The ubiquitous 'cancer mutational signature' 5 occurs specifically in cancers with deleted FHIT alleles

Abstract

The FHIT gene is located at the fragile FRA3B locus where activation by carcinogen-induced and endogenous replication stress causes FHIT deletions even in normal cells over a lifetime. Our lab has shown that loss of FHIT expression causes genome instability and provides single-strand DNA substrates for APOBEC3B hypermutation, in line with evidence that FHIT locus deletions occur in many cancers. Based on these biological features, we hypothesized that FHIT loss drives development of COSMIC mutational signature 5 and here provide evidence, including data mining of >6,500 TCGA samples, that FHIT is the cancer-associated gene with copy number alterations correlating most significantly with signature 5 mutation rate. In addition, tissues of Fhit-deficient mice exhibit a mutational signature strongly resembling signature 5 (cosine similarity value = 0.89). We conclude that FHIT loss is a molecular determinant for signature 5 mutations, which occur in all cancer types early in cancer development, are clock-like, and accelerated by carcinogen exposure. Loss of FHIT caretaker function may be a predictive and preventive marker for cancer development.

Keywords: cancer genes; clock-like signatures; data mining; exome sequences; mutational signatures.

Figure 1. Fhit knockout mutational signature compared to signature 5 profiles

(A) Previously described mutational signatures from Fhit ko mouse kidney tissue total mutation profile adapted from Figure 3 of Paisie et al [20], human mutational signature 5 of Alexandrov et al [10], signature 5^* from Kim et al [21] that used a different algorithm to define mutational signatures. {Permissions: upper panel, Paisie et al (2016) under CC BY-NC 4.0 license (https://creativecommons.org/licenses/by-nc/4.0/legalcode); middle panel, adapted by permission from Macmillan Publishers Ltd: [Nature] Alexandrov et al. 2013; lower panel, adapted by permission from Macmillan Publishers Ltd: [Nature Genetics] Kim et al. 2016}. (B) The mutation spectra for Fhit-/- lung, kidney tissues, two -/- kidney cell lines, a totipotent and differentiated -/- ESC cell line, were assessed for mutational signatures using the SomaticSignatures algorithm [22]. The upper panel (tissue culture signature) shows a signature occurring primarily in the two kidney cell lines, with a distinctive peak of C to G SBSs at GCC trinucleotides; the lower panel (FHIT loss signature) shows a mutational signature dominated by C to T and T to C SBSs that may be the murine equivalent of the human signature 5 shown in panel A.

Figure 2. Fhit expression in Acute Myelogenous Leukemias, a cancer exhibiting only mutational signatures 1 and 5

(A) Immunoblot depicting loss of Fhit protein expression in 7 of 8 AML bone marrow samples (lanes 1-6, 8 & 9), positive control H1299 D1 cells with induced Fhit expression (lane 7). (B) Fhit expression in samples accessed through Genome Data Commons, depicting reduced FHIT RNA expression in 153 AMLs derived from bone marrow vs 50 kidney samples derived from normal tissue. Neither normal bone marrow nor matched peripheral white blood cell RNA was available for comparison.

Figure 3. Features of cells with FHIT loss (above circles), and specific mutational signatures (below circles)

Figure 4. The mutational signatures in smokers vs nonsmokers

An abbreviated copy of the “smoking signatures” from Figure 2 of ref 39 {from Alexandrov LB et al. 2016. Mutational signatures associated with tobacco smoking in human cancer. Science 354: 618-622. Reprinted with permission from AAAS}, to emphasize features of this signature that make FHIT loss a strong candidate as cause of mutational signature 5: (A) illustration of the mutation spectra in 25 randomly selected cancer genomes (individual bars from smokers or nonsmokers of a given cancer type). Each bar is colored proportionately to the number of mutations/Mb of the specific mutational signatures found in the sample genome. (B) The pattern of mutational signatures observed in tobacco smoker cancers.