Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer

Abstract

Metabolic remodeling is now widely regarded as a hallmark of cancer, but it is not clear whether individual metabolic strategies are frequently exploited by many tumours. Here we compare messenger RNA profiles of 1,454 metabolic enzymes across 1,981 tumours spanning 19 cancer types to identify enzymes that are consistently differentially expressed. Our meta-analysis recovers established targets of some of the most widely used chemotherapeutics, including dihydrofolate reductase, thymidylate synthase and ribonucleotide reductase, while also spotlighting new enzymes, such as the mitochondrial proline biosynthetic enzyme PYCR1. The highest scoring pathway is mitochondrial one-carbon metabolism and is centred on MTHFD2. MTHFD2 RNA and protein are markedly elevated in many cancers and correlated with poor survival in breast cancer. MTHFD2 is expressed in the developing embryo, but is absent in most healthy adult tissues, even those that are proliferating. Our study highlights the importance of mitochondrial compartmentalization of one-carbon metabolism in cancer and raises important therapeutic hypotheses.

Figure 1. Transcriptional regulation of metabolic pathways in human tumors

(a) Differential expression (Z-score) distributions for 51 tumor-vs-normal data sets representing 19 tumor types are shown as violin plots (gray). Dots indicate Z-score for MTHFD2 in each study; red color denotes significance at < 5% false discovery rate (FDR). (b) Distribution of meta-analysis scores for all 20,103 genes interrogated across the 51 data sets. Gene symbols indicated, see text for further description. (c) Metabolic pathways detected as strongly over-expressed (among top 50 metabolic enzymes; red gene symbols) or under-expressed (among bottom 50 metabolic enzymes; blue gene symbols) in tumors. (d) Schematic of one-carbon metabolism with over-expressed (red) and under-expressed (blue) genes indicated. Gray symbols, not measured. (e) Gene set enrichment analysis for the set of 35 embryonic metabolic enzymes compared against mRNAs for all enzymes.

Figure 2. MTHFD2 expression in transformed compared to normal proliferating cells

(a) mRNA expression levels in normal postmitotic (open bars), normal proliferating (black bars) and transformed cells or tissues (red bars) for MTHFD2 and four established cancer drug targets. Normal hematopoietic cell fractions with strong expression are indicated. (b) Quantile-quantile plot for the ratio of minimal expression among transformed cells to maximum expression among normal (proliferating and postmitotic) cells, defined as in (a), for each of the 12,529 human mRNAs measured. Randomized quantiles (X-axis) were obtained by permuting samples. MTHFD2 mRNA is indicated. (c) mRNA expression of human MTHFD2 or mouse Mthfd2 and four established cancer drug targets during mouse liver regeneration following partial hepatectomy (left); human fibroblasts proliferating in response to serum stimulation (center); and human CD4+ T lymphocytes activated by CD3 and CD28 antibodies (right). Red line indicates Mthfd2/MTHFD2. (d) mRNA expression of human MTHFD2 (left) and mouse Mthfd2 (right) during early embryonic development. Error bars denote standard deviation (n = 3). (e) mRNA expression of mouse Mthfd2 during embryonic development of liver (left) and hypothalamus (right). Error bars denote standard deviation (n = 2).

Figure 3. MTHFD2 protein expression in human tumors

(a) Top, fraction of samples with none, weak, moderate or strong immunohistochemistry staining for MTHFD2 in transformed cells, across 16 solid tumor types. Bottom, same analysis as above for stromal cells. For each tumor type, tumors from 9–12 individuals were examined. (b) Representative images from each of the 16 tumor types summarized in (a), exemplifying negative (N), weak (W), moderate (M) or strong (S) staining intensities. Up arrow, stromal cells; down arrow, cancer cells. Scale bars represent 100um.