Minimally invasive biomarkers in human and non-human primate evolutionary biology: Tools for understanding variation and adaptation.

BACKGROUND: The use of minimally invasive biomarkers (MIBs - physiological biomarkers obtained from minimally invasive sample types) has expanded rapidly in science and medicine over the past several decades. The MIB approach is a methodological strength in the field of human and non-human primate evolutionary biology (HEB). Among humans and our closest relatives, MIBs provide unique opportunities to document phenotypic variation and to operationalize evolutionary hypotheses. AIMS: This paper overviews the use of MIBs in HEB. Our objectives are to (1) highlight key research topics which successfully implement MIBs, (2) identify promising yet under-investigated areas of MIB application, and (3) discuss current challenges in MIB research, with suggestions for advancing the field. DISCUSSION AND CONCLUSIONS: A range of MIBs are used to investigate focal topics in HEB, including energetics and life history variation/evolution, developmental plasticity, and social status and dominance relationships. Nonetheless, we identify gaps in existing MIB research on traits such as physical growth and gut function that are central to the field. Several challenges remain for HEB research using MIBs, including the need for additional biomarkers and methods of assessment, robust validations, and approaches that are standardized across labs and research groups. Importantly, researchers must provide better support for adaptation and fitness effects in hypothesis testing (e.g., by obtaining complementary measures of energy expenditure, demonstrating redundancy of function, and performing lifetime/longitudinal analyses). We point to continued progress in the use of MIBs in HEB to better understand the past, present, and future of humans and our closest primate relatives.

An Examination of the Development and Localization of Key Immune Cells in Developing Pouch Young of the Red-Tailed Phascogale (Phascogale calura).

Cells expressing the surface markers CD3, CD4, CD79b, IgM, MHC class II, and ModoUG (nonclassical MHC class I) were detected in red-tailed phascogale tissues using immunohistochemistry, and the appearance and localization of cells observed here was consistent with previous observations in other marsupial species. CD3+ cells were first detected at one day postpartum (dpp) in the thymus, followed by ModoUG+ cells at 5-7 dpp in the thymus and lymph nodes. CD79b+ cells were first detected at 12-14 dpp in bone marrow, spleen, and lymph nodes. IgM+ cells were first detected at 12-14 dpp in thymus, bone marrow, spleen, and lymph nodes. MHC class II+ cells were first detected at 12-14 dpp in thymus, bone marrow, and lymph nodes. CD4+ cells were detected in adult thymus and spleen only. The presence of the mature immune cell populations and their localization to characteristic T and B cell zones in mature lymphoid tissues with normal histological structure indicates that red-tailed phascogales develop immunocompetence by the end of pouch life. Anat Rec, 302:1985-2002, 2019. © 2019 American Association for Anatomy.

Molecular identification and gene expression profiles of the T cell receptors and co-receptors in developing red-tailed phascogale (Phascogale calura) pouch young.

Expressed coding sequences were identified for the T cell receptors TCRα, TCRß, TCRγ, TCRδ, TCRµ, and co-receptors CD3ε, CD4, and CD8α in the red-tailed phascogale (Phascogale calura). Expression of these genes was examined in the developing thymus and spleen of pouch young and juvenile individuals to detect any changes in expressionrelative to developmental stages. Transcripts of CD3ε, CD4, TCRδ and TCRµ were first detected in the thorax at 1 day postpartum (dpp), and transcripts of all target genes were detected in the thymus from 3 dpp, and the spleen from 17 dpp. The relative expression of all target genes changed significantly over the course of pouch life and was associated with histological milestones of both the thymus and the spleen. Peak gene expression was observed early in pouch life in the thymus, with a decrease in expression associated with timing of thymic involution, while expression peaked later in the spleen and was associated with the initial differentiation of the red and white pulp and a population of T cells forming the periarterial lymphatic sheath (PALS). Active expression of these target genes within the thymus and spleen indicates that the young marsupials are actively developing immunocompetence during pouch life.

Antimicrobial activity of red-tailed phascogale (Phascogale calura) serum.

Antimicrobial substances in serum include circulating complement proteins and acute phase proteins (APPs). We identified gene sequences for APPs, haptoglobin (Hp), C-reactive protein (CRP) and serum amyloid A (SAA) in marsupial genomes. Hp and SAA levels were measured in red-tailed phascogale (Phascogale calura) sera using commercially available assays. Hp levels were higher in males than females, while SAA levels suggest the phascogales used in this study were healthy. Serum was co-cultured with four bacterial species. Bacterial growth was inhibited after incubation at 37°C, however effectiveness differed with bacteria and incubation time. The least amount of bacterial growth was noticed after introduction to K. pneumoniae, and most when introduced to P. aeruginosa. Despite marsupials not having mature immune tissues at birth, and unable to mount specific immune responses, this study suggests other immune strategies, such as APPs in serum likely aid marsupials in their defence against pathogens.

Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen.

BACKGROUND: Reference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues. METHODS: The study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase, GAPDH; ß-actin, ACTB; 18S rRNA, 18S; 28S rRNA, 28S; and ribosomal protein L13A, RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUS software. RESULTS: Gene stability for juvenile and adult tissue samples combined show that GAPDH was most stable in liver and lung tissue, and 18S in small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except 28S were stable for lung and only 18S and 28S were stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTB and GAPDH) and adults (18S and 28S), and RPL13A was not stable for juvenile small intestine tissue. Except for 28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue. DISCUSSION: Based on expression stability, ACTB and GAPDH are suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults but RPL13A was not suitable in juveniles.

Further characterisation of cytokines in macropod marsupials: IL-10 and IL-10Δ3.

Interleukin-10 is an immunomodulatory cytokine that has been implicated, along with IFN-γ, in the disease sequelae of mycobacterial infection. In order to investigate the role of IL-10 in marsupial disease models we sequenced and characterised the IL10 gene in the tammar wallaby (Macropus eugenii) and rufous hare-wallaby (Lagorchestes hirsutus). An isoform IL-10Δ3, in which an in-frame deletion of exon 3 occurs, was discovered in both macropod species. Analysis of wallaby and other reported marsupial IL-10 homologs suggests that while marsupial IL-10 is comparable to that of human IL-10, the predicted IL-10Δ3 protein may play a more complicated role in the modulation of IL-10-directed responses. Expression of the canonical gene and splicing variant was confirmed in both wallabies, and the rufous hare-wallaby showed differential expression across lymph node, spleen and liver, with isoform expression detected in the lymph node. This characterisation and expression of IL-10 in de novo tissues provides a basis for further study into the role of IL-10 in disease models in marsupials.

Sequences and expression of pathway-specific complement components in developing red-tailed phascogale (Phascogale calura).

Marsupials are born immunologically premature, relying on cells and molecules in maternal milk for immune protection. Both immunoglobulin and complement proteins have been identified in marsupial milk, but the expression of specific complement proteins remains largely unexplored. We report partial cDNA sequences for two complement-activating proteins, C3, C1r, CFP and MASP2, in liver tissues from red-tailed phascogale (Phascogale calura). Conservation of functionally relevant motifs were identified in the translated cDNA sequences from phascogale C3, CFP and MASP2 and their eutherian homologues. Gene expression of representative molecules from each of the major complement pathways was also investigated in whole body tissues from 1 to 18 day old animals and liver tissues from 31-day to 14-month old animals. Average complement expression in whole bodies and liver tissues of C1r, CFP, MASP2 and C3 increased significantly in juveniles compared to pouch young, presumably due to the maturation of the young's own complement system. Comparing expression in liver tissues only, we found that the average CFP expression were higher in pouch young compared to juveniles, while results were still statistically similar to the average expression of all tissues for C1r, MASP2 and C3. The average complement expression then significantly decreased as the animals aged into adulthood.

Identification of the mRNA encoding interleukin-6 and its receptor, interleukin-6 receptor α, in five marsupial species.

Expressed coding sequences for interleukin-6 (IL-6) and interleukin-6 receptor α (IL-6R) were examined in five marsupial species. Full length expressed coding sequences for IL-6 and IL-6R were identified and characterized in the gray short-tailed opossum (Monodelphis domestica). For IL-6, ∼225 bp fragments of the mRNA sequence were identified in the red-tailed phascogale (Phascogale calura), kultarr (Antechinomys laniger), and stripe-faced dunnart (Sminthopsis macroura), while ∼563 bp fragments of mRNA encoding IL-6R were identified in the red-tailed phascogale, kultarr, stripe-face dunnart and fat-tailed dunnart (Sminthopsis crassicaudata). Relative expression levels of IL-6 and IL-6R were examined in the heart, muscle, lung, liver, spleen and kidney of adult red-tailed phascogales, and IL-6 gene expression was found to be significantly higher in the lung and spleen than the other tissues examined, while the expression of IL-6R was significantly higher in the liver, lung and spleen. These results now serve as a reference point for examining the role and levels of IL-6 and IL-6R in the health and disease of these marsupial species. The pro-tumorigenic nature of IL-6 is of particular interest, and the identification of these IL-6 and IL-6R coding sequences provides a platform for further work to evaluate the potential role of IL-6 in marsupial cancers.

The macropod type 2 interferon gene shares important regulatory and functionally relevant regions with eutherian IFN-γ.

Interferon-γ (IFN-γ) is an important immune regulatory molecule that plays a significant role in internal and external modulation of the mammalian immune response to intracellular pathogens. Herein, we report the 492 nt expressed sequence for the coding domain of IFN-γ from the immune tissues of two Australian macropod marsupial species: the tammar wallaby (Macropus eugenii) and the vulnerable rufous hare-wallaby (Lagorchestes hirsutus). Both 5' and 3' untranslated regions and the coding domain of M. eugenii IFN-γ revealed the presence of motifs responsible for transcriptional regulation, mRNA regulation, post-translational modifications, and receptor binding in other mammals. Since diagnostic kits for mycobacterial disease commonly rely on the assessment of interferon levels, we can now use this information to develop reagents that can be applied in clinical and laboratory settings to further our understanding of marsupial responses to disease.

Isoforms of the CD79 signal transduction component of the macropod B-cell receptor.

B cell responses and their concomitant signal transduction pathways are not well understood in marsupial mammals, despite the availability of gene expression data for key immunoglobulin genes and for elements of the CD79a/CD79b heterodimer signalling complex for two model marsupials. Broader studies of factors that influence B cell responses are still hampered by a lack of species-specific reagents and there are few reports of other factors that influence gene expression such as the potential for splice variants in BCR components, which may influence immune signalling pathways. In this study, we characterise CD79a and CD79b genes in the endangered macropod marsupial, Onychogalea fraenata (the bridled nailtail wallaby) and show that domains and residues important for the structural and functional integrity of both monomers are conserved in this species, consistent with results previously reported for the closely-related macropod, Macropus eugenii (the tammar wallaby). We extend this work to report the detection of splice variants for CD79a and CD79b in wallaby species; three CD79a isoforms and one CD79b isoform. Of these, two CD79a isoforms and the CD79b isoform have not been reported in any other mammalian species.

The development of the immune tissues in marsupial pouch young.

Current knowledge of the development of the marsupial immune system, particularly in the context of lymphoid tissue development and the appearance of lymphocytes, has been examined and limitations identified. While primary lymphoid tissues like the thymus have been extensively studied, secondary lymphoid tissues such as the spleen and lymph nodes have been examined to a lesser extent, partly due to the difficulty of macroscopically identifying these structures, particularly in very small neonates. In addition, little research has been conducted on the mucosal-associated lymphoid tissues; tissues that directly trap antigens and play an important role in the maturity of adaptive immune responses. Research on the development of the marsupial immune tissues to date serves as a solid foundation for further research, particularly on the mechanisms behind the development of the immune system of marsupials. With the recent sequencing and annotation of whole marsupial genomes, the current wealth of sequence data will be essential in the development of marsupial specific reagents, including antibodies, that are required to widen our specific knowledge of the complex marsupial immune system and its development.

Further investigation of the blood characteristics of Australian Quoll (Dasyurus spp.) species.

BACKGROUND: The Eastern and Spotted-Tailed Quolls are "near threatened" Australian dasyurid marsupials that have undergone significant reduction in their geographic ranges in the past 200 years. Captive breeding and research colonies now exist, allowing further efforts to more fully understand the physiology of these carnivorous species. OBJECTIVES: The aims of the study were to provide a more detailed study of blood chemistry and differential WBC counts for Eastern and Spotted-Tailed Quolls, and to determine the influence by 3 biologic factors. METHODS: Blood samples were taken from conscious, captive, healthy Eastern Quolls. A small number of samples from Spotted-Tailed Quolls were also available and were included in the study for comparison. Blood chemistry and differential WBC counts were compared to determine season-, age-, and sex-related differences. RESULTS: For many of the analytes, blood chemistry results were comparable to other marsupial ranges, and no significant differences between sexes were detected (P > .05). Seasonal differences were determined for total bilirubin, glucose, creatinine, and potassium concentrations in the Eastern Quoll. Generally, higher concentrations of these analytes were observed in the summer; however, amylase activity was significantly higher in autumn (southern hemisphere). Eastern Quolls one year of age and younger had significantly (P < .05) higher ALP activities than older animals. CONCLUSIONS: The normal ranges determined in this study can be used to assess clinical health of quolls and will assist with captive management and future reintroduction programs to the wild.

Molecular characterisation and expression of interleukin-6 and interleukin-6Δ2 in the Tammar wallaby (Macropus eugenii).

The pro-inflammatory cytokine, Interleukin-6 (IL-6), has not yet been fully characterised in the model macropod, Macropus eugenii, due to incomplete sequence information in publically available genome databases. Using a Rapid Amplification of cDNA Ends strategy we have confirmed the expression and complete nucleotide sequence for this molecule in lymph node tissue and activated leukocytes. Structural conservation of the mature wallaby IL-6 molecule was high when compared with human IL-6, although there was only 34% amino acid sequence identity with the human IL-6 peptide, consistent with reports of the evolutionary divergence of this cytokine. We also report the discovery of MeIL-6Δ2, a splice variant missing exon 2, which directly translates to a truncated non-functional peptide, but which may also code for an alternative peptide that is translated downstream of the canonical IL-6 start site. This putative gene product is predicted to maintain some, if not all, of the functions of macropod IL-6 and is the first IL-6 isoform reported outside of eutherian mammals.

Molecular identification and expression of Lyn tyrosine kinase isoforms in marsupials.

Lyn is a tyrosine kinase molecule required for modulation of signalling cascades in cell populations including B lymphocytes of the mammalian immune system. We have characterised the coding domain of the marsupial lyn gene of two macropod marsupials; the Tammar Wallaby (Macropus eugenii) and the Bridled Nailtail Wallaby (Onychogalea fraenata) and show the co-expression of two Lyn isoforms in cells and tissues of these and three other marsupials (Brush-tail Possum, Trichosurus vulpecula; American Grey Short-tailed Opossum, Monodelphis domestica and Red-tailed Phascogale, Phascogale calura). The predicted Lyn proteins (LynA and LynB) were highly conserved across vertebrate species, with amino acid identities of 94% with their human orthologues and conservation of key tyrosine kinase motifs that suggests that marsupial Lyn most likely functions in cell signalling. Comparison of our cDNA data to annotations for Lyn transcripts (available through the Ensembl Genome Browser) for the Tammar Wallaby confirm splice sites for a number of exons in the wallaby transcript that are missing from the current annotation. This is the first report of the expression of kinase signalling molecules that influence immunity in metatherian mammals and provides key information to support ongoing studies of immune regulation in marsupials.

Molecular characterization of interleukin-1Beta in the tammar wallaby (Macropus eugenii).

Interleukin-1beta (IL-1ß) plays a significant role in the onset and pathogenesis of inflammation in mammalian hosts. Although well characterized in a range of vertebrate species, little is known about this important cytokine in marsupial mammals. We report here the molecular cloning and characterization of IL-1ß in the tammar wallaby (Macropus eugenii). M. eugenii IL-1ß has an open-reading frame of 813 nucleotides, coding for a putative protein of 270 amino acids to the termination codon. The IL-1 family motif and potential caspase cleavage site (necessary for production of the mature protein) is also present in the sequence. Molecular characterization of tammar wallaby IL-1ß provides fundamental information necessary to progress the study of functional immune responses in this unique group of mammals.

In silico identification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammals.

BACKGROUND: Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared a common ancestor more than 180 million years ago, so it is not surprising that attempts to isolate many key marsupial cytokines using traditional laboratory techniques have been unsuccessful. This paucity of molecular data has led some authors to suggest that the marsupial immune system is 'primitive' and not on par with the sophisticated immune system of eutherian (placental) mammals. RESULTS: The sequencing of the first marsupial genome has allowed us to identify highly divergent immune genes. We used gene prediction methods that incorporate the identification of gene location using BLAST, SYNTENY + BLAST and HMMER to identify 23 key marsupial immune genes, including IFN-gamma, IL-2, IL-4, IL-6, IL-12 and IL-13, in the genome of the grey short-tailed opossum (Monodelphis domestica). Many of these genes were not predicted in the publicly available automated annotations. CONCLUSION: The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals.

A survey of type I interferons from a marsupial and monotreme: implications for the evolution of the type I interferon gene family in mammals.

Sequence data for type I interferons (IFNs) have previously only been available for birds and eutherian ('placental') mammals, but not for the other two groups of extant mammals, the marsupials and monotremes. This has left a large gap in our knowledge of the evolutionary and functional relationships of what is a complex gene family in eutherians. In this study, a PCR-based survey of type I IFN genes from a marsupial, the tammar wallaby (Macropus eugenii), and a monotreme, the short-beaked echidna (Tachyglossus aculeatus), was conducted. Along with Southern blot and phylogenetic analysis, this revealed a large number of type I IFN genes for the wallaby, rivalling that of eutherians, but relatively few type I IFN genes in the echidna. The wallaby genes include both IFNA and IFNB orthologues, indicating that the gene duplication leading to these subtypes occurred prior to the divergence of marsupials and eutherians some 130 million years ago. Results from this study support the idea that the expansion of type I IFN gene complexity in mammals coincides with a concomitant expansion in the functionality of these molecules. For example, this expansion in complexity may have, at least partially, facilitated the evolution of viviparity in marsupials and eutherians. Other evolutionary aspects of these sequences are also discussed.