Biosynthesis of heme in leukemic leukocytes

A deep profile of gene expression across 18 human cancers

Clinically and biologically valuable information may reside untapped in large cancer gene expression data sets. Deep unsupervised learning has the potential to extract this information with unprecedented efficacy but has thus far been hampered by a lack of biological interpretability and robustness. Here, we present DeepProfile, a comprehensive framework that addresses current challenges in applying unsupervised deep learning to gene expression profiles. We use DeepProfile to learn low-dimensional latent spaces for 18 human cancers from 50,211 transcriptomes. DeepProfile outperforms existing dimensionality reduction methods with respect to biological interpretability. Using DeepProfile interpretability methods, we show that genes that are universally important in defining the latent spaces across all cancer types control immune cell activation, while cancer type-specific genes and pathways define molecular disease subtypes. By linking DeepProfile latent variables to secondary tumor characteristics, we discover that tumor mutation burden is closely associated with the expression of cell cycle-related genes. DNA mismatch repair and MHC class II antigen presentation pathway expression, on the other hand, are consistently associated with patient survival. We validate these results through Kaplan-Meier analyses and nominate tumor-associated macrophages as an important source of survival-correlated MHC class II transcripts. Our results illustrate the power of unsupervised deep learning for discovery of novel cancer biology from existing gene expression data.

Upregulated heme biosynthesis, an exploitable vulnerability in MYCN-driven leukemogenesis

The increased heme biosynthesis long observed in leukemia was previously of unknown significance. Heme, synthesized from porphyrin precursors, plays a central role in oxygen metabolism and mitochondrial function, yet little is known about its role in leukemogenesis. Here, we show increased expression of heme biosynthetic genes, including UROD, only in pediatric AML samples that have high MYCN expression. High expression of both UROD and MYCN predicts poor overall survival and unfavorable outcomes in adult AML. Murine leukemic progenitors derived from hematopoietic progenitor cells (HPCs) overexpressing a MYCN cDNA (MYCN-HPCs) require heme/porphyrin biosynthesis, accompanied by increased oxygen consumption, to fully engage in self-renewal and oncogenic transformation. Blocking heme biosynthesis reduced mitochondrial oxygen consumption and markedly suppressed self-renewal. Leukemic progenitors rely on balanced production of heme and heme intermediates, the porphyrins. Porphyrin homeostasis is required because absence of the porphyrin exporter, ABCG2, increased death of leukemic progenitors in vitro and prolonged the survival of mice transplanted with Abcg2-KO MYCN-HPCs. Pediatric AML patients with elevated MYCN mRNA display strong activation of TP53 target genes. Abcg2-KO MYCN-HPCs were rescued from porphyrin toxicity by p53 loss. This vulnerability was exploited to show that treatment with a porphyrin precursor, coupled with the absence of ABCG2, blocked MYCN-driven leukemogenesis in vivo, thereby demonstrating that porphyrin homeostasis is a pathway crucial to MYCN leukemogenesis.

Porphyria cutanea tarda and hematologic malignancy--a report of 4 cases

Porphyria cutanea tarda has been reported in association with a variety of myeloproliferative and lymphoproliferative disorders, suggesting a possible association between these conditions. We describe four patients presenting within a 12 month period with sporadic porphyria cutanea tarda shortly following the diagnosis of hematologic malignancy. A review of the literature and evidence supportive of a causal association are presented.

Porphyrins, porphyrias, cancer and photodynamic therapy--a model for carcinogenesis

Porphyrins are the only and most powerful photosensitizers synthesized internally. To understand better the involvement of porphyrins in photosensitization reactions, the heme biosynthetic pathway is first described, as well as the main features of its regulation in both erythroid and hepatic cells. Most disorders of porphyrin metabolism, known as porphyrias, are characterized by porphyrin accumulation. A full discussion of these diseases, their classification and relevant biochemical and clinical signs are presented. Abnormalities in heme biosynthesis in disorders other than porphyrias, such as iron-deficient and sideroblastic anemias, lead poisoning, hereditary tyrosinemia, chronic renal disease and alcoholism, are briefly considered. A complete survey of the experimental research on the biosynthesis of porphyrins in tumors and of the important association between cancer and porphyrias is dealt with. The link to photodynamic therapy (PDT) emerges naturally and this is treated from the point of view of using porphyrins endogenously formed by the tumors for their localization and PDT. Finally, considering the nature of the alterations occurring in heme metabolism in tumors, and porphyrias and their ubiquity, a model is discussed where the abnormality of heme synthesis is involved in the initiating lesion of carcinogenesis. The model strongly predicts that the incidence of cancer will be high in cells with abnormal heme metabolism, suggesting that porphyric patients may be at greater risk of the development of cancer.

Measurement of 5-aminolevulinic acid synthase activity in whole and fractionated human bone marrow: effect of myeloid cell lysis by monoclonal antibody

A sensitive radiochemical assay for the measurement of bone marrow and erythroblast 5-aminolevulinic acid (ALA) synthase (EC 2.3.1.37) was developed and optimized with respect to sample preparation and reagent concentration. Succinylacetone (4,6-dioxoheptanoic acid) was used to prevent ALA utilization during the incubation period. Sample purification on a Sep-Pak cartridge (Waters Associates) followed by reverse-phase high-performance liquid chromatography (HPLC) allowed rapid isolation of pure ALA-pyrrole, free from radioactive succinate and other contaminants. ALA synthase activity was measured in unfractionated bone marrow and in samples from which myeloid cells had been removed by monoclonal antibody-mediated cell lysis. Myeloid-derived ALA synthase was calculated and found to contribute approximately half of the total unfractionated marrow enzyme activity. This suggests that results from previous studies using unfractionated bone marrow which have assumed that myeloid cells are an insignificant source of ALA synthase require reappraisal.

5-Aminolevulinic acid stimulation of porphyrin and hemoglobin synthesis by uninduced Friend erythroleukemic cells

Porphyrin synthesis and iron accumulation was stimulated by exogenous 5-aminolevulinic acid (ALA) in uninduced Friend erythroleukemic cells (FELC). Uroporphyrin and protoporphyrin were the major intermediated precursors produced. All porphyrin types were conjugated to protein insoluble cellular components and could be extracted only by methanol sulfuric acid esterification. Heme content of the uninduced FELC was increased 6-fold in the presence of 5 x 10(-4) M ALA. As a consequence, the synthesis of the minor murine hemoglobin component was preferentially induced, an effect similar to that expressed by exogenous hemin. Addition of exogenous ALA to 0.5% DMSO-induced cells increased total hemoglobin synthesis with a higher efficiency of the minor hemoglobin. The endogenous synthesis of porphyrin from exogenous ALA was markedly reduced by hemin. Uroporphyrin, coproporphyrin, protoporphyrin and heme were equally repressed, indicating an inhibitory effect of hemin on ALA dehydrase and urosynthetase activities. In addition, hemin repressed [3H]leucine incorporation into protein by uninduced cells. Incubation of uninduced cells in culture medium without serum in the presence of hemin blocked their protein synthesis activity, whereas addition of serum exerted a protective effect on living FELC.