Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration

Comparative proteomic analysis of tail regeneration in the green anole lizard, Anolis carolinensis

As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional replacement. Green anoles (Anolis carolinensis) can regenerate their tails through a process that involves differential expression of hundreds of genes, which has previously been analyzed by transcriptomic and microRNA analysis. To investigate protein expression in regenerating tissue, we performed whole proteomic analysis of regenerating tail tip and base. This is the first proteomic data set available for any anole lizard. We identified a total of 2,646 proteins - 976 proteins only in the regenerating tail base, 796 only in the tail tip, and 874 in both tip and base. For over 90% of these proteins in these tissues, we were able to assign a clear orthology to gene models in either the Ensembl or NCBI databases. For 13 proteins in the tail base, 9 proteins in the tail tip, and 10 proteins in both regions, the gene model in Ensembl and NCBI matched an uncharacterized protein, confirming that these predictions are present in the proteome. Ontology and pathways analysis of proteins expressed in the regenerating tail base identified categories including actin filament-based process, ncRNA metabolism, regulation of phosphatase activity, small GTPase mediated signal transduction, and cellular component organization or biogenesis. Analysis of proteins expressed in the tail tip identified categories including regulation of organelle organization, regulation of protein localization, ubiquitin-dependent protein catabolism, small GTPase mediated signal transduction, morphogenesis of epithelium, and regulation of biological quality. These proteomic findings confirm pathways and gene families activated in tail regeneration in the green anole as well as identify uncharacterized proteins whose role in regrowth remains to be revealed. This study demonstrates the insights that are possible from the integration of proteomic and transcriptomic data in tail regrowth in the green anole, with potentially broader application to studies in other regenerative models.

Protein extracts from regenerating lizard tail show an inhibitory effect on human cancer cells cultivated in-vitro

BACKGROUND

accumulating evidence indicates that during tail regeneration in lizards the initial stage of regenerative blastema is a tumor-like proliferative outgrowth that rapidly elongates into a new tail composed of fully differentiated tissues. Both oncogenes and tumor-suppressors are expressed during regeneration, and it has been hypothesized that an efficient control of cell proliferation avoids that the blastema is turned into a tumor outgrowth.

METHODS

in order to determine whether functional tumor-suppressors are present in the growing blastema we have utilized protein extracts collected from early regenerating tails of 3-5 mm that have been tested for a potential anti-tumor effect on in-vitro culture by using cancer cell lines from human mammary gland (MDA-MB-231) and prostate cancer (DU145).

RESULTS

at specific dilutions, the extract determines a reduction of viability in cancer cells after 2-4 days of culture, as supported by statistical and morphological analyses. While control cells appear viable, treated cells result damaged and produce an intense cytoplasmic granulation and degeneration.

CONCLUSIONS

this negative effect on cell viability and proliferation is absent using tissues from the original tail supporting the hypothesis that only regenerating tissues synthesize tumor-suppressor molecules. The study suggests that the regenerating tail of lizard at the stages here selected contains some molecules that determine inhibition of cell viability on the cancer cells analyzed.

Spatial Venomics─Cobra Venom System Reveals Spatial Differentiation of Snake Toxins by Mass Spectrometry Imaging

Among venomous animals, toxic secretions have evolved as biochemical weapons associated with various highly specialized delivery systems on many occasions. Despite extensive research, there is still limited knowledge of the functional biology of most animal toxins, including their venom production and storage, as well as the morphological structures within sophisticated venom producing tissues that might underpin venom modulation. Here, we report on the spatial exploration of a snake venom gland system by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in combination with standard proteotranscriptomic approaches, to enable in situ toxin mapping in spatial intensity maps across a venom gland sourced from the Egyptian cobra (Naja haje). MALDI-MSI toxin visualization on the elapid venom gland reveals a high spatial heterogeneity of different toxin classes at the proteoform level, which may be the result of physiological constraints on venom production and/or storage that reflects the potential for venom modulation under diverse stimuli.

A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection

Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2, in India, during the early days of the pandemic in 2020, by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.

Immunolocalization of tumor suppressors arhgap28 and retinoblastoma in the lizard Podarcis muralis suggests that they contribute to the regulated regeneration of the tail

Tail regeneration in lizards is an outstanding and unique postembryonic morphogenetic process. This developmental process is regulated by poorly known factors, but recent studies have suggested that it derives from a balanced activity between oncoproteins and tumor suppressors. Transcriptome and expression data have indicated that arhgap28 and retinoblastoma proteins are among the main tumor suppressors activated during tail regeneration. However, their cellular localization is not known. Therefore, in the present immunohistochemical study, two proteins have been detected in various tissues at the beginning of their differentiation. Both proteins are present especially in the new scales, axial cartilage, and muscle bundles of the regenerating tail, the main tissues forming the new tail. Sparse or occasionally labeled cells are observed in the blastema, but intense labeling is seen in the basal layers of the wound (regenerating) epidermis and in external differentiating epidermal layers. Numerous keratinocytes also show a nuclear localization for both proteins, suggesting that the latter may activate a gene program for tissue differentiation after the inhibition of cell multiplication. Based on microscopic, molecular, experimental, and in vitro studies, a hypothesis on the "inhibition of contact" among the apical cells of the blastema and those of proximal differentiating tissues is proposed to explain the permanence of an active blastema only at the apex of the regenerating tail without tail growth can degenerate into a tumorigenic outgrowth.

De Novo Transcriptome Sequencing and Analysis of Differential Gene Expression among Various Stages of Tail Regeneration in Hemidactylus flaviviridis

Across the animal kingdom, lizards are the only amniotes capable of regenerating their lost tail through epimorphosis. Of the many reptiles, the northern house gecko, Hemidactylus flaviviridis, is an excellent model system that is used for understanding the mechanism of epimorphic regeneration. A stage-specific transcriptome profile was generated in the current study following an autotomized tail with the HiSeq2500 platform. The reads obtained from de novo sequencing were filtered and high-quality reads were considered for gene ontology (GO) annotation and pathway analysis. Millions of reads were recorded for each stage upon de novo assembly. Up and down-regulated transcripts were categorized for early blastema (EBL), blastema (BL) and differentiation (DF) stages compared to the normal tail (NT) by differential gene expression analysis. The transcripts from developmentally significant pathways such as FGF, Wnt, Shh and TGF-β/BMP were present during tail regeneration. Additionally, differential expression of transcripts was recorded from biological processes, namely inflammation, cell proliferation, apoptosis and cell migration. Overall, the study reveals the stage-wise transcriptome analysis in conjunction with cellular processes as well as molecular signaling pathways during lizard tail regeneration. The knowledge obtained from the data can be extrapolated to configure regenerative responses in other amniotes, including humans, upon loss of a complex organ.

Gramicidin S and melittin: potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection

The COVID19 pandemic has led to multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of the well-studied antibacterial peptides gramicidin S and melittin obtained from Bacillus brevis and bee venom respectively. The EC50 values for gramicidin S and melittin were 1.571 µg and 0.656 µg respectively based on in vitro antiviral assay. Significant decrease in the viral load as compared to the untreated group with no/very less cytotoxicity was observed. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 h onwards with a maximal viral clearance after 24 h post infection. Proteomics analysis indicated that more than 250 proteins were differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 h post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.

Immunolocalization of Adenomatous Polyposis Coli protein (apc) in the regenerating lizard tail suggests involvement in tissue differentiation and regulation of growth

Lizard tail regeneration is likely regulated by the balanced activity of oncogenes and tumor suppressors that control cell proliferation avoiding tumorigenic degeneration. One of the main tumor suppressor genes present in the regenerating tail is the "adenomatous polyposis coli (apc)" but the localization of its coded protein (apc) is not known. This protein may be involved in regulation of apical-basal tail regeneration in lizards. The present immunohistochemical study shows that apc is localized in apical wound epidermis and regenerating ependyme, two tissues that proliferate and also express onco-genes. Apc is not present in blastema cells but localizes in differentiating cells of regenerating scales, muscles and less intensely in the non-apical ependymal epithelium and cartilage. This suggests that apc is involved in the induction of their differentiation. The apc immunolabeling is mainly nuclear in the basal epidermal layer of the apical wound epidermis where it may be involved in modulating keratinocytes proliferation, like in the forming scales. In regenerating muscle and cartilage apc is mainly cytoplasmic while sparse labeled nuclei are seen in proliferative areas of these tissues. In the regenerating spinal cord, the nuclear and cytoplasmic apc labeling is present in ependymal cells of the distal-most ependymal ampulla but the labeling fades in more proximal regions and mainly remains in the cytoplasm facing the central canal and in sparse nuclei. It is suggested that the pattern of immunolabeling for apc indicates that this tumor suppressor may contribute to tissue differentiation within the regenerating tail. This article is protected by copyright. All rights reserved.

Review. Limb regeneration in lizards under natural and experimental conditions with considerations on the induction of appendages regeneration in amniotes

BACKGROUND

Study on the failure of limb regeneration in lizards evidences the difficult problems met from amniotes to regenerate organs. Contrary to the tail, limb loss in terrestrial environment is generally fatal and no selection for its regeneration occurred during lizard evolution.

METHODS

Experimentally amputated limbs were fixed and embedded for microscopy.

RESULTS

After limb loss an intense inflammatory reaction occurs and immune cells are recruited underneath a wound epidermis, forming a vascularized granulation tissue. The regenerating epidermis takes 2-3 weeks to cover the limb stump since degenerating long bones must be excised first while a dense connective tissue is formed and no limb growth occurs. Cell proliferation occurs in granulation tissues and wound epidermis during the initial 2-3 weeks of wound healing but disappears later determining the arrest of growth. Transcriptome data indicates that the limb, contrary to the tail, activates numerous genes involved in inflammation, immunity and fibroplasia while down-regulates some proliferative and most myogenic genes. Attempts to stimulate limb regeneration, by implants of nervous tissues or growth factors such as FGFs only maintain proliferation for few weeks but eventually the scarring program prevails and only short outgrowths missing of autopodial elements are regenerated.

CONCLUSIONS

While lizard limbs show the typical scarring outcome of mammals, the comparison of genes activated in the regenerating tail has allowed identifying key genes implicated in organ regeneration in amniotes.

Review: Regeneration of the tail in lizards appears regulated by a balanced expression of oncogenes and tumor suppressors

BACKGROUND

Tail regeneration in lizards is the only case of large multi-tissue organ regeneration in amniotes.

METHODS

The present Review summarizes numerous immunolocalization and gene-expression studies indicating that after tail amputation in lizards the stump is covered in 7-10 days by the migration of keratinocytes. This allows the accumulation of mesenchymal-fibroblasts underneath the wound epidermis and forms a regenerative blastema and a new tail.

RESULTS

During migration keratinocytes transit from a compact epidermis into relatively free keratinocytes in a process of "Epithelial Mesenchymal Transition" (EMT). While EMT has been implicated in carcinogenesis no malignant transformation is observed during these cell movements in the regenerative blastema. Immunolabeling for E-cadherin and snail shows that these proteins are present in the cytoplasm and nuclei of migrating keratinocytes. The basal layer of the wound epithelium of the apical blastema express onco-proteins (wnt2b, egfr, c-myc, fgfs, fgfr, rhov, etc.) and tumor suppressors (p53/63, fat2, ephr, apc, retinoblastoma, arhgap28 etc.). This suggests that their balanced action regulates proliferation of the blastema.

CONCLUSIONS

While apical epidermis and mesenchyme are kept under a tight proliferative control, in more proximal regions of the regenerating tail the expression of tumor-suppressors triggers the differentiation of numerous tissues, forming the large myomeres, axial cartilage, simple spinal cord and nerves, new scales, arteries and veins, fat deposits, dermis and other connective tissues. Understanding gene expression patterns of developmental pathways activated during tail regeneration in lizards is useful for cancer research and for future attempts to induce organ regeneration in other amniotes including humans.