, but their performance was significantly improved for two subtypes (monocyte vs. promonocytes + blasts). Our findings (1) support the concept that morphologic distinction between monocytic cells of various differentiation level is difficult; (2) suggest that combining blasts and promonocytes into a single category is desirable for improved accuracy; and (3) show that CNN models can reach accuracy comparable to human reviewers (0.78 ± 0.10 vs. 0.86 ± 0.05). As far as we know, this is the first study to separate monocytes from their precursors using CNN.
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http://dx.doi.org/10.3390/jcm10112264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8197234PMC
May 2021

Machine learning and augmented human intelligence use in histomorphology for haematolymphoid disorders.

Pathology 2021 Apr 25;53(3):400-407. Epub 2021 Feb 25.

Division of Hematopathology, Mayo Clinic, Rochester, MN, USA. Electronic address:

Advances in digital pathology have allowed a number of opportunities such as decision support using artificial intelligence (AI). The application of AI to digital pathology data shows promise as an aid for pathologists in the diagnosis of haematological disorders. AI-based applications have embraced benign haematology, diagnosing leukaemia and lymphoma, as well as ancillary testing modalities including flow cytometry. In this review, we highlight the progress made to date in machine learning applications in haematopathology, summarise important studies in this field, and highlight key limitations. We further present our outlook on the future direction and trends for AI to support diagnostic decisions in haematopathology.
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http://dx.doi.org/10.1016/j.pathol.2020.12.004DOI Listing
April 2021

Important Pathologic Considerations for Establishing the Diagnosis of Myelofibrosis.

Authors:
Mohamed E Salama

Hematol Oncol Clin North Am 2021 Apr 14;35(2):267-278. Epub 2021 Jan 14.

Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic School of Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA. Electronic address:

Diagnostic criteria for primary myelofibrosis as defined by the 2017 revised World Health Organization (WHO) classification system incorporate clinical and laboratory findings, including driver mutational status (JAK2, MPL, CALR. and triple negative). The WHO emphasized the role of histopathology in making an accurate diagnosis of primary myelofibrosis and successfully incorporated a fibrosis scoring system and scoring schemas for collagen fibrosis and osteosclerosis. These steps represent a significant addition to the standardization of myelofibrosis evaluation and minimize the risk for misdiagnosis. This article reviews important pathologic considerations along with highlights of potentially relevant pitfalls relevant to histopathological diagnosis of myelofibrosis.
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http://dx.doi.org/10.1016/j.hoc.2020.11.002DOI Listing
April 2021

Phase 2 study of ruxolitinib and decitabine in patients with myeloproliferative neoplasm in accelerated and blast phase.

Blood Adv 2020 10;4(20):5246-5256

Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.

Myeloproliferative neoplasms (MPN) that have evolved into accelerated or blast phase disease (MPN-AP/BP) have poor outcomes with limited treatment options and therefore represent an urgent unmet need. We have previously demonstrated in a multicenter, phase 1 trial conducted through the Myeloproliferative Neoplasms Research Consortium that the combination of ruxolitinib and decitabine is safe and tolerable and is associated with a favorable overall survival (OS). In this phase 2 trial, 25 patients with MPN-AP/BP were treated at the recommended phase 2 dose of ruxolitinib 25 mg twice daily for the induction cycle followed by 10 mg twice daily for subsequent cycles in combination with decitabine 20 mg/m2 for 5 consecutive days in a 28-day cycle. Nineteen patients died during the study follow-up. The median OS for all patients on study was 9.5 months (95% confidence interval, 4.3-12.0). Overall response rate (complete remission + incomplete platelet recovery + partial remission) was 11/25 (44%) and response was not associated with improved survival. We conclude that the combination of decitabine and ruxolitinib was well tolerated, demonstrated favorable OS, and represents a therapeutic option for this high-risk patient population. This trial was registered at www.clinicaltrials.gov as #NCT02076191.
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http://dx.doi.org/10.1182/bloodadvances.2020002119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7594401PMC
October 2020

Is the Time Right to Start Using Digital Pathology and Artificial Intelligence for the Diagnosis of Lymphoma?

J Pathol Inform 2020 26;11:16. Epub 2020 Jun 26.

University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.4103/jpi.jpi_16_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513776PMC
June 2020

Could Bordetella pertussis vaccine protect against coronavirus COVID-19?

J Glob Antimicrob Resist 2020 09 16;22:803-805. Epub 2020 Jul 16.

The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA. Electronic address:

According to the World Health Organization (WHO), as of today, there are 2.165.500 confirmed cases of the novel coronavirus disease (COVID-19) and 145.705 deaths in over 185 countries. Unfortunately, despite the tremendous efforts to develop a vaccine initiated by various leading health institutions all over the world, it may be 18 months before a vaccine against the coronavirus is publicly available. We are proposing a theory about testing the use of the Bordetella pertussis vaccine to protect against COVID-19. We deliver this theory to the scientific community, aiming to raise the concern about it, and to provide us with support by realistic and experimental evidence.
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http://dx.doi.org/10.1016/j.jgar.2020.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7365096PMC
September 2020

Improving Augmented Human Intelligence to Distinguish Burkitt Lymphoma From Diffuse Large B-Cell Lymphoma Cases.

Am J Clin Pathol 2020 05;153(6):743-759

Department of Pathology, Mayo Clinic, Rochester, MN.

Objectives: To assess and improve the assistive role of a deep, densely connected convolutional neural network (CNN) to hematopathologists in differentiating histologic images of Burkitt lymphoma (BL) from diffuse large B-cell lymphoma (DLBCL).

Methods: A total of 10,818 images from BL (n = 34) and DLBCL (n = 36) cases were used to either train or apply different CNNs. Networks differed by number of training images and pixels of images, absence of color, pixel and staining augmentation, and depth of the network, among other parameters.

Results: Cases classified correctly were 17 of 18 (94%), nine with 100% of images correct by the best performing network showing a receiver operating characteristic curve analysis area under the curve 0.92 for both DLBCL and BL. The best performing CNN used all available training images, two random subcrops per image of 448 × 448 pixels, random H&E staining image augmentation, random horizontal flipping of images, random alteration of contrast, reduction on validation error plateau of 15 epochs, block size of six, batch size of 32, and depth of 22. Other networks and decreasing training images had poorer performance.

Conclusions: CNNs are promising augmented human intelligence tools for differentiating a subset of BL and DLBCL cases.
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http://dx.doi.org/10.1093/ajcp/aqaa001DOI Listing
May 2020

Practical Approaches on CD30 Detection and Reporting in Lymphoma Diagnosis.

Am J Surg Pathol 2020 02;44(2):e1-e14

Departments of Pathology and Dermatology, University of Virginia, Charlottesville, VA.

While our understanding of the biology of CD30 in lymphoma continues to evolve, our need to detect and measure its expression at the protein level remains critically important for diagnosis and patient care. In addition to its diagnostic and prognostic utility, CD30 has emerged as a vehicle for drug targeting through the antibody-drug conjugate brentuximab-vedotin (BV). Given the numerous ways that CD30 is utilized and its emergence as a predictive/prognostic biomarker, pathologists must come to a general consensus on the best reporting structure and methodology to ensure appropriate patient care. In this manuscript, we review the indications for testing, various modalities for testing, technical challenges, pitfalls, and potential standards of reporting. The following questions will try to be addressed in the current review article: What defines a "POSITIVE" level of CD30 expression?; How do we evaluate and report CD30 expression?; What are the caveats in the evaluation of CD30 expression?
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http://dx.doi.org/10.1097/PAS.0000000000001368DOI Listing
February 2020

Machine learning applications in the diagnosis of leukemia: Current trends and future directions.

Int J Lab Hematol 2019 Dec 9;41(6):717-725. Epub 2019 Sep 9.

Oncology Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

Machine learning (ML) offers opportunities to advance pathological diagnosis, especially with increasing trends in digitalizing microscopic images. Diagnosing leukemia is time-consuming and challenging in many areas globally and there is a growing trend in utilizing ML techniques for its diagnosis. In this review, we aimed to describe the literature of ML utilization in the diagnosis of the four common types of leukemia: acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), acute myeloid leukemia (AML), and chronic myelogenous leukemia (CML). Using a strict selection criterion, utilizing MeSH terminology and Boolean logic, an electronic search of MEDLINE and IEEE Xplore Digital Library was performed. The electronic search was complemented by handsearching of references of related studies and the top results of Google Scholar. The full texts of 58 articles were reviewed, out of which, 22 studies were included. The number of studies discussing ALL, AML, CLL, and CML was 12, 8, 3, and 1, respectively. No studies were prospectively applying algorithms in real-world scenarios. Majority of studies had small and homogenous samples and used supervised learning for classification tasks. 91% of the studies were performed after 2010, and 74% of the included studies applied ML algorithms to microscopic diagnosis of leukemia. The included studies illustrated the need to develop the field of ML research, including the transformation from solely designing algorithms to practically applying them clinically.
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http://dx.doi.org/10.1111/ijlh.13089DOI Listing
December 2019

Identification and Characterization of Tumor-Initiating Cells in Multiple Myeloma.

J Natl Cancer Inst 2020 05;112(5):507-515

Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA.

Background: Treatment failures in cancers, including multiple myeloma (MM), are most likely due to the persistence of a minor population of tumor-initiating cells (TICs), which are noncycling or slowly cycling and very drug resistant.

Methods: Gene expression profiling and real-time quantitative reverse transcription polymerase chain reaction were employed to define genes differentially expressed between the side-population cells, which contain the TICs, and the main population of MM cells derived from 11 MM patient samples. Self-renewal potential was analyzed by clonogenicity and drug resistance of CD24+ MM cells. Flow cytometry (n = 60) and immunofluorescence (n = 66) were applied on MM patient samples to determine CD24 expression. Therapeutic effects of CD24 antibodies were tested in xenograft MM mouse models containing three to six mice per group.

Results: CD24 was highly expressed in the side-population cells, and CD24+ MM cells exhibited high expression of induced pluripotent or embryonic stem cell genes. CD24+ MM cells showed increased clonogenicity, drug resistance, and tumorigenicity. Only 10 CD24+ MM cells were required to develop plasmacytomas in mice (n = three of five mice after 27 days). The frequency of CD24+ MM cells was highly variable in primary MM samples, but the average of CD24+ MM cells was 8.3% after chemotherapy and in complete-remission MM samples with persistent minimal residual disease compared with 1.0% CD24+ MM cells in newly diagnosed MM samples (n = 26). MM patients with a high initial percentage of CD24+ MM cells had inferior progression-free survival (hazard ratio [HR] = 3.81, 95% confidence interval [CI] = 5.66 to 18.34, P < .001) and overall survival (HR = 3.87, 95% CI = 16.61 to 34.39, P = .002). A CD24 antibody inhibited MM cell growth and prevented tumor progression in vivo.

Conclusion: Our studies demonstrate that CD24+ MM cells maintain the TIC features of self-renewal and drug resistance and provide a target for myeloma therapy.
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http://dx.doi.org/10.1093/jnci/djz159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7225664PMC
May 2020

Characterization of myeloid malignancies with TP53 mutations and comparison to P53 expression by immunohistochemical staining methods.

Int J Lab Hematol 2020 04 7;42(2):e35-e37. Epub 2019 Aug 7.

Department of Pathology, Mayo Clinic, Rochester, Minnesota.

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http://dx.doi.org/10.1111/ijlh.13088DOI Listing
April 2020

American Registry of Pathology Expert Opinions: Immunohistochemical evaluation of classic Hodgkin lymphoma.

Ann Diagn Pathol 2019 Apr 6;39:105-110. Epub 2019 Feb 6.

Mayo Clinic, Rochester, MN, United States of America.

The diagnosis of classic Hodgkin lymphoma requires immunohistochemical confirmation in most cases and one can argue for these studies as standard-of-care in the diagnostic workup. The authors propose a panel of studies for primary identification of CHL to include: CD3, CD20, CD15, CD30 and PAX5. When pattern discordances are identified, additional assessment is recommended. In the case of overexpression of B lineage markers by Hodgkin/Reed-Sternberg cells, or a differential diagnosis that includes large B-cell lymphoma or variants, additional markers recommended are: CD45, OCT2, BOB1, CD79a and MUM1/IRF4. If primary mediastinal large B cell lymphoma is considered in the differential diagnosis, suggested additional markers include: P63, CD23, CD45 and CD79a. When considering a differential diagnosis that includes anaplastic large cell lymphoma we suggest: ALK, CD45, pan T cell antigens (such as CD2, CD5, CD7, and CD43), and cytotoxic markers (granzyme, perforin, and TIA1). If peripheral T cell lymphoma or T cell lymphomas of follicular helper origin are considered in the differential diagnosis, the following panel is recommended: pan T cell antigens, CD4, CD8, one or more follicular dendritic cell markers, and assessment for Epstein-Barr virus (EBV) infection, preferably EBV encoded RNA (EBER) as assessed by in situ hybridization When the differential diagnosis includes nodular lymphocyte predominant Hodgkin lymphoma, recommended additional studies include OCT2, CD21 and/or CD23, PD1, and assessment for EBV infection. The authors recognize that these panels may not be adequate to completely characterize other lymphomas, but these panels will usually be sufficient to distinguish classic Hodgkin lymphoma from other lymphoma types.
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http://dx.doi.org/10.1016/j.anndiagpath.2019.02.001DOI Listing
April 2019

Quantitative Image Analysis of Human Epidermal Growth Factor Receptor 2 Immunohistochemistry for Breast Cancer: Guideline From the College of American Pathologists.

Arch Pathol Lab Med 2019 10 15;143(10):1180-1195. Epub 2019 Jan 15.

From the Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, Florida (Dr Bui); the Department of Pathology, University of Texas MD Anderson Cancer Center, Houston (Dr Riben); the Department of Pathology, Stanford University Medical Center, Stanford, California (Dr Allison); Premier Laboratory, Longmont, Colorado (Ms Chlipala); Surveys (Mses Colasacco and Thomas), College of American Pathologists, Northfield, Illinois; the Department of Pathology, University of South Alabama, Mobile (Dr Kahn); Policy and Advocacy, American Society of Clinical Oncology, Alexandria, Virginia (Ms Lacchetti); the Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio (Dr Madabhushi); the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Pantanowitz); the Department of Pathology, University of Utah/ARUP Laboratories Inc, Salt Lake City (Dr Salama); the Department of Pathology, University of Kentucky, Lexington (Dr Stewart); the Department of Pathology and Anatomical Sciences, University at Buffalo, State University of New York, Buffalo (Dr Tomaszewski); and the Department of Pathology, University of Utah School of Medicine and Intermountain Healthcare, Salt Lake City (Dr Hammond).

Context.—: Advancements in genomic, computing, and imaging technology have spurred new opportunities to use quantitative image analysis (QIA) for diagnostic testing.

Objective.—: To develop evidence-based recommendations to improve accuracy, precision, and reproducibility in the interpretation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) for breast cancer where QIA is used.

Design.—: The College of American Pathologists (CAP) convened a panel of pathologists, histotechnologists, and computer scientists with expertise in image analysis, immunohistochemistry, quality management, and breast pathology to develop recommendations for QIA of HER2 IHC in breast cancer. A systematic review of the literature was conducted to address 5 key questions. Final recommendations were derived from strength of evidence, open comment feedback, expert panel consensus, and advisory panel review.

Results.—: Eleven recommendations were drafted: 7 based on CAP laboratory accreditation requirements and 4 based on expert consensus opinions. A 3-week open comment period received 180 comments from more than 150 participants.

Conclusions.—: To improve accurate, precise, and reproducible interpretation of HER2 IHC results for breast cancer, QIA and procedures must be validated before implementation, followed by regular maintenance and ongoing evaluation of quality control and quality assurance. HER2 QIA performance, interpretation, and reporting should be supervised by pathologists with expertise in QIA.
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http://dx.doi.org/10.5858/arpa.2018-0378-CPDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629520PMC
October 2019

Nuclear-Cytoplasmic Transport Is a Therapeutic Target in Myelofibrosis.

Clin Cancer Res 2019 04 18;25(7):2323-2335. Epub 2018 Dec 18.

Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah.

Purpose: Myelofibrosis is a hematopoietic stem cell neoplasm characterized by bone marrow reticulin fibrosis, extramedullary hematopoiesis, and frequent transformation to acute myeloid leukemia. Constitutive activation of JAK/STAT signaling through mutations in , or is central to myelofibrosis pathogenesis. JAK inhibitors such as ruxolitinib reduce symptoms and improve quality of life, but are not curative and do not prevent leukemic transformation, defining a need to identify better therapeutic targets in myelofibrosis.

Experimental Design: A short hairpin RNA library screening was performed on JAK2-mutant HEL cells. Nuclear-cytoplasmic transport (NCT) genes including and were among top candidates. JAK2-mutant cell lines, human primary myelofibrosis CD34 cells, and a retroviral JAK2-driven myeloproliferative neoplasms mouse model were used to determine the effects of inhibiting NCT with selective inhibitors of nuclear export compounds KPT-330 (selinexor) or KPT-8602 (eltanexor).

Results: JAK2-mutant HEL, SET-2, and HEL cells resistant to JAK inhibition are exquisitely sensitive to RAN knockdown or pharmacologic inhibition by KPT-330 or KPT-8602. Inhibition of NCT selectively decreased viable cells and colony formation by myelofibrosis compared with cord blood CD34 cells and enhanced ruxolitinib-mediated growth inhibition and apoptosis, both in newly diagnosed and ruxolitinib-exposed myelofibrosis cells. Inhibition of NCT in myelofibrosis CD34 cells led to nuclear accumulation of p53. KPT-330 in combination with ruxolitinib-normalized white blood cells, hematocrit, spleen size, and architecture, and selectively reduced JAK2-mutant cells .

Conclusions: Our data implicate NCT as a potential therapeutic target in myelofibrosis and provide a rationale for clinical evaluation in ruxolitinib-exposed patients with myelofibrosis.
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http://dx.doi.org/10.1158/1078-0432.CCR-18-0959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445677PMC
April 2019

Safety and efficacy of combined ruxolitinib and decitabine in accelerated and blast-phase myeloproliferative neoplasms.

Blood Adv 2018 12;2(24):3572-3580

Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.

Myeloproliferative neoplasms (MPN), including polycythemia vera, essential thrombocythemia, and primary myelofibrosis, have a propensity to evolve into accelerated and blast-phase disease (MPN-AP/BP), carrying a dismal prognosis. Conventional antileukemia therapy has limited efficacy in this setting. Thus, MPN-AP/BP is an urgent unmet clinical need. Modest responses to hypomethylating agents and single-agent ruxolitinib have been reported. More recently, combination of ruxolitinib and decitabine has demonstrated synergistic in vitro activity in human and murine systems. These observations led us to conduct a phase 1 study to explore the safety of combined decitabine and dose-escalated ruxolitinib in patients with MPN-AP/BP. A total of 21 patients were accrued to this multicenter study. Ruxolitinib was administered at doses of 10, 15, 25, or 50 mg twice daily in combination with decitabine (20 mg/m per day for 5 days) in 28-day cycles. The maximum tolerated dose was not reached. The most common reasons for study discontinuation were toxicity/adverse events (37%) and disease progression (21%). Fourteen patients died during study treatment period or follow-up. The median overall survival for patients on study was 7.9 months (95% confidence interval, 4.1-not reached). Among evaluable patients, the overall response rate by protocol-defined criteria (complete remission with incomplete count recovery + partial remission) was 9/17 (53%) and by intention-to-treat analysis was 9/21 (42.9%). The combination of decitabine and ruxolitinib was generally well tolerated by patients with MPN-AP/BP and demonstrates potentially promising clinical activity. A phase 2 trial evaluating the efficacy of this combination regimen is ongoing within the Myeloproliferative Disorder Research Consortium.
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http://dx.doi.org/10.1182/bloodadvances.2018019661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306885PMC
December 2018

The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment.

Immunity 2018 10;49(4):764-779.e9

Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA. Electronic address:

The major types of non-small-cell lung cancer (NSCLC)-squamous cell carcinoma and adenocarcinoma-have distinct immune microenvironments. We developed a genetic model of squamous NSCLC on the basis of overexpression of the transcription factor Sox2, which specifies lung basal cell fate, and loss of the tumor suppressor Lkb1 (SL mice). SL tumors recapitulated gene-expression and immune-infiltrate features of human squamous NSCLC; such features included enrichment of tumor-associated neutrophils (TANs) and decreased expression of NKX2-1, a transcriptional regulator that specifies alveolar cell fate. In Kras-driven adenocarcinomas, mis-expression of Sox2 or loss of Nkx2-1 led to TAN recruitment. TAN recruitment involved SOX2-mediated production of the chemokine CXCL5. Deletion of Nkx2-1 in SL mice (SNL) revealed that NKX2-1 suppresses SOX2-driven squamous tumorigenesis by repressing adeno-to-squamous transdifferentiation. Depletion of TANs in SNL mice reduced squamous tumors, suggesting that TANs foster squamous cell fate. Thus, lineage-defining transcription factors determine the tumor immune microenvironment, which in turn might impact the nature of the tumor.
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http://dx.doi.org/10.1016/j.immuni.2018.09.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197489PMC
October 2018

Ruxolitinib Therapy Followed by Reduced-Intensity Conditioning for Hematopoietic Cell Transplantation for Myelofibrosis: Myeloproliferative Disorders Research Consortium 114 Study.

Biol Blood Marrow Transplant 2019 02 8;25(2):256-264. Epub 2018 Sep 8.

Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.

We evaluated the feasibility of ruxolitinib therapy followed by a reduced-intensity conditioning (RIC) regimen for patients with myelofibrosis (MF) undergoing transplantation in a 2-stage Simon phase II trial. The aims were to decrease the incidence of graft failure (GF) and nonrelapse mortality (NRM) compared with data from the previous Myeloproliferative Disorders Research Consortium 101 Study. The plan was to enroll 11 patients each in related donor (RD) and unrelated donor (URD) arms, with trial termination if ≥3 failures (GF or death by day +100 post-transplant) occurred in the RD arm or ≥6 failures occurred in the URD. A total of 21 patients were enrolled, including 7 in the RD arm and 14 in the URD arm. The RD arm did not meet the predetermined criteria for proceeding to stage II. Although the URD arm met the criteria for stage II, the study was terminated owing to poor accrual and a significant number of failures. In all 19 transplant recipients, ruxolitinib was tapered successfully without significant side effects, and 9 patients (47%) had a significant decrease in symptom burden. The cumulative incidences of GF, NRM, acute graft-versus-host disease (GVHD), and chronic GVHD at 24 months were 16%, 28%, 64%, and 76%, respectively. On an intention-to-treat basis, the 2-year overall survival was 61% for the RD arm and 70% for the URD arm. Ruxolitinib can be integrated as pretransplantation treatment for patients with MF, and a tapering strategy before transplantation is safe, allowing patients to commence conditioning therapy with a reduced symptom burden. However, GF and NRM remain significant.
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http://dx.doi.org/10.1016/j.bbmt.2018.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339828PMC
February 2019

Molecular Fingerprinting of Anatomically and Temporally Distinct B-Cell Lymphoma Samples by Next-Generation Sequencing to Establish Clonal Relatedness.

Arch Pathol Lab Med 2019 01 6;143(1):105-111. Epub 2018 Jul 6.

From the Department of Pathology, University of Utah School of Medicine, Salt Lake City (Drs Matynia, Li, Salama, and Kelley); and ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Drs Szankasi and Liew and Mr Schumacher).

Context.—: B-cell lymphomas exhibit balanced translocations that involve immunoglobulin loci and result from aberrant V(D)J recombination, class switch recombination, or somatic hypermutation. Although most of the breakpoints in the immunoglobulin loci occur in defined regions, those in the partner genes vary; therefore, it is unlikely that 2 independent clones would share identical breakpoints in both partners. Establishing whether a new lesion in a patient with history of lymphoma represents recurrence or a new process can be relevant. Polymerase chain reaction (PCR)-based clonality assays used in this setting rely only on evaluating the length of a given rearrangement. In contrast, next-generation sequencing (NGS) provides the exact translocation breakpoint at single-base resolution.

Objective.—: To determine if translocation breakpoint coordinates can serve as a molecular fingerprint unique to a distinct clonal population.

Design.—: Thirty-eight follicular lymphoma/diffuse large B-cell lymphoma samples collected from different anatomic sites and/or at different time points from 18 patients were analyzed by NGS. For comparison, PCR-based B-cell clonality and fluorescence in situ hybridization studies were performed on a subset of cases.

Results.—: IGH-BCL2 rearrangements were detected in all samples. The breakpoint coordinates on derivative chromosome(s) were identical in all samples from a given patient, but distinct between samples derived from different patients. Additionally, 5 patients carried a second rearrangement also with conserved breakpoint coordinates in the follow-up sample(s).

Conclusions.—: Breakpoint coordinates in the immunoglobulin and partner genes can be used to establish clonal relatedness of anatomically/temporally distinct lesions. Additionally, an NGS-based approach has the potential to detect secondary translocations that may have prognostic and therapeutic significance.
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http://dx.doi.org/10.5858/arpa.2017-0497-OADOI Listing
January 2019

The characteristics of vessel lining cells in normal spleens and their role in the pathobiology of myelofibrosis.

Blood Adv 2018 05;2(10):1130-1145

Division of Hematology/Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY; and.

The CD34CD8α, sinusoid lining, littoral cells (LCs), and CD34CD8α, splenic vascular endothelial cells (SVECs) represent 2 distinct cellular types that line the vessels within normal spleens and those of patients with myelofibrosis (MF). To further understand the respective roles of LCs and SVECs, each was purified from normal and MF spleens, cultured, and characterized. Gene expression profiling indicated that LCs were a specialized type of SVEC. LCs possessed a distinct gene expression profile associated with cytoskeleton regulation, cellular interactions, endocytosis, and iron transport. LCs also were characterized by strong phagocytic activity, less robust tube-forming capacity and a limited proliferative potential. These characteristics underlie the role of LCs as cellular filters and scavengers. Although normal LCs and SVECs produced overlapping as well as distinct hematopoietic factors and adhesion molecules, the gene expression profile of MF LCs and SVECs distinguished them from their normal counterparts. MF SVECs were characterized by activated interferon signaling and cell cycle progression pathways and increased vascular endothelial growth factor receptor, angiopoietin-2, stem cell factor, interleukin (IL)-33, Notch ligands, and IL-15 transcripts. In contrast, the transcription profile of MF LCs was associated with mitochondrial dysfunction, reduced energy production, protein biosynthesis, and catabolism. Normal SVECs formed in vitro confluent cell layers that supported MF hematopoietic colony formation to a greater extent than normal colony formation. These data provide an explanation for the reduced density of LCs observed within MF spleens and indicate the role of SVECs in the development of extramedullary hematopoiesis in MF.
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http://dx.doi.org/10.1182/bloodadvances.2017015073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965045PMC
May 2018

Autocrine Tnf signaling favors malignant cells in myelofibrosis in a Tnfr2-dependent fashion.

Leukemia 2018 11 18;32(11):2399-2411. Epub 2018 Apr 18.

Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.

Tumor necrosis factor alpha (TNF) is increased in myelofibrosis (MF) and promotes survival of malignant over normal cells. The mechanisms altering TNF responsiveness in MF cells are unknown. We show that the proportion of marrow (BM) cells expressing TNF is increased in MF compared to controls, with the largest differential in primitive cells. Blockade of TNF receptor 2 (TNFR2), but not TNFR1, selectively inhibited colony formation by MF CD34 and mouse JAK2 progenitor cells. Microarray of mouse MPN revealed reduced expression of X-linked inhibitor of apoptosis (Xiap) and mitogen-activated protein kinase 8 (Mapk8) in JAK2 relative to JAK2 cells, which were normalized by TNFR2 but not TNFR1 blockade. XIAP and MAPK8 were also reduced in MF CD34 cells compared to normal BM, and their ectopic expression induced apoptosis. Unlike XIAP, expression of cellular IAP (cIAP) protein was increased in MF CD34 cells. Consistent with cIAP's role in NF-κB activation, TNF-induced NF-κB activity was higher in MF vs. normal BM CD34 cells. This suggests that JAK2 reprograms TNF response toward survival by downregulating XIAP and MAPK8 through TNFR2. Our results reveal an unexpected pro-apoptotic role for XIAP in MF and identify TNFR2 as a key mediator of TNF-induced clonal expansion.
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http://dx.doi.org/10.1038/s41375-018-0131-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224399PMC
November 2018

US Food and Drug Administration Approval of Whole Slide Imaging for Primary Diagnosis: A Key Milestone Is Reached and New Questions Are Raised.

Arch Pathol Lab Med 2018 11 30;142(11):1383-1387. Epub 2018 Apr 30.

From the Laboratory Medicine Program, Department of Pathology, University Health Network, Toronto, Ontario, Canada (Dr Evans); the Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, New York (Dr Bauer); the Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, Florida (Dr Bui); the Department of Pathology, University of Colorado Denver, Aurora (Dr Cornish); Economic and Regulatory Affairs, College of American Pathologists, Washington, DC (Ms Duncan); Affiliated Pathologists Medical Group, Rancho Dominguez, California (Dr Glassy); the Medical Brain Team, Google, San Francisco, California (Dr Hipp); Covance, Indianapolis, Indiana (Dr McGee); the Surveys Department, College of American Pathologists, Northfield, Illinois (Mr Murphy); the Department of Pathology, Emory University Hospital, Atlanta, Georgia (Dr Myers); the Department of Pathology, Manchester Memorial Hospital, Manchester, Connecticut (Dr O'Neill); the Department of Pathology, Ohio State University Wexner Medical Center, Columbus (Dr Parwani); the Department of Pathology, Dell Medical School, University of Texas at Austin (Dr Rampy); ARUP Laboratories Incorporated, Salt Lake City, Utah (Dr Salama); and the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Pantanowitz).

April 12, 2017 marked a significant day in the evolution of digital pathology in the United States, when the US Food and Drug Administration announced its approval of the Philips IntelliSite Pathology Solution for primary diagnosis in surgical pathology. Although this event is expected to facilitate more widespread adoption of whole slide imaging for clinical applications in the United States, it also raises a number of questions as to the means by which pathologists might choose to incorporate this technology into their clinical practice. This article from the College of American Pathologists Digital Pathology Committee reviews frequently asked questions on this topic and provides answers based on currently available information.
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http://dx.doi.org/10.5858/arpa.2017-0496-CPDOI Listing
November 2018

Combination of the low anticoagulant heparin CX-01 with chemotherapy for the treatment of acute myeloid leukemia.

Blood Adv 2018 02;2(4):381-389

Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT.

Relapses in acute myelogenous leukemia (AML) are a result of quiescent leukemic stem cells (LSCs) in marrow stromal niches, where they resist chemotherapy. LSCs employ CXCL12/CXCR4 to home toward protective marrow niches. Heparin disrupts CXCL12-mediated sequestration of cells in the marrow. CX-01 is a low-anticoagulant heparin derivative. In this pilot study, we combined CX-01 with chemotherapy for the treatment of AML. Induction consisted of cytarabine and idarubicin (7 + 3) with CX-01. Twelve patients were enrolled (median age, 56 years; 3 women). Three, 5, and 4 patients had good-, intermediate-, and poor-risk disease, respectively. Day 14 bone marrows were available on 11 patients and were aplastic in all without detectable leukemia. Eleven patients (92%) had morphologic complete remission after 1 induction (CR1). Eight patients were alive at a median follow-up of 24 months (4 patients in CR1). Three patients received an allogeneic stem cell transplant in CR1. Median disease-free survival was 14.8 months. Median overall survival was not attained at the maximum follow-up time of 29.4 months. No CX-01-associated serious adverse events occurred. Median day to an untransfused platelet count of at least 20 × 10/L was 21. CX-01 is well tolerated when combined with intensive therapy for AML and appears associated with enhanced count recovery and treatment efficacy.
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http://dx.doi.org/10.1182/bloodadvances.2017013391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858478PMC
February 2018

Variability of PD-L1 expression in mastocytosis.

Blood Adv 2018 02;2(3):189-199

Department of Pathology, University of New Mexico, Albuquerque, NM.

Mastocytosis is a rare disease with heterogeneous clinical manifestations and few effective therapies. Programmed death-1 (PD-1) and its ligands (PD-L1 and PD-L2) protect tissues from immune-mediated damage and permit tumors to evade immune destruction. Therapeutic antibodies against PD-1 and PD-L1 are effective in the treatment of a variety of neoplasms. In the present study, we sought to systematically analyze expression of PD-1 and PD-L1 in a large number of patients with mastocytosis using immunohistochemistry and multiplex fluorescence staining. PD-L1 showed membrane staining of neoplastic mast cells (MCs) in 77% of systemic mastocytosis (SM) cases including 3 of 3 patients with MC leukemia, 2 of 2 with aggressive SM, 1 of 2 with smoldering SM, 3 of 4 with indolent SM, and 9 of 12 with SM with an associated hematologic neoplasm (SM component only). Ninety-two percent (23 of 25) of cutaneous mastocytosis (CM) cases and 1 of 2 with myelomastocytic leukemia expressed PD-L1, with no expression found in 15 healthy/reactive marrows, 18 myelodysplastic syndromes (MDSs), 16 myeloproliferative neoplasms (MPNs), 5 MDS/MPNs, and 3 monoclonal MC activation syndromes. Variable PD-L1 expression was observed between and within samples, with PD-L1 staining of MCs ranging from 10% to 100% (mean, 50%). PD-1 dimly stained 4 of 27 CM cases (15%), with no expression in SM or other neoplasms tested; PD-1 staining of MCs ranged from 20% to 50% (mean, 27%). These results provide support for the expression of PD-L1 in SM and CM, and PD-1 expression in CM. These data support the exploration of agents with anti-PD-L1 activity in patients with advanced mastocytosis.
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http://dx.doi.org/10.1182/bloodadvances.2017011551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812326PMC
February 2018

A phase 1 study of the Janus kinase 2 (JAK2) inhibitor, gandotinib (LY2784544), in patients with primary myelofibrosis, polycythemia vera, and essential thrombocythemia.

Leuk Res 2017 10 31;61:89-95. Epub 2017 Aug 31.

University of Utah School of Medicine, Division of Hematology, 30 North 1900 East, Salt Lake City, UT 84132, USA. Electronic address:

Mutations in Janus kinase 2 (JAK2) are implicated in the pathogenesis of Philadelphia-chromosome negative myeloproliferative neoplasms, including primary myelofibrosis, polycythemia vera, and essential thrombocythemia. Gandotinib (LY2784544), a potent inhibitor of JAK2 activity, shows increased potency for the JAK2 mutation. The study had a standard 3+3 dose-escalation design to define the maximum-tolerated dose. Primary objectives were to determine safety, tolerability, and recommended oral daily dose of gandotinib for patients with JAK2-positive myelofibrosis, essential thrombocythemia, or polycythemia vera. Secondary objectives included estimating pharmacokinetic parameters and documenting evidence of efficacy by measuring clinical improvement. Thirty-eight patients were enrolled and treated (31 myelofibrosis, 6 polycythemia vera, 1 essential thrombocythemia). The maximum-tolerated dose of gandotinib was 120mg daily, based on dose-limiting toxicities of blood creatinine increase or hyperuricemia at higher doses. Maximum plasma concentration was reached 4h after single and multiple doses, and mean half-life on day 1 was approximately 6h. Most common treatment-emergent adverse events were diarrhea (55.3%) and nausea (42.1%), a majority of which were of grade 1 severity. Best response of clinical improvement was achieved by 29% of myelofibrosis patients. A ≥50% palpable spleen length reduction was observed at any time during therapy in 20/32 evaluable patients. Additionally, ≥50% reduction in the Total Symptom Myeloproliferative Neoplasm Symptom Assessment Form Score was seen in 11/21 (52%) and 6/14 patients (43%) receiving ≥120mg at 12 and 24 weeks respectively. Gandotinib demonstrated an acceptable safety and tolerability profile, and findings at the maximum-tolerated dose of 120mg supported further clinical testing. Clinicaltrials.gov identifier: NCT01134120.
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http://dx.doi.org/10.1016/j.leukres.2017.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8207330PMC
October 2017
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