Nuclear and kinetoplastic DNA from trypanosomes

NLRC5 regulates expression of MHC-I and provides a target for anti-tumor immunity in transmissible cancers

Purpose

Downregulation of MHC class I (MHC-I) is a common immune evasion strategy of many cancers. Similarly, two allogeneic clonal transmissible cancers have killed thousands of wild Tasmanian devils (Sarcophilus harrisii) and also modulate MHC-I expression to evade anti-cancer and allograft responses. IFNG treatment restores MHC-I expression on devil facial tumor (DFT) cells but is insufficient to control tumor growth. Transcriptional co-activator NLRC5 is a master regulator of MHC-I in humans and mice but its role in transmissible cancers remains unknown. In this study, we explored the regulation and role of MHC-I in these unique genetically mis-matched tumors.

Methods

We used transcriptome and flow cytometric analyses to determine how MHC-I shapes allogeneic and anti-tumor responses. Cell lines that overexpress NLRC5 to drive antigen presentation, and B2M-knockout cell lines incapable of presenting antigen on MHC-I were used to probe the role of MHC-I in rare cases of tumor regressions.

Results

Transcriptomic results suggest that NLRC5 plays a major role in MHC-I regulation in devils. NLRC5 was shown to drive the expression of many components of the antigen presentation pathway but did not upregulate PDL1. Serum from devils with tumor regressions showed strong binding to IFNG-treated and NLRC5 cell lines; antibody binding to IFNG-treated and NRLC5 transgenic tumor cells was diminished or absent following B2M knockout.

Conclusion

MHC-I could be identified as a target for anti-tumor and allogeneic immunity. Consequently, NLRC5 could be a promising target for immunotherapy and vaccines to protect devils from transmissible cancers and inform development of transplant and cancer therapies for humans.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00432-021-03601-x.

What do unicellular organisms teach us about DNA methylation?

DNA methylation is an epigenetic hallmark that has been studied intensively in mammals and plants. However, knowledge of this phenomenon in unicellular organisms is scanty. Examining epigenetic regulation, and more specifically DNA methylation, in these organisms represents a unique opportunity to better understand their biology. The determination of their methylation status is often complicated by the presence of several differentiation stages in their life cycle. This article focuses on some recent advances that have revealed the unexpected nature of the epigenetic determinants present in protozoa. The role of the enigmatic DNA methyltransferase Dnmt2 in unicellular organisms is discussed.

Isolation and characterization of a gene from Trypanosoma cruzi encoding a 46-kilodalton protein with homology to human and rat tyrosine aminotransferase

The complete sequence of a gene encoding a 46-kDa protein of Trypanosoma cruzi is presented. The first ATG complies with the consensus sequence for initiation of translation. A single band of 2 kb was highlighted by hybridizing a probe from the 46-kDa protein gene to a Northern filter containing total T. cruzi RNA. The gene is present in 50-80 copies per cell and most of them are contained in 2 tandem arrays on large T. cruzi chromosomes (> 2000 kb). A strong homology with rat and human tyrosine aminotransferase was detected. Homology with a Trypanosoma brucei retrotransposon was found in the nonsense strand of the intergenic region.

Nuclear and kinetoplast DNA synthesis in Trypanosoma cruzi, autoradiographical study with DNA polymerase inhibitors

DNA synthesis in epimastigote forms of Trypanosoma cruzi was studied autoradiographically by incorporation of [3H]thymidine in the nuclear and kinetoplast DNA. Both DNA were heavily labelled. Three eukaryotic DNA polymerase inhibitors (aphidicolin, aracytidine, and dideoxythimidine) were chosen to study the nuclear and kinetoplast DNA synthesis in vivo. Inhibition was mainly observed with the nuclear DNA.

DNA methylation in Trypanosoma cruzi

DNA isolated from the protozoan Trypanosoma cruzi has been found to contain 5-methylcytosine. Analysis of T. cruzi DNA by both HpaII and MspI restriction endonucleases suggests that the sequence -CCGG- is not methylated. Probably T. cruzi DNA also contains N6-methyladenine. This report constitutes the first clear demonstration of the presence of methylated bases in the nuclear DNA from trypanosomes.

On the DNA content of Trypanosoma cruzi

The DNA contents of three different Trypanosoma cruzi strains were compared by direct microfluorometry. The maximal difference found was 40% of the lowest value. Two of the cloned strains, reported in an earlier study to differ by 48% in their total DNA content, showed a difference of 33%. The kinetoplast of the Y strain made up about one third of its total genome. The absolute DNA content of T. cruzi was estimated at 125 to 200 fg.

Quantitation of total DNA per cell in an exponentially growing population using the diphenylamine reaction and flow cytometry

The diphenylamine assay used to estimate the absolute mass of DNA/cell as well as absolute differences in DNA content between cell populations is based upon the assumption that all of the cells are in the G0 or G1 phase of the DNA synthetic cycle. However, if cells are in exponential growth and synthesizing DNA, portions of the population will be in S or G2 phases and the diphenylamine assay will overestimate the total mass of DNA/cell. Conversely, flow cytometry (FCM) can estimate relative differences in total DNA/cell and the proportions of an exponentially growing population in G1, S, and G2 but cannot estimate absolute mass or differences in DNA/cell. In this report, we describe a methodology of combined diphenylamine and FCM assays of total DNA/cell which is applicable to any eukaryotic cell population. The method involves using the two assay methods concurrently and correcting the diphenylamine data for the FCM-derived distribution of the cells within the DNA synthetic cycle. The methodology was tested on single-cell-derived stocks of the obligate intracellular protozoan parasite Trypanosoma cruzi which displays marked but stable intraspecific heterogeneity.

An isolation method of DNA from Pneumocystis carinii: a quantitative comparison to known parasitic protozoan DNA

1. A method for isolating DNA from Pneumocystis carinii is described. 2. The DNA content per nucleus is 0.22-0.34 pg. 3. This finding is consistent with other parasitic protozoa DNA content per nuclei.

Schizodeme analyses of Trypanosoma cruzi zymodemes from Chile

Kinetoplast DNA was isolated from Chilean Trypanosoma cruzi populations and digested with the restriction endonucleases EcoRI, HinfI, HpaII, MspI, and HaeIII. Three major schizodeme groups were discriminated. There was a correlation between the Chilean schizodeme groups (S1, S2, or S3) and the zymodemes known to occur in Chile (Z1, Brazilian Z2 and Bolivian Z2, respectively), although heterogeneity was seen within the schizodeme groups S2 and S3. Standard Brazilian and Bolivian T. cruzi clones (X10 clone 1, Esmeraldo clone 3, SC43 clone 1, and CAN III clone 1) and laboratory strains (Tulahuen and Y) were included in the schizodeme comparisons. SC43 clone 1 had obvious affinities with S3 and X10 clone 1 shared some features with S1 but the other reference stocks could not be definitely assigned to S1, S2, or S3. Fragment patterns and densitometric traces following digestion with HpaII or MspI suggested that kDNA sequences were not methylated.

In situ microfluorometry of kinetoplast and nuclear DNAs in Trypanosoma gambiense. Unusual repairment of DNA after treatment with bleomycin

The blood stream form of Trypanosoma gambiense was smeared on a nonfluorescent slide glass with 1 microgram/ml of Hoechst 33258 in 1 mM Tris-HCl buffer (pH 7.2) containing 1% 2-mercaptoethanol and subjected to the in situ microfluorometry. Effects of bleomycin (BL) on the kinetoplast (K)-DNA and nuclear (N)-DNA of T. gambiense were examined in the time course to 6 h after injection of BL into the infected mice. An enhancement of fluorescence occurred 30 min after the injection and then slowed down. This enhancement was due to DNA synthesis both in the K-DNA and N-DNA. This suggests that the strong repairment occurs in both DNAs after treatment with BL.

Isoenzyme changes during the life cycle of Trypanosoma cruzi

The isoenzyme profiles, for 14 enzymes, of amastigotes, trypomastigotes and epimastigotes were compared in various cloned and uncloned T. cruzi stocks belonging to different zymodemes. A culture method with a human diploid cell line was developed and produced either pure amastigotes or trypomastigotes in high yields. Trypomastigotes were also isolated from rat blood and from liquid culture. Epimastigotes were harvested from various acellular media and from the overlay of cell monolayers. The isoenzyme patterns of each life-cycle stage showed consistent differences in the number, position and intensity of the electrophoretic bands for certain enzymes. With the single exception of one peptidase, the variable patterns were stage-specific regardless of whether the organisms were harvested from animals or from various cultures at different temperatures.

Introduction of plasmid DNA into the trypanosomatid protozoan Crithidia fasciculata

Crithidia fasciculata cells were treated with a plasmid (pDK96) containing pBR322 sequences, a Leishmania tarentolae maxicircle autonomously replicating sequence, and the bacterial gene for aminoglycoside 3' phosphotransferase I inserted between the yeast alcohol dehydrogenase 1 promotor and terminator sequences. Resistant colonies were selected on agar plates containing paromomycin and screened for vector DNA by hybridization. Approximately 1% of the resistant colonies contained detectable vector DNA, which was present as extrachromosomal closed circular molecules ranging in copy number from 1 to 160 per cell. The plasmids could be recovered from Escherichia coli transformed to ampicillin resistance with Crithidia total cell DNA. Most of the recovered plasmids were a deleted product of pDK96, which lacked the maxicircle autonomously replicating sequence and contained a unique fragment of Crithidia nuclear DNA present at a low copy number in the wild-type genome. The plasmid DNA in resistant Crithidia was unstable even under selective conditions and was lost within 30 cell divisions.

Tubulin genes are tandemly linked and clustered in the genome of trypanosoma brucei

We have isolated cDNA and genomic clones containing alpha- and beta-tubulin genes from Trypanosoma brucei. Each clone has been mapped, and the identity of the tubulin genes has been established by cross-hybridization with cloned chicken tubulin genes and by hybridization-selection and translation of trypanosome tubulin mRNA. In contrast with the dispersed organization of tubulin genes in other organisms, trypanosome alpha- and beta-tubulin genes are physically linked and clustered in tandem repeats of approximately 13-17 copies per haploid genome of alternating alpha- and beta-tubulin sequences.

Trypanosoma cruzi: flow cytometric analysis. I. Analysis of total DNA/organism by means of mithramycin-induced fluorescence

Total DNA/organism was determined by flow cytometry on stocks of 33 single-cell-isolate clones and one strain of mithramycin-stained Trypanosoma cruzi. Interstrain differences in mean total DNA/group of 34% and interclone differences in total DNA/organism of 41% were found. Microspectrofluorometric analyses of the trypomastigote stage of selected clones confirmed the flow cytometry data and indicated that the total DNA/organism differences were due to differences in DNA of both the nucleus and kinetoplast with the nucleus being the major contributing factor. These data imply that the potential for genetic diversity in T. cruzi may be very large.

On the DNA content and ploidy of trypanosomes

We have determined the nuclear and kinetoplast DNA content of two trypanosomatids by quantitative absorption and fluorescence cytophotometry of individual Feulgen-pararosaniline stained cells. For the insect trypanosomatid Crithidia fasciculata we find nuclear and kinetoplast DNA contents of 0.095 and 0.032 pg per non-replicating cell. For the African trypanosome Trypanosoma brucei these values are 0.097 and 0.004 pg. A sub-population of T. brucei cells with two kinetoplasts and one nucleus was found to contain 0.181 pg/nucleus. The DNA values of bloodstream form T. brucei and the procyclic culture from were not significantly different. In DNA-DNA renaturation experiments the haploid amount of DNA in T. brucei was previously found to be 0.041 pg/nucleus (Borst, P., Fase-Fowler, F., Frasch, A.C.C., Hoeijmakers, J.H.J. and Weijers, P.J. (1980) Mol. Biochem. Parasitol. 1,221-246). Our data, therefore, indicate that T. brucei is diploid. No sub-population of haploid cells was observed in T. brucei grown in rats or in culture.

The kinetoplast of DNA of Trypanosoma gambiense: comparison with the kDNA of Trypanosoma equiperdum

The molecular components of the kinetoplast DNA (kDNA) network of Trypanosoma gambiense have been studied and compared with those of the very closely related species T. equiperdum, previously studied in detail. The kDNA of T. gambiense contains about 80 maxicircles of 20 kilobase pairs and 4000 minicircles of 1 kilobase pairs. The restriction cleavage sites of 7 restriction endonucleases have been mapped on the T. gambiense maxicircle. The majority of these sites were also found in T. equiperdum maxicircles; however their relative positions which are different do not allow us to conclude to relatedness of maps. Maxicircles of the Cairn or of the rolling circle type have been observed and thought to be replicative intermediates. Experiments on renaturation kinetics and hybridization after blotting transfer, show that T. gambiense and T. equiperdum maxicircles have base sequences in common. The T. gambiense minicircles are heterogeneous in base sequence, in contrast to the T. equiperdum minicircles which are homogeneous. The minicircles of the two species have also common base sequences.

Complexity and content of the DNA and RNA in Trypanosoma cruzi

The content and sequence complexity of the nuclear DNA and messenger RNA for epimastigotes of Trypanosoma cruzi were determined. From analysis of nuclear DNA reassociation studies and microspectrofluorometric measurements of laser induced fluorescence of cellular DNA, T. cruzi is found to be a diploid organism with a nuclear DNA content of 2.5 x 10(8) nucleotide pairs (2.8 x 10(-13) g) and a kinetoplast DNA content of 4.9 x 10(7) nucleotide pairs (5.4 x 10(-14) g). Reassociation kinetics of nuclear DNA of average length 0.4 kb reveals three kinetic components: a moderately repetitive component with a reiteration frequency of 5.1 x 10(3) present in 9% of the fragments, a lowly repetitive component with a reiteration frequency of 32 present in 51% of the fragments, and a single-copy component present in 23% of the fragments. By saturation hybridization of total polysomal RNA to 3H-labeled single-copy DNA, it was determined that 68% of the single-copy DNA was represented in the epimastigote polysomal RNA. This corresponds to ca. 12 000 different mRNA species. Of these, ca. 9000 are present as poly(A)+-RNA, while the remaining 3000 appear not to be polyadenylated. Kinetic analysis of the poly(A)+-RNA population indicates it is composed of at least three classes of RNA's of different abundancy levels: two sequences which occur ca. 3000 per cell, ca. 750 sequences which occur about 20 times per cell, and ca. 15 500 sequences which occur 1-2 times per cell.

Sub-cellular fractionation of Trypanosoma brucei. Isolation and characterization of plasma membranes

A procedure is described for the isolation of sub-cellular fractions from bloodstream forms of Trypanosoma brucei. The method leaves intact most of the nuclei, mitochondria and microbodies. All the fractions have been chemically characterized and tested for 10 enzymatic markers. About 5% of total cell protein was isolated as a microsomal fraction containing mostly plasma membranes and endoplasmic reticulum vesicles. Plasma membranes were purified by high-speed centrifugation on magnesium-containing Dextran, and on linear sucrose-density gradients. The yield of membranes was approximately 0.3% of the total cell protein. The purified material had a sucrose density of 1.14 g/cm3 and consisted of smooth vesicles. Specific activity of the membrane markers Na+, K+, ouabain-sensitive ATPase and adenylate cyclase were 26- and 20-fold higher, respectively, than in total cells. Neither DNA nor RNA was detected. The sum of the cholesterol and phospholipid content was 0.99 mg/mg protein. The cholesterol/phospholipid molar ratio was 1:2.

Absence of kinetoplast DNA in a late antigenic variant of Trypanosoma equiperdum

We have analysed by several biochemical techniques the DNA components of two antigenic variants isolated from Trypanosoma equiperdum. We did not observe any kinetoplast DNA (kDNA) structures or networks in the late antigen variant BoTat 28. Furthermore, the results of reassociation kinetics of in vitro labelled kDNA show that neither kDNA minicircle sequences nor kDNA maxicircle sequences of BoTat 1, the basic antigen type, can be detected in the total DNA of BoTat 28.

Novel expression-linked copies of the genes for variant surface antigens in trypanosomes

Pathogenic African trypanosomes evade the immune system of their mammalian hosts by the sequential expression of alternative cell-surface glycoproteins (reviewed in refs 1,2). Variant surface glycoproteins (VSGs) purified from cloned variants of Trypanosoma brucei have similar molecular weights (about 60,000), but differ in amino acid composition, N-terminal amino acid sequence and C-terminal structure. We have cloned DNA complementary to the messenger RNA's for four immunologically distinct VSGs and hybridised these complementary DNAs (cDNAs) with restriction digests of T. brucei nuclear DNA, fractionated by gel electrophoresis and transferred to nitrocellulose strips. Each cDNA recognises a unique set of fragments and this basic set is present unaltered in the nuclear DNAs from the four variants. In addition, each probe recognises an extra fragment only in nuclear DNA isolated from cells expressing the VSG corresponding to the cDNA probe. We infer that activation of a VSG gene involves the production of an expression-linked copy of that gene.

Properties of DNA from some malarial parasites

The base compositions of DNA from some species of malarial parasite have been estimated by measurement of density in CsCl gradients and of thermal denaturation temperatures. Species from avian (Plasmodium gallinaceum) and rodent (P. bergheiandP. vinckei) hosts – often used as model systems in malarial studies – contain single DNA components with base compositions of about 20% G + C. By contrast, species from primate hosts (P. knowlesiandP. falciparum) contain major DNA components of about 40% G + C and minor ones of about 20% G + C. These differences could be reflexions of markedly different genomes within these two groups of the genusPlasmodium.

Apart from differences in base composition, the physico-chemical properties of the main components of DNA from primate and rodent malarial parasites are very similar to those of DNA from mammalian cells. DNA from avian malarial parasites appears to have some unusual properties.

One of us (P.I.T.) received financial assistance from the World Health Organization. We thank Dr F. Hawking and Dr J. Williamson for many helpful discussions, Dr W. H. G. Richards, Dr A. Voller and Dr D. C. Warhurst for the provision of some of the strains and Miss Jane Dunnett, Mrs A. C. Gutteridge and Mr T. Scott-Finnigan for technical assistance.