Deep learning predicts therapy-relevant genetics in acute myeloid leukemia from Pappenheim-stained bone marrow smears.

ABSTRACT: The detection of genetic aberrations is crucial for early therapy decisions in acute myeloid leukemia (AML) and recommended for all patients. Because genetic testing is expensive and time consuming, a need remains for cost-effective, fast, and broadly accessible tests to predict these aberrations in this aggressive malignancy. Here, we developed a novel fully automated end-to-end deep learning pipeline to predict genetic aberrations directly from single-cell images from scans of conventionally stained bone marrow smears already on the day of diagnosis. We used this pipeline to compile a multiterabyte data set of >2 000 000 single-cell images from diagnostic samples of 408 patients with AML. These images were then used to train convolutional neural networks for the prediction of various therapy-relevant genetic alterations. Moreover, we created a temporal test cohort data set of >444 000 single-cell images from further 71 patients with AML. We show that the models from our pipeline can significantly predict these subgroups with high areas under the curve of the receiver operating characteristic. Potential genotype-phenotype links were visualized with 2 different strategies. Our pipeline holds the potential to be used as a fast and inexpensive automated tool to screen patients with AML for therapy-relevant genetic aberrations directly from routine, conventionally stained bone marrow smears already on the day of diagnosis. It also creates a foundation to develop similar approaches for other bone marrow disorders in the future.

The Role of Clonal Evolution on Progression, Blood Parameters, and Response to Therapy in Multiple Myeloma.

Introduction: A variety of biomarkers are considered for diagnosis (e.g., ß2-microgobulin, albumin, or LDH) and prognosis [e.g., cytogenetic aberrations detected by fluorescence in situ hybridization (FISH)] of multiple myeloma (MM). More recently, clonal evolution has been established as key. Little is known on the clinical implications of clonal evolution. Methods: We performed in-depth analyses of 25 patients with newly diagnosed MM with respect to detailed clinical information analyzing blood samples collected at several time points during follow-up (median follow-up: 3.26 years since first diagnosis). We split our cohort into two subgroups: with and without new FISH clones developing in the course of disease. Results: Each subgroup showed a characteristic chromosomal profile. Forty-three percent of patients had evidence of appearing new clones. The patients with new clones showed an increased number of translocations affecting chromosomes 14 (78% vs. 33%; p = 0.0805) and 11, and alterations in chromosome 4 (amplifications and translocations). New clones, on the contrary, were characterized by alterations affecting chromosome 17. Subsequent to the development of the new clone, 6 out of 9 patients experienced disease progression compared to 3 out of 12 for patients without new clones. Duration of the therapy applied for the longest time was significantly shorter within the group of patients developing new clones (median: 273 vs. 406.5 days; p = 0.0465). Discussion: We demonstrated that the development of new clones, carrying large-scale alterations, was associated with inferior disease course and shorter response to therapy, possibly affecting progression-free survival and overall survival as well. Further studies evaluating larger cohorts are necessary for the validation of our results.

Chromosomal Abnormalities and Prognosis in NPM1-Mutated Acute Myeloid Leukemia: A Pooled Analysis of Individual Patient Data From Nine International Cohorts.

PURPOSE: Nucleophosmin 1 (NPM1) mutations are associated with a favorable prognosis in acute myeloid leukemia (AML) when an internal tandem duplication (ITD) in the fms-related tyrosine kinase 3 gene (FLT3) is absent (FLT3-ITDneg) or present with a low allelic ratio (FLT3-ITDlow). The 2017 European LeukemiaNet guidelines assume this is true regardless of accompanying cytogenetic abnormalities. We investigated the validity of this assumption. METHODS: We analyzed associations between karyotype and outcome in intensively treated patients with NPM1mut/FLT3-ITDneg/low AML who were prospectively enrolled in registry databases from nine international study groups or treatment centers. RESULTS: Among 2,426 patients with NPM1mut/FLT3-ITDneg/low AML, 2,000 (82.4%) had a normal and 426 (17.6%) had an abnormal karyotype, including 329 patients (13.6%) with intermediate and 83 patients (3.4%) with adverse-risk chromosomal abnormalities. In patients with NPM1mut/FLT3-ITDneg/low AML, adverse cytogenetics were associated with lower complete remission rates (87.7%, 86.0%, and 66.3% for normal, aberrant intermediate, and adverse karyotype, respectively; P < .001), inferior 5-year overall (52.4%, 44.8%, 19.5%, respectively; P < .001) and event-free survival (40.6%, 36.0%, 18.1%, respectively; P < .001), and a higher 5-year cumulative incidence of relapse (43.6%, 44.2%, 51.9%, respectively; P = .0012). These associations remained in multivariable mixed-effects regression analyses adjusted for known clinicopathologic risk factors (P < .001 for all end points). In patients with adverse-risk chromosomal aberrations, we found no significant influence of the NPM1 mutational status on outcome. CONCLUSION: Karyotype abnormalities are significantly associated with outcome in NPM1mut/FLT3-ITDneg/low AML. When adverse-risk cytogenetics are present, patients with NPM1mut share the same unfavorable prognosis as patients with NPM1 wild type and should be classified and treated accordingly. Thus, cytogenetic risk predominates over molecular risk in NPM1mut/FLT3-ITDneg/low AML.

Postnatal follow-up of prenatally diagnosed trisomy 16 mosaicism.

OBJECTIVE: To determine the long-term outcome of pregnancies prenatally diagnosed with trisomy 16 and identify variables associated with the outcome. METHODS: We reviewed all published and our unpublished data from trisomy 16 pregnancies for which outcomes were available for children of greater than 1 year of age. RESULTS: Nineteen cases were diagnosed with trisomy 16 on chorionic villus sampling (CVS) and 17 cases at amniocentesis. Age at last follow-up ranges from 1 to 13 years. Among the CVS group, four out of five patients, with a birth weight and/or length below -2 SD and postnatal growth information, showed catch-up growth (80%). Among the amniotic fluid (AF) group, the birth weight was available in 13 cases. Eleven of the 13 cases had a birth weight less than -2 SD. In eight cases, the length was also below -2 SD (length data unavailable in one case). Nine out of ten cases (90%) and seven out of eight (87.5%) showed catch-up growth for weight and length, respectively. In terms of development, no cases of CVS mosaicism had global developmental delay. One child had a history of delay in speech development. Among the AF-detected cases, 4/17 cases had global developmental delay. All four children with global developmental delay had more than one major malformation compared to 6 out of 32 children in the group with normal development (p = 0.004). The finding of uniparental disomy (UPD) was not associated with developmental delay. CONCLUSIONS: The majority of prenatally diagnosed trisomy 16 mosaic cases have a good postnatal outcome. However, the finding of mosaicism on AF and the presence of major congenital anomalies are associated with an increased risk of developmental delay.

Establishment of a benign meningioma cell line by hTERT-mediated immortalization.

Meningioma represents the most common intracranial tumor, but well-characterized cell lines derived from benign meningiomas are not available. A major reason for the lack of benign tumor cell lines is senescence of nonmalignant cells in vitro, while malignant cells are often immortal. We have developed a meningioma cell line by retrovirally transducing primary cells derived from a human WHO grade I meningothelial meningioma with the human telomerase reverse transcriptase (hTERT) gene, which enables bypassing cellular senescence. Five clones have been cultured for more than 21 months so far, while corresponding nontransfected cells ceased proliferation within 3 months. Quantitative RT-PCR and a telomeric repeat amplification protocol (TRAP) assay revealed high hTERT mRNA levels and high telomerase activity in all transduced populations, while nontransduced cells were negative. The average telomere size of transduced cells was considerably longer than that of parental cells and the biopsy specimen. One clone, designated Ben-Men-1, was characterized in more detail, and exhibited typical cytological, immunocytochemical, ultrastructural and genetical features of meningioma, including whorl formation, expression of epithelial membrane antigen, desmosomes and interdigitating cell processes, as well as -22q. Following subdural transplantation into nude mice, tumor tissue with typical histological features of meningothelial meningioma was found. We conclude that Ben-Men-1 represents an immortalized yet differentiated cell line useful for biological and therapeutical studies on meningioma.

Mild phenotype in two unrelated patients with a partial deletion of 21q22.2-q22.3 defined by FISH and molecular studies.

We describe two unrelated patients with cytogenetically visible deletions of 21q22.2-q22.3 and mild phenotypes. Both patients presented minor dysmorphic features including thin marfanoid build, facial asymmetry, downward-slanting palpebral fissures, depressed nasal bridge, small nose with bulbous tip, and mild mental retardation (MR). FISH and molecular studies indicated common deleted areas but different breakpoints. In patient 1, the breakpoint was fine mapped to a 5.2 kb interval between exon 5 and exon 8 of the ETS2 gene. The subtelomeric FISH probe was absent on one homologue 21 indicating a terminal deletion spanning approximately 7.9 Mb in size. In patient 2, the proximal breakpoint was determined to be 300-700 kb distal to ETS2, and the distal breakpoint 2.5-0.3 Mb from the 21q telomere, indicating an interstitial deletion sized approximately 4.7-7.3 Mb. The 21q- syndrome is rare and typically associated with a severe phenotype, but different outcomes depending on the size and location of the deleted area have been reported. Our data show that monosomy 21q of the area distal to the ETS2 gene, representing the terminal 7.9 Mb of 21q, may result in mild phenotypes comprising facial anomalies, thin marfanoid build, and mild MR, with or without signs of holoprosencephaly.

The cellular immune response of children is specifically decreased against their parents but not vice versa, independent of pregnancy, age, or HLA or HY antigens.

PROBLEM: The fetal immune response against the mother and the father is specifically altered. Up to now it is unclear whether the immune response between adult children and their parents is also specifically altered. METHODS: Seven female and seven male adults and five male and five female newborns and all their parents were enrolled in the study. Cyotoxicity, apoptosis and proliferation properties of the parents' lymphocytes were measured against those of their children and vice versa using two-way mixed lymphocyte cultures (MLCs). RESULTS: The immune response of adult children against both their parents is reproducibly decreased compared with that of both parents against their children in cytotoxicity, apoptosis and proliferation, independent of sex or age. CONCLUSION: The cellular immune response of children is decreased against both their parents but not vice versa independent of pregnancy, age, or HLA or HY antigens. This might be acquired during pregnancy or genetically determined.

Neonatal lymphocytes dominate against lymphocytes of their own mother but not against allogenic maternal or adult lymphocytes in bidirectional mixed lymphocyte cultures.

OBJECTIVE: Recent studies have shown a regular prenatal transfer of maternal immunocompetent cells into the fetal circulation. However, these cells engraft and proliferate only in a few exceptional cases if the fetus reaches an immunocompetent state. Thus the fetus has to have an immunologic defense mechanism against the engraftment of maternal cells. In the current study we investigated whether the fetus has such an immune defense and whether this defense mechanism specifically attacks cells of the mother. PATIENTS, MATERIAL AND METHODS: Blood samples were obtained from 15 mothers and 15 newborns directly after delivery. We compared individual vitality and spontaneous cytotoxicity between fetal and maternal lymphocytes in a cell ratio of 1:1 in nonstimulated bidirectional mixed lymphocyte cultures (MLC). The distribution of each cell population within the MLC was visualized by fluorescence in situ hybridization and X/Y-DNA probes. This was compared to MLCs between unrelated fetal and maternal as well as between unrelated adult lymphocytes. RESULTS: After 72 h, a significant cell shift was observed only in the MLC with neonatal lymphocytes mixed with cells of their own mother; there was a significantly higher number of neonatal cells (0.71 vs. 0.29) present. All other groups continued to have a cell distribution of 1:1. CONCLUSION: Our results show that neonatal lymphocytes specifically dominate against maternal but not allogenous maternal or adult lymphocytes in nonstimulated bidirectional MLCs.

Differentiation of single populations in a bidirectional mixed lymphocyte culture using X and Y chromosome-specific FiSH markers.

OBJECTIVE: To validate a new combination of a viability assay and Fluorescence in Situ Hybridsation (FiSH) techniques using X- or Y-DNA probes to assay the viability of each single population within bidirectional mixed lymphocyte cultures (MLCs). STUDY DESIGN: We determined the absolute viable lymphocyte counts of each population in bidirectional maternal-fetal MLCs as well as in bidirectional MLCs between male and female unrelated adults using a combination of a viability assay and additional sex discrimination by FiSH, and compared the results with the classical tritiated thymidine incorporation assay and with sex discrimination by metaphase number. RESULTS: The results of the total viability assay correlated with those of the tritiated thymidine incorporation assay. The differentiation of each single population by FiSH showed, as in the metaphase assay, that the relationship between viable maternal and neonatal cells was shifted significantly (p<0.05) towards the neonatal cells, while the relationship of the viable cells in the MLCs between unrelated adults was balanced. CONCLUSION: Our results show that X/Y discrimination by FiSH would be a useful tool for analyzing the immunologic network by bidirectional MLCs. The main advantage over sex discrimination by metaphase counting is that not only the proliferating cells but all viable cells are taken into account. An additional aspect would be the possibility to sort the cells according to surface markers (e.g. CD8+ HLA DR+) before discrimination by X and Y chromosomes.