Biology subjects

Caicci, F.

Publications and source records attributed to Caicci, F..

12 recordsLinked to original sources

bioRxiv2026

A Living Oncogenic Microcell Isolated from Mammalian Cancers

The biological mechanisms underlying oncogenesis are traditionally interpreted within the frameworks of somatic mutation, clonal evolution, and, in some cases, viral infection. Here, we report the isolation, purification and characterization of a distinct class of autonomous microcellular organisms consistently recovered from independent mammalian neoplastic tissues. These entities measure approximately 1-3 microns in diameter and exhibit a reproducible organic wall assembly with internal compartmentalization revealed by transmission and scanning electron microscopy. Biochemical and molecular analyses demonstrated a predominantly RNA-based genetic system associated with intrinsic reverse transcriptase activity. High-throughput sequencing revealed a highly distributed multipartite genetic repertoire comprising approximately 2.63 Mb organized across 1,597 independent RNA units. Canonical bacterial signatures, including 16S ribosomal RNA, were not detected, and the recovered architecture lacked the genomic organization characteristic of known retroviruses. Instead, multiple RNA units contained domains related to reverse transcriptase, mobile genetic elements, regulatory functions, and oncogene-associated sequences. Purified preparations containing intact microcells induced rapid cellular transformation in vitro and aggressive malignancies in murine models. In contrast, matched preparations filtered through a 0.2 micron membrane failed to exhibit reverse transcriptase activity, cellular transformation, or tumorigenicity, demonstrating that the observed biological effects reside within intact micron-scale particles rather than filterable viral agents or soluble components. Furthermore, vaccination targeting the microcellular organisms was associated with tumour regression and restoration of tissue architecture in dogs with naturally occurring cancers. Collectively, these findings describe a previously unrecognized autonomous microcell lineage within mammalian hosts possessing distinctive structural, genetic and biological properties. The combination of cellular organization, a highly distributed multipartite RNA repertoire, intrinsic reverse transcriptase activity, and oncogenic potential suggest a biological strategy not readily accommodated within current frameworks of cancer biology, virology or cellular evolution.

cancer biology↗

bioRxiv2026

Morphological comparison between cell-like entities from mammalian tissues and Precambrian microfossils

The fossil record of the Precambrian era preserves some of the earliest evidence of life, yet these ancient microfossils primarily reveal morphology rather than function, leaving unresolved questions about how early cells lived, replicated and evolved. The RNA world hypothesis proposes that primordial organisms relied on RNA for both information storage and catalysis, but direct living systems reflecting such biology remain poorly characterized. Here we describe cell-like entities isolated from mammalian tissues, measuring approximately 1-3 m in diameter and exhibiting morphological similarity to a range of Precambrian microfossils. Ultrastructural comparisons reveal a high degree of correspondence with fossil taxa spanning the Paleoproterozoic to Ediacaran intervals ([~]1.8 Ga to [~]551 Ma). In addition to these morphological features, the entities display biochemical characteristics, including RNA-dominant nucleic acid content and particle-associated reverse transcriptase activity. These observations indicate that the cell-like entities described are not inert, but represent biologically active systems. The combined ultrastructural and biochemical features raise the possibility that biologically active entities comparable to those observed in Precambrian microfossils may occur in contemporary biological contexts.

paleontology↗

bioRxiv2023

Efficient Prohibitin 2 exposure during mitophagy depends on Voltage-dependent anion-selective channel protein 1.

Autophagic elimination of depolarized mitochondria (mitophagy) depends on Ubiquitin proteasome complex to expose the inner mitochondrial membrane-resident protein-Prohibitin 2 (PHB2). This uncovering facilitates its interaction with autophagosomal membrane-associated protein LC3. It remains unclear whether PHB2 is uncovered randomly through mitochondrial rupture sites. Prior knowledge and initial screening indicated that Voltage-dependent anion-selective channel protein 1 (VDAC1) might play a role in this process. Through in vitro biochemical assays and imaging, we have found that VDAC1-PHB2 interaction increases during mitochondrial depolarization. Subsequently, this interaction enhances the efficiency of PHB2 exposure and mitophagy. To investigate the relevance in vivo, we utilized a Porin (equivalent to VDAC1) knockout Drosophila line. Our findings demonstrate that during rotenone-induced mitochondrial stress, Porin is essential for PHB2 exposure, PHB2-LC3 interaction, and mitophagy. This study highlights that VDAC1 predominantly synchronizes efficient PHB2 exposure through mitochondrial rupture sites during mitophagy. These findings may provide insights to understand progressive neurodegeneration.

cell biology↗

bioRxiv2023

New permanent stem cell niche for development and regeneration in a chordate

Stem cell niches are defined as the microenvironments where stem cells home, receiving stimuli defining their fate. In vertebrates, stem cell niches are stable and physically confined compartments. Botryllus schlosseri is an invertebrate colonial chordate where temporary stem cell niches have been identified in adult individuals that are cyclically resorbed and replaced by a new generation of clonal zooids. B. schlosseri also displays remarkable regenerative abilities, being capable of whole-body regeneration, but the cellular source of these processes is still unknown. Here we identified by means of a high-resolution morphological characterization a new putative stem cell niche in the ampullae of the circulatory system acting as a stem cell source during asexual reproduction. Stem cells of the ampullae travel via the circulatory system and contribute to the development of several organs and could explain where stem cells contributing to whole-body regeneration are stored. The ampullae niches are stable during the life cycle and regeneration of B. schlosseri, while additional niches of the zooid are dynamically established and colonised by circulating stem cells. Our results reveal an unprecedented dynamicity of stem cell niches in highly regenerative invertebrates.

cell biology↗

bioRxiv2023

NON-TOXIC ACID-FREE GLYOXAL FIXATIVE FOR VETERINARY HISTOPATHOLOGY, IMMUNOHISTOCHEMISTRY AND MOLECULAR ANALYSIS

Formaldehyde fixation is worldwide the most used system for histopathological examination. However, its toxicity is well known, and preservation of proteins and nucleic acids is not optimal. Alternative fixatives warranting similar morphological quality of tissues and costs, but lacking toxicity and allowing better preservation of proteins and nucleic acids would therefore increase both safety of operators and quality of molecular analysis in pathology. This multi-institutional study aimed to compare the morphological, histochemical, immunohistochemical (IHC), and molecular analyses outcomes of a newly patented, non-toxic, acid-free Glyoxal (GAF) fixative with neutral buffered formaldehyde (NBF). Tissues from a total of 73 subjects were analyzed, including 13 necropsies. Gross features were preserved after GAF fixation, with no tissue hardening or discoloration. Cellular ultrastructure was also better preserved with GAF and histology and histochemistry on GAF-fixed samples showed good results when compared to NBF-fixed samples, with the exception of loss of tinctorial affinity of erythrocytes and mast cell granules. IHC analyses also showed comparable results with only slight and rare protocol adjustment. DNA and RNA yields were higher from GAF-fixed samples (P<0.05) and the tested genes (p53 and COX1) were better amplified. RNA scope showed positive results for c-KIT expression in GAF-fixed mast cell tumors. Based on these data, the non-toxic GAF fixative allows good macroscopical, histological and immunohistochemical analyses of tissue samples, including on-field application, and better molecular analyses when compared to NBF. This represents a promising possibility for teaching, diagnostic, and research in veterinary pathology.

pathology↗

bioRxiv2023

USP8 inhibition promotes Parkin-independent mitophagy in the Drosophila brain and in human neurons

Stress-induced mitophagy, a tightly regulated process that targets dysfunctional mitochondria for autophagy-dependent degradation, mainly relays on two proteins, PINK1 and Parkin, which genes are mutated in some forms of familiar Parkinsons Disease (PD). Upon mitochondrial damage, the protein kinase PINK1 accumulates on the organelle surface where it controls the recruitment of the E3-ubiquitin ligase Parkin. On mitochondria, Parkin ubiquitinates a subset of mitochondrial resident proteins located on the outer mitochondrial membrane, leading to the recruitment of downstream cytosolic autophagic adaptors, and subsequent autophagosome formation. Importantly, PINK1/Parkin-independent mitophagy pathways also exist that can be counteracted by specific deubiquitinating enzymes (DUBs). Downregulation of these specific DUBs can presumably enhances basal mitophagy, and be beneficial in models in which accumulation of defective mitochondria is implicated. Among these DUBs, USP8 is an interesting target because of its role in the endosomal pathway and autophagy, and its beneficial effects, when inhibited, in models of neurodegeneration. Based on this, we evaluated autophagy and mitophagy levels when USP8 activity is altered. We used genetic approaches in D. melanogaster to measure autophagy and mitophagy in vivo, and complementary in vitro approaches to investigate the molecular pathway that regulates mitophagy via USP8. We found an inverse correlation between basal mitophagy and USP8 levels, in that inhibition of USP8 correlates with increased Parkin-independent mitophagy. These results suggest the existence of a yet uncharacterized mitophagic pathway that is inhibited by USP8.

cell biology↗

bioRxiv2022

Single extracellular vesicle analysis in human amniotic fluid shows evidence of phenotype alterations in preeclampsia

Amniotic fluid surrounding the developing fetus is a complex biological fluid rich in metabolically active bio-factors. The presence of extracellular vesicles (EVs) in amniotic fluid has been mainly related to fetal urine. We here characterized EVs from term amniotic fluid in terms of surface marker expression using different orthogonal techniques. EVs appeared to be a heterogeneous population expressing markers of renal, placental, epithelial and stem cells. Moreover, we compared amniotic fluid EVs from normal pregnancies with those of preeclampsia, a hypertensive disorder affecting up to 8% of pregnancies worldwide. An increase of CD105 (endoglin) expressing EVs was observed in preeclamptic amniotic fluid by bead-based cytofluorimetric analysis, and further confirmed using a chip-based analysis. HLA-G, a typical placental marker, was not co-expressed by the majority of CD105+ EVs, suggesting their origin from amniotic fluid cells. At a functional level, preeclampsia-derived EVs, but not normal pregnancy EVs, showed an antiangiogenic effect, possibly due to the decoy effect of endoglin. In addition, several miRNAs were differentially expressed in preeclampsia-derived EVs and directly related to the modulation of angiogenesis and trophoblast function. Our results provide a characterization of term amniotic fluid-EVs, supporting their origin from fetal and placental cells. In preeclampsia, the observed antiangiogenic characteristics of amniotic fluid-EVs may reflect the hypoxic and antiangiogenic microenvironment and could possibly impact on the developing fetus or on the surrounding fetal membranes.

molecular biology↗

bioRxiv2021

Stemness activity underlying whole brain regeneration in a basal chordate

Central nervous system (CNS) regeneration extent is highly diverse across the metazoans, with adult mammals demonstrating limited ability1,2. Understanding how neurons regenerate following injury remains a central challenge in regenerative medicine. Although conserved pathways associated with neural regeneration have been identified3,4, a study describing the stepwise morphogenetic changes that take place throughout a complete CNS regeneration is lacking. Utilizing the highly regenerative tunicate model Polycarpa mytiligera5, we characterized the morphological, cell proliferation, and transcriptomic dynamics that lead to entire CNS regeneration. The regenerated CNS of adult P. mytiligera expressed key neurodevelopmental markers that are not otherwise present in the adult CNS. Removal of the entire CNS resulted in high cell proliferation in the regenerated area. Transcriptome analysis revealed enhanced stem-cell related gene activity, with high expression of P53 and piRNA pathways preceding the activation of Notch, Wnt, and Nanos pathways. The CNS regeneration atlas created here depicts the transcriptomic landscape of the entire CNS regeneration process, revealing the core pathways that regulate neuronal response to injury, and the regeneration stage at which they are most pronounced. The molecular and cellular mechanisms controlling regenerative capacity that this atlas reveals could be used to develop approaches to enhancing neurogenesis in closely-related chordate species, including humans.

developmental biology↗

bioRxiv2021

Revealing conserved mechanisms of neurodegeneration in a colonial chordate

Loss of the brains functional ability is a common symptom of aging and neurodegenerative diseases1,2. While the genetic and molecular mechanisms underlying human neurodegeneration are studied in-depth3-6, very little is known about the evolutionary origin of these traits and their involvement in loss of nervous system function in aged invertebrate species. Here we study evolutionarily conserved elements of brain degeneration using the colonial chordate model species Botryllus schlosseri. B. schlosseri reproduces both sexually and asexually7, with adult brains regenerating and degenerating multiple times throughout its adult life. Combining microscopy, transcriptomics and behavioral assays, we characterized adult brains from diverse stages and ages. We found that the number of neurons fluctuates each week, reaching a maximum of [~]1000 cells, and thereafter decreasing while the number of immunocytes increases. Comparing the number of neurons in the adult brains of young and old colonies, we found that older brains are smaller and contain fewer cells. Both during weekly degeneration cycles and overall with age, the decrease in neuron number correlates with reduced response to stimuli and with significant changes in the expression of genes with mammalian homologs associated with neural stem cells and neurodegenerative pathways. These results suggest persistent neural stem cell activity across ages and that cellular and molecular mechanisms of neurodegeneration are evolutionary conserved between tunicates and humans.

neuroscience↗

bioRxiv2020

A transforming giant virus discovered in Canine Transmissible Venereal Tumour: Stray dogs and Tasmanian devils opening the door to a preventive cancer vaccine.

BackgroundCanine Transmissible Venereal Tumour (CTVT) along with Tasmanian Devil Facial Tumour and transmissible leukaemia in Mya Arenaria soft shell-clams are the only examples of contagious cancers occurring in nature. In particular, CTVT is the oldest contagious cancer present in the wild world. The attempts to detect a transmissible virus as a causative agent in these forms of contagious cancer proved conflicting and the current consensus view is that a transformed somatic cell itself is transmitted and starts the tumor in a new animal, as a parasitic allograft. We modify this perception and report for the first time the isolation of an acutely transforming agent from CTVT. MethodsLarge particles were successfully isolated from CTVT specimens through a sucrose gradient, examined at electron microscopy, fully sequenced, used for transformation tests on NIH-3T3 cells and tumorigenic experiments in dogs. A neutralizing therapeutic vaccine was also administered in dogs with natural, not-induced CTVT. ResultsThe particles, isolated from CTVT, are infectious living entities with large dimension. Electron Microscopy reconstructed an organic wall assemblage pattern typical of early life fossils from the Precambrian age, time at which Earth began to form 4.6 billion years ago. Astonishingly, our agents are not fossils, but unicellular organisms biologically active and acutely transforming. They transformed NIH-3T3 cells in vitro and initiated the typical CTVT lesions in healthy dogs, just one week post-infection. Only the fraction containing these infectious entities were able to induce cancer, while a filtered supernatant did not. This ruled out the presence of conventional filterable viruses. RNA sequencing and bioinformatics analyses disclosed a large genome composed by an almost complete Orphan genes dataset, with retro-elements distinct from the host genome. Five doses of a neutralizing vaccine against these oncogenic organisms, drastically reduced the neoplastic mass in dogs with natural, not-induced CTVT. Analogous infectious agents, acutely transforming were also isolated from several human neoplasms. ConclusionsModifying the current believe that contagious cancers are transmitted by a somatic cells allograft, we identified a living agent that infects and starts the typical CTVT in healthy dogs, while its neutralization with a vaccine induces cancer regression in animals with cancer. Significance StatementThese infectious living single-cell agents establish a new family of oncogenic organisms that resist current classifications and affect humans and animals in the wild. While only a dozen of proteins compose a classic virus, these organisms are small infectious cells, but very distinct from somatic eukaryotic cells. The identification of causative unicellular organisms that start cancer in healthy subjects and the possibility to induce cancer regression with a neutralizing vaccine change some perspectives in cancer. The Precambrian features and the genetic composition suggest that these unicellular entities are infectious living RNA protocells that finally gives form to what was considered only a hypothesis drafted by the Nobel laureate Walter Gilmore: the RNA world, the origin of life and RNA protocells.

cancer biology↗

bioRxiv2019

Discovery Of The First Human Retro-Giant Virus: Description of its morphology, retroviral kinase and ability to induce tumours in mice

BackgroundThe study of retroviruses dates back to the early 1900s during investigations on neoplastic diseases in chickens. Subsequently, Robert Gallo reported the first human retrovirus HLTV in 1980. What we report here is not an archetypal retrovirus, but the discovery of an oncogenic giant microbial agent with a mega-genome, where the transforming retroviral nature co-exists with multiple archaeal oncogenes. MethodsAfter their isolation from human T cells Leukaemia, these organisms were examined at electron microscopy, tested for reverse transcriptase activity, fully sequenced, used for transformation tests on NIH-3T3 cells in vitro and tumours formation in mice. Same type of particles were also isolated from Canine Transmissible Venereal Tumour (CTVT), the oldest contagious cancer in nature. ResultsEM showed the presence of giant viral particles displaying retroviral antigens. These microbial entities harbour in their mega-genome a transforming retroviral kinase, cell-based oncogenes and have reverse transcriptase activity. The purified viral particles transformed NIH-3T3 cells and induced metastatic tumours in nude mice, three weeks post infection. Ruling out the possible presence of filterable retroviruses, a filtered supernatant did not display RT activity and did not transforms. ConclusionsWe discovered an ancestral microbial agent, acutely transforming. For its giant dimensions, the ability to retain the Gram stain, the presence of a mega-genome and its retroviral nature, we tentatively named the agent Retro-Giant-Virus (RGV). However, distinct from amoeba giant Mimiviruses, this transforming human agent has a different nature and does not require for its isolation amoeba co-culture, since amoeba is not its natural host. The morphology, biology and genetic features allocate this mammalian giant microbe halfway in between a classic oncogenic virus and an infectious cancer cell. Its transforming nature goes with its constant ability to induce tumours formation in mice.

cancer biology↗

bioRxiv2019

Molecular and Morphological Signatures of Chordate Development: Two Distinct Pathways, One Tunicate

All chordates, including urochordates such as tunicates, develop through embryogenesis. The chordate larvae of colonial tunicates metamorphose to lose all chordate structures such as notochord, neural tube, segmented musculature, and then develop by asexual reproduction [blastogenesis], whereby stem cells form tissues and organs. These two developmental pathways establish the same body axis, morphogenetic patterning and organ formation. It is unknown if this convergent morphology implies convergent cellular and molecular mechanisms, and whether the stem cells that mediate these processes differ. Using the colonial tunicate Botryllus schlosseri, we combined transcriptome sequencing and multiple microscopy techniques to study the molecular and morphological signatures of cells at each developmental stage of embryogenesis and blastogenesis. This revealed that the molecular programs are distinct, but the blastogenic tissue-specific stem cells and embryonic precursor populations share similar molecular profiles. By comparing embryogenesis in other chordates we found shared developmental principles, highlighting transcription factors as key evolutionary conserved elements. This study establishes a platform for advancing the science of stem cell biology and regulation of development and regeneration.

developmental biology↗