- Research Article
- Open Access
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans
Infectious Agents and Cancer volume 14, Article number: 46 (2019)
Earlier we suggested a new hypothesis of the possible evolutionary role of hereditary tumors (Kozlov, Evolution by tumor Neofunctionalization, 2014), and described a new class of genes – tumor specifically expressed, evolutionarily novel (TSEEN) genes - that are predicted by this hypothesis (Kozlov, Infect Agents Cancer 11:34, 2016). In this paper we studied evolutionarily novel genes expressed in fish tumors after regression, as a model of evolving organs. As evolutionarily novel genes may not yet have organismal functions, we studied the acquisition of new gene functions by comparing fish evolutionarily novel genes with their human orthologs. We found that many genes involved in development of progressive traits in humans (lung, mammary gland, placenta, ventricular septum, etc.) originated in fish and are expressed in fish tumors and tumors after regression. These findings support a possible evolutionary role of hereditary tumors, and in particular the hypothesis of evolution by tumor neofunctionalization.
Earlier we described a new class of genes that are tumor-specifically expressed and evolutionarily novel (TSEEN). As the functions of TSEEN genes are often uncertain, we decided to study TSEEN genes of fishes so that we could trace the appearance of their new functions in higher vertebrates. We found that many human genes which are involved in development of progressive traits (placenta development, mammary gland and lung development etc.,) originated in fishes and are expressed in fish tumors.
We are interested in the possible role of tumors in evolution. In previous publications [22,23,24,25,26,27] the hypothesis of the possible evolutionary role of hereditary tumors was formulated. According to this hypothesis, hereditary tumors at earlier stages of progression, or benign tumors, were the source of extra cell masses which could be used during the evolution of multicellular organisms for the expression of evolutionarily novel genes, for the origin of new differentiated cell types with novel functions, and for building new structures that constitute evolutionary innovations and morphological novelties. Hereditary tumors could play an evolutionary role by providing conditions (space and resources) for the expression of genes that have newly-arisen in the germline. As a result of the expression of such novel genes, tumor cells may acquire new functions and differentiate in new directions, which might in turn lead to the origin of new cell types, tissues and organs .
This hypothesis makes several nontrivial predictions. One prediction is that tumors could be beneficial to the organism by performing new functional roles. This prediction was addressed in previous work [26, 29], where it was shown that the «hoods» of some varieties of gold fishes such as Lionhead, Oranda, etc. are benign tumors. These tumors have been selected by breeders for hundreds of years until they eventually formed new organ, the «hood». The origin of simbiovilly in voles is the result of natural selection of early papillomatosis (Vorontsov, 2003), and the origin of macromelanophores in swordtails is the result of sexual selection . These examples were discussed in detail in . They support the prediction about the possibility of selection of hereditary tumors for new organismal functions.
Another prediction of the hypothesis is that evolutionarily young and novel genes should often be specifically (or preferentially) expressed in tumors. This prediction was verified in a number of papers from our laboratory ([6, 20, 28, 30, 40,41,42, 44]; Dobyunin et al., 2013 ;). We have described several evolutionarily young and novel genes with tumor-predominant or tumor-specific expression in humans, and even the evolutionary novelty of an entire class of genes – cancer/testis genes – which includes evolutionary young and novel genes expressed predominantly in tumors (reviewed in ).
The functional role of evolutionarily novel genes is often uncertain. Therefore, we were further interested in studying evolutionarily novel genes of fishes, so that we could trace the evolutionary trajectory of the appearance of their new functions in higher vertebrates. Our hypothesis predicts that some fish TSEEN genes should have acquired functions that determine progressive traits during evolution in higher vertebrates including humans. In the present study, we have used the transgenic inducible hepatoma model in zebrafish described earlier , because we suppose that transgenic tumors, after regression, may be an approximation to an evolving organ. So, we studied evolutionarily novel genes in fish, that are expressed both in tumors and in tumors after regression.
Materials and methods
Transgenic inducible hepatoma model
The krasV12-induced tumor progression was conducted on 100 transgenic zebrafish fishes maintained in water containing 2 μM mifepristone. Fishes were treated at age of reproduction, more than 2 month pf (post fertilization), between 4 and 6 month old. All experimental zebrafish can be described as siblings, as progeny of single pair of parents. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular carcinoma within 4 weeks of induction. Observation of tumor development and hepatocellular carcinoma staging of tumorigenesis was conducted as described .
For tumor regression the group of 15 fishes with hepatocellular carcinoma stage (according to ) was transferred to mifepristone-free water. Gross observation revealed shrinkage of tumor and dissappearence of GFP. Notably, complete tumor regression with scarred fibrosis of the former tumor tissue was observed after 4 weeks of mifepristone withdrawal.
Liver tumors from mifipristone induced transgenic fishes with hepatocellular carcinoma, livers after tumor regression (from fishes after mifepristone withdrawal) and normal livers from non-induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.
RNA sequencing and sequence data analysis
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and treated with DNase I to remove genomic DNA contamination. mRNA was purified using Dynabeads Oligo (dT) EcoP (Invitrogen) and subjected to cDNA synthesis. Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA-SAGE (serial analysis of gene expression) sequencing was performed on ABI SOLiD platform by Mission Biotech (Taiwan) according to manufacturer’s protocol and 10–23 million reads were generated from each sample (Additional files 1, 2, 3). The tags were mapped to the NCBI RefSeq (Reference Sequence)  mRNA database for zebrafish with a criterion of maximum 2 nucleotide mismatches.
All RNA-Seq data were submitted to Gene Expression Omnibus database  and are accessible through GEO Series accession number GSE93965.
Tag counts for each transcript were normalized to TPM (transcripts per million) to facilitate comparison among different samples.
Transcriptome coverage estimation
In order to estimate RNA-Seq sensitivity we chose several housekeeping genes with known expression level in normal liver. The list of these genes is presented in Additional file 4. Relative copy number value was studied for each these genes. For further transcriptome analysis we chose gluconeogenesis metabolic pathway (15 genes according to GO,0006094; GO:0006111; GO:0035948; GO:0045722; GO:0045721).
Selection of genes activated in tumors and expressed after regression
After RNA deep sequencing the lists of transcripts in control, tumor and regressed tumor samples (the original data after raw Blast from the company) were analyzed.
We manually selected genes which were expressed in liver carcinomas and in liver after regression of tumors but not in normal liver.
The search of orthologs
Danio rerio genome was retrieved from Danio rerio genome sequencing project (GRCz10). GRCz10 (Genome Reference Consortium Zebrafish Build 10, INSDC Assembly GCA_000002035.3, Sep 2014).
For the search of orthologs we chose the following genomes: lamprey (Petromyzon marinus, Pmarinus_7.0); spotted gar (LepOcu1, Lepisosteus oculatus), atlantic cod (gadMor1, Gadus morhua); clawed frog (JGI 4.2, Xenopus tropicalis); human (GRCh38, Homo sapiens).
These genomes were downloaded via ensembl ftp browser, the command line used are presented in the Supplementary text.
For the search of orthologs we used BLAST command line applications developed at the National Center for Biotechnology Information (NCBI). We required to run BLAST locally and to support automatic resolution of sequence identifiers . Documentation about this procedure can be found in ftp://ftp.ncbi.nlm.nih.gov/blast/db/README.
The blastx, and psiblast were considered search applications, as they execute the BLAST search .
We ran NCBI’s blastx alignment search for all nucleotide sequences of the coding regions of our genes from the sample against Nucleotide database of genomes chosen above. The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB.
We ran NCBI’s psiblast comparisons of all proteins encoded by annotated genes of our sample against all the proteins encoded by genes annotated in any chosen genome, with a E-value threshold of 1 × 10 − 3.
For any further consideration, we also required the coverage of at least 25% of any of the protein sequences in the alignments.
We imported the output of blastx and psiblast into a MySQL database where we filtered the matches to sequences with alignment coverage more then 25% and E-value below the chosen cut off (1 × 10 − 3). The final E-value 1 × 10− 3 cutoff value was based on our analysis of the single genes from our sample as a compromise between specificity and sensitivity. Orthology data from EnsemblCompara resource  were loaded into the same MySQL database. The final results of the search of orthologs were annotated via SQL queries by joining tables using ensembl Gene ID, Additional file 23.
OMA («orthologous matrix»)
As an alternative method for seeking orthologs we used OMA (Orthologous MAtrix) for large-scale orthology inference . The advantages of this approach are the use of evolutionary distances instead of BLAST scores, consideration of distance inference uncertainty, including many-to-many orthologous relations, and accounting for differential gene losses. In our search we used the following genomes: elephant shark (Callorhinchus_milii-6.1.3, Callorhinchus milii), common carp (ASM127010v1, Cyprinus carpio), tunicate (KH, Ciona intestinalis), atlantic herring (ASM96633v1, Clupea harengus), coelacanth (latCha1, Latimeria chalumnae), lamprey (Petromyzon marinus, Pmarinus_7.0), Hagfish (Eptatretus burger, Eburgeri_3.2 (GCA_900186335.2)), spotted gar (LepOcu1, Lepisosteus oculatus), red-bellied piranha (Pygocentrus_nattereri-1.0.2, Pygocentrus nattereri), whale shark (ASM164234v2, Rhincodon typus); atlantic salmon (ASM23337v1, Salmo salar), asian bonytongue (ASM162426v1, Scleropages formosus), chimpanzee (Pan_tro 3.0, Pan troglodytes), orangutan (Susie_PABv2, Pongo abelii), platypus (Ornithorhynchus_anatinus-5.0.1, Ornithorhynchus anatinus), opossum (MonDom5, Monodelphis domestica), mouse (GRCm38.p6, Mus musculus), rat (Rnor_6.0, Rattus norvegicus), sea urchin (Spur_4.2, Strongylocentrotus purpuratus), clawed frog (Xenopus_tropicalis_v9.1, Xenopus tropicalis), yeast (Sc_YJM993_v1, Saccharomyces cerevisiae) and human (GRCh38, Homo sapiens).
The panels from various normal human tissues containing a set of normalized single-strand cDNA, produced from poly(A) + RNA were obtained from Clontech, USA. We used the following panels: Human MTC™ Panel I (Cat. no. 636742), Human MTC™ Panel 2 (Cat. no. 637643), Human Fetal MTC™ Panel (Cat. no. 636747). According to the manufacturer’s information, the panels were free from genomic DNA and were normalized to expression levels of four house-keeping genes. According to the manufacturer’s information, each cDNA sample comes from a pool of tissue samples obtained from donors of different age and sex, with 2–550 donors in each pool, and the fetal tissue samples were obtained from spontaneously aborted fetuses at 18 to 36 weeks of gestational age. The relevant ethics statement is available from manufacturer’s website: Takara Bio Inc., USA.
A cDNA panel from human tumors containing a total of 10 of cDNA samples were obtained from BioChain Instutute, USA (Cat. nos. C1235035–10, C1235086, C1235090, C1235142, C1235152, C1235183–10, C1235188–10, C1235201–10, C1235248, C1235274). The samples were produced by the manufacturer from various human tumors obtained by surgerical resection. Each sample came from one patient and was histologically characterized. cDNA was produced from poly(A) + mRNA that was free from genomic DNA and normalized by b-actin gene expression level. The relevant ethics statement is available from manufacturer’s website: BioChain Institute Inc., USA.
Zebrafish normal liver and cancers tissues
Zebrafish were maintained according to established protocols . All experimental procedures with fishes, such as gross observation and sampling of materials were carried out in accordance with regulations of institutional ethical committee.
Each sample from zebrafish was histologically characterized. We used tissues of spontaneous hepatocellular carcinoma and spermatocytic seminoma, and pooled samples of normal liver from 4 to 5 fishes.
RNA purification and cDNA synthesis for gene expression experiments
The total RNA from fish liver and tumor samples was extracted using TRIzol Reagent (Invitrogen, USA) following the standard protocol. The isolated RNA had an A260/280 ratio of ≥1.7 when diluted into distilled water. Ethidium bromide staining of RNA in agarose gels visualizes two predominant bands of small and large ribosomal RNA, a bands of low molecular mass RNA.
cDNA synthesis was performed from equal amounts of RNA using Revert Aid® First Strand cDNA Synthesis Kit (Thermo, USA) with random hexanucleotide, following the manufacturer guidelines. The obtained cDNA was stored at − 20 °C.
The PCR mixture contained 2.5 μl of cDNA, PCR-buffer (67 mMTris-HCl, pH 8.9, 4 mM MgCl2, 16 mM (NH4)2SO4, 10 mM 2-mercaptoetanol), 200 μM dNTP, 1 unit of Taq DNA polymerase (Fermentas, Lithuania), and 10 pmol of forward and reverse primers in a total of 25-μl reaction. Amplification was performed in a thermal cycler C1000TM Thermal Cycler, Bio-Rad, USA.
All primers targeting zebrafish genes were chosen to cross exon-intron junctions in order to avoid amplifying genomic DNA. The following PCR conditions were used: 3 min at 95 °C; 35 cycles consisting of 30 s at 95 °C, 30 s at 58 °C, 30 s at 72 °C; and final elongation at 72 °C for 5 min. We used zebrafish gapdh gene primers as a positive control for gene expression. Primer sequences used for PCR and the expected size of amplicons are included in Additional file 7.
Primer sequences for experimental studies of expression of human orthologs of fish TSEEN genes in cDNA panels from human normal tissues and the expected size of amplicons are included in Table of Additional file 7. Amplification was performed with the following conditions: 3 min at 95 °C; 35 cycles consisting of 30 s at 95 °C, 30 s at 58 °C, 30 s at 72 °C; and final elongation at 72 °C for 5 min. We used human GAPDH gene primers as a positive control for gene expression; the following PCR conditions were used 3 min at 95 °C; 30 cycles consisting of 30 s at 95 °C, 30 s at 68 °C, 1 min at 72 °C; and final elongation at 72 °C for 5 min. The expected size of the GAPDH – specific product was 983 bp.
All PCR products were analyzed by electrophoresis in 1.8% agarose gel and detected by staining with ethidium bromide. The results of electrophoresis are presented as truncated images of gels.
The study of gene expression in normal zebrafish tissues treated with mifepristone
In order to exclude the possible gene expression activation by mifepristone, 20 to 50 fishes were treated at 5 mkM of mifepristone for 5 days. In 5 day old fishes the liver is already developed.
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) and treated with DNase (QIAGEN) in accordance with the manufacturer’s instructions. 2 μg of total RNA was reverse transcribed using RevertAid First Strand cDNA Synthesis Kit (Thermo ScientificTM) and 50–70 ng cDNA were used in triplicate for qPCR. Quantitative real-time PCR reactions were performed with the SYBER Green (KAPA Biosystem) in MicroAmp Optical 96-well plates using a StepOnePlus System (Applied Biosystems). See Additional file 15 for a complete list of qRT-PCR primer sequences used in this study.
Functional annotation was accomplished with the help of the Gene Ontology tool . GO annotation for genes from our samples were retrieved from EnsemblBiomart resource (Ensembl 89: May 2017) and stored in MySQL database. Several tables were created, depending on evolutionary novelty of genes and GO evidence codes (Additional files 9, 10, 11 and 12).
The Experimental Evidence codes are the following: inferred from experiment (EXP), inferred from direct assay (IDA), inferred from physical interaction (IPI), inferred from mutant phenotype (IMP), inferred from genetic interaction (IGI), inferred from expression pattern (IEP).
In order to estimate the GO enrichment of human orthologs of fish TSEEN genes GeneOntology enrichment analysis and visualization tool was used [33, 45]. As a background we used a list of all human genes.
After filtering against multiple hits for tagged sequences and re-annotation, Additional file 1 contains the list of 16,083 normal liver transcripts and their descriptions, Additional file 2– the list of 14,334 carcinoma transcripts and their description, Additional file 3– the list of 8812 transcripts expressed in liver after tumor regression. Transcriptome normalization was made by housekeeping gene transcripts abundance estimation, Additional file 4, based on the measured transcript levels of all genes involved in gluconeogenesis metabolic pathway (15 genes according to GO:0006094; GO:0006111; GO:0035948; GO:0045722; GO:0045721).
By comparison of the results of deep sequencing of RNA from normal liver, liver tumor and liver after tumor regression we manually selected a sample of 1502 genes which were activated in tumors and expressed after tumor regression, as described in materials and methods (Fig. 1 and Additional file 5).
From these 1502 genes, we selected 870 genes that had stable Ensembl gene IDs (Fig. 1). Among these 870 genes with the Ensembl gene IDs, 868 are protein coding, 1 is a polymorphic pseudogene and 1 is a lncRNA not present in control liver tissues (Additional file 6).
We sought orthologs for the set of 870 genes in 5 genomes of different species, which were selected relative to the phylogenetic position of zebrafish. We estimated the number of genes that have orthologs in the chosen genomes using three algorithms, based both on blast alignments and tree construction (cut off e-value < 10− 3 and matching > 25% of the total protein length) (Table 1). Among the 870 genes with Ensembl gene IDs, 461 had lamprey orthologs, and 409 had no lamprey orthologs (Fig. 1). We defined the 409 genes with no orthologs in genomes of lamprey as evolutionarily novel to fishes. These genes are tumor and tumor-after-regression expressed, evolutionarily novel (TTRgrEEN) genes.
In order to confirm the evolutionary novelty of fish TTRgrEEN genes we used an alternative ortholog search method, OMA (see Materials and Methods). Using this method, we detected 680 evolutionarily-novel genes in the sample of 870 fish genes expressed in tumors after regression. Of 409 Ensembl TTRgrEEN genes, OMA confirmed 306 genes. OMA also confirmed all genes in Table 3 (see below).
To experimentally confirm the tumor-specific expression of some fish TTRgrEEN genes identified as described above, we selected 12 genes from Table 3, 2 from Table 4 and 9 from the confirmed set of 306 TTRgrEEN genes, and performed PCR with primers specific for these genes on cDNA from zebrafish normal and tumor tissues (Additional file 7). Histological data for fish tumor tissues are presented in Additional file 8. For 12 fish genes this analysis showed no or low expression in normal fish liver and increased expression in fish tumor tissues (Fig. 2), confirming the tumor-specific expression aspect of their TSEEN nature. For 7 other analyzed genes, overexpression in tumor tissues was detected (Fig. 3).
In order to study the possible evolutionary appearance of new functions for the novel fish genes, we looked for human orthologs of the zebrafish Ensembl TTRgrEEN genes, and found that the 296 fish TTRgrEEN genes have 343 human orthologs, and that the remaining 113 fish Ensembl TTRgrEEN genes have no human orthologs (Fig. 1). Hence, of 409 fish tumor-activated genes with no lamprey orthologs 296 (72.4%) have human orthologs (Fig. 1). Of the total 22,897 novel fish genes, as compared to lamprey, only 8230 (35.9%) are conserved in humans.
To estimate the possible functions of zebrafish TTRgrEEN genes and their human orthologs, we used the Gene Ontology (GO) approach (Additional files 9, 10, 11 and 12 and Table 2). Gene samples studied by GO are those represented in Fig. 1. Additional file 9 contains gene ontology annotation with all evidence codes for all 870 tumor-activated fish genes with Ensemble IDs. Additional file 10 contains gene ontology annotation with all evidence codes for the 296 fish TTRgrEEN genes with human orthologs. Additional file 11 contains gene ontology annotation with all evidence codes for 343 human orthologs of the 296 fish TTRgrEEN genes. Gene ontology annotation for the 113 fish TTRgrEEN genes without human orthologs is in the Additional file 12.
GO functions are grouped in Table 2 as genes involved in developmental processes, genes involved in transcription, genes involved in different signaling pathways, and genes involved in the immune system. As we see from Table 2, fish TTRgrEEN genes have fewer corresponding annotated functions than their human orthologs. The increase of the number of gene function annotations for human orthologs is especially evident for functions involved in developmental process and immune system, as compared to transcription regulation and signaling pathways (Additional file 13 contains full version of the Table 2). Some of 296 fish TTRgrEEN genes have annotated functions of DNA binding, sequence specific DNA binding and regulation of DNA-templated transcription. Their human orthologs, in addition to the above mentioned functions, have annotated functions of anatomical structure development, anatomical structure involved in morphogenesis, and development of particular cell types and organs.
Statistical analysis of the GO enrichment analysis of human orthologs of fish TTRgrEEN genes was made with the PANTHER13.1 functional clustering tool . As a background we used all human genes. Results are presented in Additional file 14. We discovered enriched functional-related morphogenetic gene groups, e.g. in anatomical structure development (Fold enrichment: 19,360, raw P-value 1.93х10− 7) and system development (Fold enrichment: 21,916, raw P-value 3.02х10− 7) (Additional file 14).
Among 343 human orthologs of fish TTRgrEEN genes, we found genes with functions that constitute progressive traits evolved on the way to humans, which do not exist in fish (Table 3), e.g., genes of lung development, mammary gland development, mammalian placenta development, ventricular septum development, etc.
To exclude the possibility of activation of the expression of 12 genes from Table 3 by mifepristone (which was used to induce tumorigenesis in our transgenic model), normal (non-transgenic) zebrafishes were treated with 5 υM mifepristone for 5 days, and their total RNA was studied in qPCR with specific primers. The results are presented in Additional file 16. From the presented data it is evident that mifepristone does not stimulate the expression of these genes in normal, nontransgenic fishes.
We experimentally verified the expression of several human genes from Table 3 (i.e. those which were selected both by Ensembl and OMA) in normal human tissues. We detected the expression of human gene LEP, the function of which is connected with the human placenta according to GO, in human placenta. Likewise, human gene NR2E1, the function of which is connected with brain according to GO, is expressed in brain and fetal brain tissue. LMX1B is expressed in placenta in accordance with GO (Fig. 4). On the contrary, LEP and NR2E1 genes have little or no expression in human tumors (Fig. 5).
The hypothesis of the possible evolutionary role of tumors was recently published by A.P. Kozlov («Evolution by Tumor Neofunctionalization», ). According to this hypothesis, heritable tumors at earlier stages of progression, or heritable benign tumors may play an evolutionary role by providing extra cell masses that allow or promote the expression of evolutionarily-novel genes and can contribute to the origin of new cell types, tissues and organs. It is presumed that novel genes originate in the germline, not in tumor cells, that is why the new cell type is inherited in progeny generations. In this theory tumors are considered as search engines for expression of evolutionary novel and evolving genes, and of new combinations of genes [25, 26].
Tumors have features that could be used in evolution. Tumors are excessive cell masses which are functionally not necessary to the organism. Many unusual genes and gene combinations are activated in tumors. Tumors may differentiate with the loss of malignancy and have morphogenetic potential.
Many tumors never kill their hosts. Benign tumors are widespread in nature, and the available data suggest that tumors are represented throughout phylogenetic tree. Tumors may also be selected at earlier stages of progression for organismal functions. The list of tumors which could be used in evolution, discussed in , includes fetal, neonatal and infantile tumors; carcinomas in situ and pseudodiseases; tumors that spontaneously regress, and sustainable tumor masses. Examples of tumors that have played roles in evolution include eutherian placenta, the hoods of goldfishes, root nodules in legumes, symbiovilli of voles, macromelanophores of Xiphophorus fishes, head outgrowths in hardosaurs and prepupal horn primordia in beetles. These and other examples have been discussed in , and the list of such examples may be continued.
The widespread occurrence of tumors (discussed in  and in subsequent reviews [2, 3]); the hereditary nature of many tumors; the evidence that considerable proportion of tumors never kill their hosts; the features of tumors that could be used in evolution; and the presence of common features of tumors that are shared with embryonic development – all this evidence suggests that hereditary tumors could play positive role in evolution of host organisms, like mutational process did.
Tumors may be considered as atypical organs: they consist of parenchyma and stroma, they have vasculature and a hierarchy of cancer stem cells and more differentiated cells . Hence, we have suggested that atypical tumor organs could evolve to normal organs in the course of progressive evolution .
The model of transgenic inducible fish hepatoma can be considered as an approximate model of an evolving organ, because the tumor scar after regression contains parenchyma cells different from normal liver parenchyma and stromal cells . Thus we consider liver after tumor regression as a model of a «new» evolving organ. Such consideration is supported by a recent publication  that showed reversion of tumor hepatocytes to normal hepatocytes, although with somewhat different properties, during liver tumor regression in an oncogene transgenic zebrafish model. That is why we performed a study of expression of evolutionary novel genes in transgenic zebrafish tumors after their regression in experimental conditions.
RNA deep sequencing analysis demonstrated that at least 1502 genes not expressed in normal liver are expressed in liver cells after tumor regression. Annotations of 870 of these 1502 genes are found in the Ensembl database. The search for lamprey orthologs of these genes, by three different approaches, demonstrated that many of them may have no lamprey orthologs, implying that they are relatively evolutionarily-novel in fish (Table 1 and Fig. 1). Thus, based on Ensembl, there are 409 zebrafish tumor-activated genes without lamprey orthologs. These are tumor and tumor after regression expressed, evolutionarily novel (TTRgrEEN) genes.
We understand that comparison only with the lamprey genome has its limitations, because lamprey may have lost some genes, which were present in other ancestral species. For example, tapt1a gene is lost in lamprey genome but present in other genomes (ascidian Ciona savignyi, Ciona intestinalis etc.) and may be considered as evolutionary conserved. However, after substraction this gene was in the list of 409 zebrafish genes without lamprey homologs and therefore could be classified as novel for fishes as compared to lamprey. This is an example of a gene with complex evolutionary history which may not have a single well defined age . That is why we also used another method of estimation of gene orthology, OMA (Orthologous MAtrix). This method uses a reciprocal best hit approach and determines evolutionary distances instead of scores. It also considers the uncertainty of distance inference, includes many-to-many orthologous relations, and accounts the differential gene loss. Using OMA, we obtained a larger number of fish TTRgrEEN genes (680) from the sample of 870 fish genes expressed in fish tumors after regression. This is probably because direct alignment, which determined the ortholog in the lamprey genome, was not confirmed by reverse alignment, which determined the reciprocal homology in the fish genome. That decreased the number of orthologs in lamprey genome and increased the number of TTRgrEEN genes, even though OMA operated with several genomes, not only lamprey genome (Additional file 17). According to Ensembl Genes 90 Zebrafish genes (GrCz11), there are 35,117 genes in zebrafish genome. Straightforward comparison with the lamprey genome qualifies 23,308 genes as evolutionary-novel, using this as the only criterion. Such a big proportion of evolutionary-novel (compared to lamprey) genes may be explained by the whole genome duplications that occurred in fishes .
We found that 296 of 409 zebrafish TTRgrEEN genes have 343 human orthologs. The other 113 fish genes have no human orthologs, i.e. either were lost during evolution or appeared after divergence of the ancestors of fishes and humans. The fact that the number of human orthologs is greater than that of the 296 zebrafish genes is due to origin of additional genes by gene duplication, as shown by the gene gain/loss trees in Ensembl . More fish TTRgrEEN genes (72.37%) are conserved in humans vs. all evolutionary-novel zebrafish genes (35.94%), P-value X2 test: 6.47х10− 52. This may indicate the importance of expression in tumors for selection and conservation of novel genes. This is in accordance with positive selection of many human tumor-related genes in primate lineage (reviewed in [25, 26]).
Gene Ontology analysis of the 296 fish TTRgrEEN genes with human orthologs shows much fewer number of morphogenetic/developmental, immunological and other annotated functions of those genes in the fish as compared to corresponding human genes (total 1813 annotated fish functions vs. total 6300 annotated human functions, Table 2). The 296 fish TTRgrEEN genes with human orthologs may represent proto-genes which acquire additional functions during the evolution of higher vertebrates. Proto-genes are considered as gene precursors which have not acquired functions yet . Since the increase of the number of annotated gene functions in human orthologs is especially evident for functions involved in developmental process and immune system, as compared to transcription regulation and signaling pathways, we may conclude that evolution of fish proto-gene functions in higher vertebrates involved more organismic than molecular functions.
GO enrichment analysis of human orthologs of fish TTRgrEEN genes also showed functional themes involved in development, i.e. anatomical structure development and system development (Additional file 14).
Protein kinase, DNA binding and transcriptional regulation functions are all highly represented among fish TTRgrEEN genes (Table 2). It is known that protein kinase, DNA binding and transcriptional regulation domains are the most common domains encoded by cancer genes [8, 19]. Thus, the original functions of many fish proto-genes and of some of their human orthologs could be related to carcinogenesis. Human orthologs of fish TTRgrEEN genes include oncogenes (12 as determined using COSMIC database and 6 using TSG database ) and tumor suppressor genes (35 found in TSG database and 2 in TAG database ).
The acquisition of new progressive functions by fish proto-genes in non-fish vertebrates is supported by finding that human orthologs of some of fish TTRgrEEN genes are involved in development of traits which do not exist in fish, such as mammalian placental development, ovulation from ovarian follicle, lung development, mammary gland development, cerebral cortex development, and ventricular septum development (Tables 3 and 4). These additional functions may have been added to a smaller set of original functions of fish proto-genes in the course of evolution, and may be related to original functions of DNA binding, transcription regulation and protein kinase activity.
The fish tgfbr2b (transforming growth factor beta receptor 2b) gene illustrates the addition of progressive functions in higher vertebrates (Additional file 18). TGFß receptors are serine/threonine kinases that activate transcription factors. In metazoans, the transforming growth factor ß (TGFß) receptor family is the only class of receptors with intrinsic serine/ threonine kinase activity. The TGFß receptors bind to ligands such as TGFß, activin, bone morphogenetic proteins (BMPs), and nodal that regulate developmental cell fate and proliferation. In humans, there are ~ 12 distinct receptors in TGFß family, which can be functionally divided into two classes (type I and type II). All have a similar overall structure, with a single membrane-spanning domain and an intracellular serine/threonine kinase domain . In fishes, tgfbr2b has protein kinase activity and few other molecular and cellular functions (Additional file 18). In humans, among many developmental and morphogenetic functions, this gene acquired functions in lung, mammary gland and ventricular septum development, not encountered in fishes (Table 3 and Additional file 18).
Fishes lack ventricular septation. It evolved independently in mammals and in birds and crocodilians . The origin of the right ventricle of the vertebrate heart needed, besides duplication of Hand gene, the recruitment of a novel population of precursor cells instead of the simple expansion of pre-existing precursor cells . There are two heart fields with progenitor cells that participate in building the mammalian heart . The Tgfß – Smad signaling pathway specifies the anterior heart field which forms the right ventricle of the heart and outflow tract where specialized expression of Hand 2 takes place . Interestingly, TGFß mediates tumor suppression in normal cells and facilitates cancer progression in malignant cells .
The other examples are nr2e1, mycn, fosl1a and dazap1 genes. In fishes, GO determines only molecular functions of DNA binding, DNA binding transcription factor activity, regulation of transcription (DNA tempated or from RNA polymerase II promoter), nucleic acid binding and RNA binding (Additional files 19, 20, 21, 22). In humans, NR2E1, MYCN, FOSL1 and DAZAP1 acquired additional functions connected with differentiation and development, including cerebral cortex development, lung development, placenta blood vessel development and maternal placenta development (Table 3 and Additional files 19, 20, 21, 22). MYCN and FOSL1 are known as cellular oncogenes [7, 47].
It was already mentioned above that domains involved in DNA binding, transcriptional regulation and protein kinase activity are among most common domains that are encoded by cancer genes . The addition of novel progressive functions may balance the original oncogenic potential of fish TSEEN proto-genes. The similar situation – that some evolutionarily novel genes appear to promote tumorigenesis while evolving new advantageous functions – was described by other authors . Evolution of new advantageous function may bring negative effects for survival of organisms, as discussed in recent selection, pleiotropy and compensation hypothesis (SPC) .
Tumor specificity of expression in Danio rerio was experimentally confirmed in vitro for lepa, nr2e1, lmx1b, sobpa and ccdc40 fish genes from Table 3. The expression of their human orthologs from Table 3 (LEP, NR2E1, LMX1B, SOBP and CCDC40) was experimentally confirmed in normal human organs, which have no analogs in fish. For LEP and NR2E1 little or no expression in human tumors is experimentally confirmed. Thus at least some human orthologs of fish TTRgrEEN genes acquire progressive functions, are expressed in normal human tissues and not expressed in human tumors.
According to the GO database, the majority of progressive traits of the genes we studied were inferred from their mutant phenotypes. As far as progressive traits listed in Tables 3 and 4 do not exist in fishes, we may be sure that they will never be discovered in fish TTRgrEEN genes. The acquisition of progressive functions which are not encountered in fish by human orthologs suggests that the functional difference between fish and human orthologs is not due to accuracy of annotation (incomplete knowledge of functions of fish genes provided by GO approach), but represents the real biological phenomenon.
As we have shown in our previous works [6, 15, 20, 27, 40, 44] human TSEEN genes are expressed in wide variety of tumors. In a similar way, the 296 fish TTRgrEEN genes may be expressed not only in hepatomas, but in tumors of other localizations as well, that could lead to the origin of wide variety of morphogenetic gene functions. This is supported by our experimental data on the expression of the fish TTRgrEEN genes (Fig. 2) and of their human orthologs in various normal human tissues (Fig. 4).
Here, we propose that many genes that are involved in development of progressive traits in humans (such as placenta, mammary gland, lungs, ventricular septum, etc.) originated as proto-genes in fish and were expressed in fish tumors and in tumors after regression. This is exactly what the theory of evolution by tumor neofunctionalization predicted [25, 26].
Some of the human orthologs of fish TTRgrEEN genes are involved in development of several progressive traits. Thus TGFBR2 participates in lung development, mammary gland morphogenesis and ventricular septum development; ID2 – in mammary gland and ventricular septum development; and WNT7B – in lung development, placenta morphogenesis and mammary gland development. Conversely, development of some progressive traits involves several of the human orthologs of fish TTRgrEEN genes. For example, ETNK2, FOSL1, LEP and DAZAP1 all participate in placenta development; TGFBR2, SOX9 and SPRY1– in lung development; TGFBR2, ID2 and SOX9– in mammary gland development, etc., Additional files 18, 19, 20, 21 and 22.
We suggest to call fish evolutionarily-novel genes that are expressed in fish tumors and that acquire morphogenetic, developmental and other important functions involved in evolution of progressive traits in higher orders of vertebrates with increased complexity, “carcino-evo-devo” genes, to stress their role in evolution of ontogenesis  and as analogy with carcinoembryonic antigens described earlier by Abelev and co-authors . Our preliminary data obtained using newly available fish transcriptomes in public databases suggest that the carcino-evo-devo genes described in this paper include TSEEN genes (e.g. lepa), cancer/testis antigen genes (e.g. ccr11.1), carcino-embryonic genes (e.g. ephb3a) and genes expressed in normal fish tissues other than liver (e.g. id2a, reck).
Carcino-evo-devo genes were predicted by the hypothesis of evolutionary role of tumors [24,25,26,27]. That is why their discovery in this paper may be considered as support of the hypothesis of evolution by tumor neofunctionalization [25, 26].
Availability of data and materials
All data generated or analysed during this study are included in this published article (and its supplementary information files).
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Note added in proof
In the recent paper of Li et al.,  the authors have shown that after reversion of tumor hepatocytes to normal hepatocytes during liver tumor regression in an oncogene transgenic zebrafish model, some tumor signaling pathways remain activated in tumor-reverted hepatocytes, according to transcriptomes analysis. This is in accordance with the data obtained in the present article.
This study was supported by 5–100-2020 program grant at Peter the Great St. Petersburg Polytechnic University and a grant No833 from Ministry of Education and Science of the Russian Federation to A.P.K.
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The List of normal liver transcripts.
The List of carcinoma transcripts.
The List of tumor after regression transcripts.
The List of housekeeping genes with known expressionlevel in normal liver.
The List of manually curated sample of 1502 genes, not expressed in normal liver, expressed in tumors and in tumors after regression.
Ensembl data for 870 genes expressed in tumors and in liver after tumor regression.
Primer sequences used for PCR.
Histological data for tissues of spontaneous hepatocellular carcinoma and spermatocytic seminoma.
GO annotation with all evidence codes for 870 fish genes from the sample.
GO annotation with all evidence codes for 296 fish evolutionary novel genes with human orthologs.
GO annotation with all evidence codes for 343 human orthologs of 296 fish evolutionary novel genes.
GO annotation with all evidence codes for the 113 fishevolutionary novel genes without human orthologs.
Table S2. Full version.
GO enrichment functional clustering, using Panther algorithm.
Primers for qPCR on set of genes selected to study the possibility of mifepristone influence on gene expression
Results of the study of gene expression in the presence and absence of mifepristone, Figure.
680 TTregEEN genes detected by OMA.
GO annotation of fish TSEEN tgfbr2b and it’s human ortholog TGFBR2.
GO annotation of fish TSEEN dazap1 and it’s human ortholog DAZAP1.
GO annotation of fish TSEEN nr2e1 and it’s human ortholog NR2E1.
GO annotation of fish TSEEN mycn and it’s human ortholog MYCN
GO annotation of fish TSEEN fosl1a and it’s human ortholog FOSL1.
Source code of Original scripts “Alignment BLAST”, (BLAST database creation, Fasta slasher, OMA parameters).
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Matyunina, E.A., Emelyanov, A.V., Kurbatova, T.V. et al. Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. Infect Agents Cancer 14, 46 (2019). https://doi.org/10.1186/s13027-019-0262-5
- Gene expression
- Tumor specific expression
- Evolutionarily novel