Deep learning for diagnosis of acute promyelocytic leukemia via recognition of genomically imprinted morphologic features.

Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML), classified by a translocation between chromosomes 15 and 17 [t(15;17)], that is considered a true oncologic emergency though appropriate therapy is considered curative. Therapy is often initiated on clinical suspicion, informed by both clinical presentation as well as direct visualization of the peripheral smear. We hypothesized that genomic imprinting of morphologic features learned by deep learning pattern recognition would have greater discriminatory power and consistency compared to humans, thereby facilitating identification of t(15;17) positive APL. By applying both cell-level and patient-level classification linked to t(15;17) PML/RARA ground-truth, we demonstrate that deep learning is capable of distinguishing APL in both discovery and prospective independent cohort of patients. Furthermore, we extract learned information from the trained network to identify previously undescribed morphological features of APL. The deep learning method we describe herein potentially allows a rapid, explainable, and accurate physician-aid for diagnosing APL at the time of presentation in any resource-poor or -rich medical setting given the universally available peripheral smear.

Conditional reprogramming culture conditions facilitate growth of lower-grade glioma models.

BACKGROUND: The conditional reprogramming cell culture method was developed to facilitate growth of senescence-prone normal and neoplastic epithelial cells, and involves co-culture with irradiated fibroblasts and the addition of a small molecule Rho kinase (ROCK) inhibitor. The aim of this study was to determine whether this approach would facilitate the culture of compact low-grade gliomas. METHODS: We attempted to culture 4 pilocytic astrocytomas, 2 gangliogliomas, 2 myxopapillary ependymomas, 2 anaplastic gliomas, 2 difficult-to-classify low-grade neuroepithelial tumors, a desmoplastic infantile ganglioglioma, and an anaplastic pleomorphic xanthoastrocytoma using a modified conditional reprogramming cell culture approach. RESULTS: Conditional reprogramming resulted in robust increases in growth for a majority of these tumors, with fibroblast conditioned media and ROCK inhibition both required. Switching cultures to standard serum containing media, or serum-free neurosphere conditions, with or without ROCK inhibition, resulted in decreased proliferation and induction of senescence markers. Rho kinase inhibition and conditioned media both promoted Akt and Erk1/2 activation. Several cultures, including one derived from a NF1-associated pilocytic astrocytoma (JHH-NF1-PA1) and one from a BRAF p.V600E mutant anaplastic pleomorphic xanthoastrocytoma (JHH-PXA1), exhibited growth sufficient for preclinical testing in vitro. In addition, JHH-NF1-PA1 cells survived and migrated in larval zebrafish orthotopic xenografts, while JHH-PXA1 formed orthotopic xenografts in mice histopathologically similar to the tumor from which it was derived. CONCLUSIONS: These studies highlight the potential for the conditional reprogramming cell culture method to promote the growth of glial and glioneuronal tumors in vitro, in some cases enabling the establishment of long-term culture and in vivo models.

Recurrent DICER1 Hotspot Mutations in Malignant Thyroid Gland Teratomas: Molecular Characterization and Proposal for a Separate Classification.

Thyroid gland teratomas are rare tumors that span a wide clinicopathologic spectrum. Although benign and immature teratomas arise in infants and young children and generally have good outcomes, malignant teratomas affect adults and follow an aggressive course. This divergent behavior raises the possibility that benign/immature and malignant teratomas are separate entities rather than different grades of a single tumor. However, the histogenesis and molecular underpinnings of thyroid gland teratomas are poorly understood regardless of grade. In this study, we performed next-generation sequencing on 8 thyroid gland teratomas, including 4 malignant, 3 benign, and 1 immature. We identified DICER1 hotspot mutations in all 4 malignant cases (100%) but not in any benign/immature cases (0%). No clinically significant mutations in other genes were found in either group. We also performed immunohistochemistry to characterize the primitive components of malignant teratomas. Not only did all cases consistently contain immature neural elements (synaptophysin and INSM1 positive), but also spindled cells with rhabdomyoblastic differentiation (desmin and myogenin positive) and bland epithelial proliferations of thyroid follicular origin (TTF-1 and PAX8 positive). Although DICER1 mutations have previously been implicated in multinodular hyperplasia and well-differentiated thyroid carcinomas, these findings demonstrate the first recurrent role for DICER1 in primitive thyroid tumors. The combined neural, rhabdomyoblastic, and homologous epithelial elements highlighted in this series of malignant thyroid gland teratomas parallel the components of DICER1-mutated tumors in other organs. Overall, these molecular findings further expand the differences between benign/immature teratomas and malignant teratomas, supporting the classification of these tumors as separate entities.

Tetraploid Partial Hydatidiform Moles: Molecular Genotyping and Determination of Parental Contributions.

DNA genotyping studies have established that most partial hydatidiform moles (PHMs) are diandric dispermic triploid conceptions. Rare triandric tetraploid PHMs have been described, but genotyping cannot determine the manner in which three paternal chromosome complements are derived (one sperm with triplication, two sperm with one duplication, three different sperm, or one diploid and one haploid sperm). In a large prospective analysis of potentially molar products of conception, five tetraploid PHMs were encountered among 235 PHMs. Single-nucleotide polymorphism (SNP) arrays were used to define different paternal chromosomal contributions. Short tandem repeat analysis of the five tetraploid PHMs established that these contained three paternal and one maternal chromosome complements. In each case, the corresponding SNP array found five tracts with segmented absence of the central tract across approximately 25% of the genome. Meiotic crossovers could be observed directly in the chromosomes via the total number of starts and stops of regions of loss of heterozygosity. The findings are consistent with each conceptus having three different paternal contributions and one maternal contribution. These findings suggest that tetraploid PHMs arise when three different sperm fertilize a single, normal ovum. SNP array is useful to determine the parental contributions in triploid/tetraploid conceptuses. It also allows for direct visualization of meiotic crossover frequency and sites in these conceptions, providing insight into their biology.

Clinical validation of coexisting driver mutations in colorectal cancers.

Mutational profiling is recommended for selecting targeted therapy and predicting prognosis of metastatic colorectal cancer (CRC). Detection of coexisting mutations within the same pathway, which are usually mutually exclusive, raises the concern for potential laboratory errors. In this retrospective study for quality assessment of a next-generation sequencing assay, we examined BRAF, KRAS, and NRAS genes within the mitogen-activated protein kinase (MAPK) pathway and the PIK3CA gene within the phosphatidylinositol 3-kinase (mTOR) pathway in 744 CRC specimens submitted to our clinical diagnostics laboratory. Although coexistence of mutations between the MAPK and mTOR pathways was observed, it rarely occurred within the MAPK pathway. Retrospective quality assessments identified false detection of coexisting activating KRAS and NRAS mutations in 1 specimen and confirmed 2 activating KRAS mutations in 2 specimens and coexisting activating KRAS and NRAS mutations in 2 specimens, but no coexisting activating RAS and BRAF mutations. There were 15 CRCs with a kinase-impaired BRAF mutation, including 3 with a coexisting activating KRAS mutation, which may have therapeutic implications. Multiregional analysis based on different histologic features demonstrated that coexisting KRAS and NRAS mutations may be present in the same or different tumor populations and showed that invasion of adenomas by synchronous adenocarcinomas of different clonal origin may result in detection of coexisting mutations within the MAPK pathway. In this study, we proposed an operating procedure for clinical validation of unexpected coexisting mutations. Further studies are warranted to elucidate the biological significance and clinical implications of coexisting mutations within the MAPK pathway.

Transfusion of leukoreduced blood products and risk of antibody-mediated rejection of renal allografts.

BACKGROUND: Antibody-mediated rejection (AMR) is a major barrier to the long-term function of renal allografts. White blood cells, which may be present in red blood cell (RBC) units, and platelets (PLTs) express HLA antigens that may increase the risk of AMR by inducing or increasing humoral sensitization to HLA. STUDY DESIGN AND METHODS: A retrospective cohort study of HLA-incompatible (HLAi) renal transplant recipients between 2004 and 2015 was conducted. Data on apheresis PLT and leukoreduced RBC transfusions within 4 weeks of transplantation, demographic information, and biopsy-proven AMR were collected from medical records and the Scientific Registry of Transplant Recipients. Patients were evaluated until they showed evidence of AMR or until 1 year posttransplant, whichever came first. Multivariable analysis with Cox modeling was performed. RESULTS: Of 244 individuals, 182 (74.6%) received RBCs and 20 (8.2%) of those also received PLTs. During the first year posttransplant, 97 (39.8%) had AMR. RBC-alone or RBC and PLT transfusions were not associated with increased risk of AMR after adjustment for panel-reactive antibody, years on dialysis, HLA antibody strength, and number of therapeutic plasma exchange treatments (adjusted hazard ratio [adjHR] 1.00, 95% confidence interval [95% CI] 0.59-1.69; and adjHR 0.68, 95% CI 0.28-1.68, respectively). For each 1-unit increase in RBC transfusions, there was no association with AMR (adjHR 0.94, 95% CI 0.85-1.05). Only HLA antibody strength before transplantation was associated with AMR (adjHR 2.23, 95% CI 1.10-4.52; cytotoxic crossmatch compared to crossmatch negative but detectable donor-specific HLA antibodies). CONCLUSIONS: Patients who receive an HLAi transplant who are transfused with leukoreduced RBCs or PLTs in the peritransplant period are at no higher risk of AMR than nontransfused patients.

Importance of Flow Cytometry in the Cytopathologic Evaluation of Lymphoid Lesions Involving the Kidney.

BACKGROUND: Cytomorphology alone is often insufficient for the diagnosis and subclassification of lymphomas, so flow cytometry (FC) may be used as an adjuvant test. METHODS: Renal fine-needle aspirations (FNAs) performed from January 1993 to August 2014 were reviewed for FC data or a diagnosis of lymphoma. RESULTS: A total of 586 renal FNAs were collected. Thirty-three cases (5.1%) had FC analysis. Lymphoma was diagnosed 35 times (6%), and FC was performed in 21 (60%) cases. Both cytomorphology and FC were consistent with lymphoma in 20 cases. Cytomorphology alone was diagnostic of lymphoma in 15 cases. In 28 cases, biopsy from the kidney or another site was diagnostic of lymphoma. One subsequent biopsy revealed that a kidney FNA, which showed no definitive morphologic or FC evidence of lymphoma, likely represented necrotic diffuse large B-cell lymphoma. CONCLUSION: FC is a useful adjuvant diagnostic test for renal FNAs, particularly for subclassification and confirmation of the diagnosis when there is insufficient material for immunohistochemistry. FC should be interpreted with caution when a sample is limited or when there is suspicion of Hodgkin lymphoma, and further work-up is warranted when cytomorphology suggests lymphoma but FC is negative.

Invasive Complete Hydatidiform Moles: Analysis of a Case Series With Genotyping.

Complete hydatidiform moles (CHM) are purely androgenetic conceptions, with most (∼85%) arising from fertilization of an egg lacking maternal DNA by a single sperm that duplicates (homozygous/monospermic 46,XX) and a small subset arising via fertilization by 2 sperms (heterozygous/dispermic 46,XY or 46,XX). It remains controversial if heterozygous/dispermic CHMs have a significantly greater risk of persistent gestational trophoblastic disease. Analysis of zygosity of CHMs with and without invasion at presentation, including invasive CHMs with concurrent atypical trophoblastic proliferations concerning for or consistent with choriocarcinoma, has not been specifically addressed. In a prospective series of 1024 products of conception specimens subjected to immunohistochemical analysis of p57 expression and molecular genotyping with short tandem-repeat markers, 288 CHMs were diagnosed, of which 126 were genotyped, including 16 invasive CHMs. Zygosity was compared between those with and without invasion. Of the 16 study cases, 12 (75%) were homozygous/monospermic XX and 4 (25%) were heterozygous/dispermic (3 XY and 1 XX). Of the 110 genotyped noninvasive CHMs, 96 (87%) were homozygous/monospermic XX and 14 (13%) were heterozygous/dispermic (12 XY, 2 XX). Comparison of the zygosity results for the invasive CHMs (study group) with the noninvasive CHMs in the database did not demonstrate a statistically significant difference (P=0.24, Fisher exact test). In addition, of the 3 cases associated with metastatic gestational trophoblastic disease (pulmonary nodules) at presentation, 2 were homozygous/monospermic XX, indicating that this form is not without risk of significant gestational trophoblastic disease. Thus, the current study has demonstrated a higher frequency of heterozygous/dispermic CHMs among invasive cases compared with those lacking invasion, but does not support the use of zygosity data for risk assessment of CHMs. A persistent, unresolved diagnostic challenge identified in some invasive CHMs is interpretation of accompanying florid atypical trophoblastic proliferations which raise concern for choriocarcinoma. Future studies should address the need for reproducible diagnostic criteria and molecular biomarkers for distinguishing florid hyperplastic from malignant neoplastic trophoblastic proliferations.

Impact of flow cytometry in liver cytopathology.

BACKGROUND: Fine needle aspiration (FNA) is commonly used as a diagnostic tool for the evaluation of lymphoproliferative diseases. Cytomorphology alone is often insufficient for the diagnosis and subclassification of lymphoma; therefore, flow cytometry (FC) plays an important role in the characterization of lymphoproliferative disorders. This study reviews our experience with FC on liver FNA at the Johns Hopkins Hospital. METHODS: 2,424 liver FNAs performed over a 21-year period were reviewed for clinical FC data (n=74) or a subsequent diagnosis of lymphoma in the liver without FC data (n=40). RESULTS: In our study, 114 cases (4.7%) were included out of the 2,424 liver FNAs performed during the study period. Lymphoma was diagnosed 79 times. Cytomorphology alone was diagnostic of lymphoma in 45 cases, and in 33 cases both the cytomorphology and the FC were consistent with a diagnosis of lymphoma. Neither FC nor cytomorphology were diagnostic of lymphoma on 1 specimen. In 39 cases, FC had negative results on a lesion suspicious for lymphoma based on cytomorphology. In several nonlymphoma cases, FC provided information that allowed further subclassification of the neoplasm. CONCLUSION: FC is a useful adjuvant diagnostic test for liver FNAs performed on patients with lymphoproliferative disorders.

Cerebrospinal fluid cytology of an endolymphatic sac tumor.

Endolymphatic sac tumor (ELST) is a rare neoplasm which is seldom evaluated by cytopathology. We report the clinicopathologic course and cytologic cerebrospinal fluid (CSF) findings in a 58-year-old patient with brainstem lesions who originally presented with vertigo but progressed to having left 7th, 8th, 9th, and 10th cranial nerve palsies, right-sided weakness, and occipital headaches. Cytospin of the CSF revealed large epithelioid cells similar to cells seen in a surgical resection of a brain mass three months previously. Review of the surgical specimen revealed a well-differentiated glandular and papillary neoplasm, most consistent with an endolymphatic sac tumor.