Kurzgesagt – In a Nutshell
Sources – Virome
We are thankful to the experts for their critical reading and input to the script:
Professor Colin Hill
School of Microbiology, University College Cork, Ireland
Associate Professor Jeremy Barr
Head of Bacteriophage Biology Research Group, Monash University, Australia
– A new frontier of science, something truly new that we are only just beginning to understand. Let us dive into the wild world of the human virome.
#Bai GH, Lin SC, Hsu YH, Chen SY. The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses. 2022
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876576/
Quote: “The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships.”
– You are a living, breathing ecosystem made of up to 40 trillion cells. This metropolis of flesh is home to the human microbiome, another 40 trillion bacteria that have a contract with your body: They get to live here and in return they break down your meals. They synthesise vitamins in your gut, neutralise acid in your mouth, help balance your immune system, and they take up space preventing harmful bacteria from getting in.
To simplify things, we will mention bacteria here. However, the human microbiome consists of numerous other microorganisms, such as viruses and fungi.
#Bai GH, Lin SC, Hsu YH, Chen SY. The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses. 2022
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876576/
Quote: “A wide range of microorganisms are found in the human body, including viruses, bacteria, archaea, fungi, and protozoa. The communities of microorganisms and their interactions both with one another and the host have strong impacts on human health and disease [1]. The virome is the viral fraction of the microbiome, and it is dominated by bacteriophages that infect bacteria as well as eukaryotic viruses that infect human cells.”
#Hatton et al. The human cell count and size distribution. 2023.
https://www.pnas.org/doi/full/10.1073/pnas.2303077120#sec-2
Quote: “We consider the body of a representative male (70 kg), which allows further estimates of a female (60 kg) and 10-y-old child (32 kg). We build a hierarchical interface for the cellular organization of the body, giving easy access to data, methods, and sources (https://humancelltreemap.mis.mpg.de/). In total, we estimate total body counts of ≈36 trillion cells in the male, ≈28 trillion in the female, and ≈17 trillion in the child.”
#Ron Sender, Shai Fuchs ,Ron Milo. Revised Estimates for the Number of Human and Bacteria Cells in the Body. 2016.
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533
Quote: “Reported values in the literature on the number of cells in the body differ by orders of magnitude and are very seldom supported by any measurements or calculations. Here, we integrate the most up-to-date information on the number of human and bacterial cells in the body. We estimate the total number of bacteria in the 70 kg "reference man" to be 3.8·10^13. For human cells, we identify the dominant role of the hematopoietic lineage to the total count (≈90%) and revise past estimates to 3.0·10^13 human cells. Our analysis also updates the widely-cited 10:1 ratio, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and their total mass is about 0.2 kg.”
Hou, K., Wu, ZX., Chen, XY. et al. Microbiota in health and diseases. Sig Transduct Target Ther 7, 135 (2022).
https://doi.org/10.1038/s41392-022-00974-4
Quote: “The composition of microbiota varies from site to site (depicted in Fig. 1). Gut microbiota is considered the most significant one in maintaining our health.4 The gut bacteria serve several functions, such as fermentation of food, protection against pathogens, stimulating immune response, and vitamin production.5”
#Begic, G. et al. (2023): Streptococcus salivarius as an Important Factor in Dental Biofilm Homeostasis: Influence on Streptococcus mutans and Aggregatibacter actinomycetemcomitans in Mixed Biofilm. International Journal of Molecular Science, Vol. 24 (8)
https://www.mdpi.com/1422-0067/24/8/7249
Quote: “However, it does not tolerate low pH levels. S. salivarius has a urease system and can lower pH by creating an alkaline microenvironment [58,59].”
– This is a fragile balance – bacteria really only look out for themselves, multiplying and testing their boundaries. To keep their numbers in check, your body's ecosystem needs a group of deadly predators: Viruses. At least ten trillion.
#Liang, G. & Bushman, F. D. (2021): The human virome: assembly, composition and host interactions. Nature Reviews Microbiology (19)
https://www.nature.com/articles/s41579-021-00536-5
Quote: “The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the ‘virome’. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity.”
– They are literally everywhere in your body, tens of thousands of different species.
Estimates vary widely, from tens of thousands to hundreds of thousands in the gut alone.
#Camarillo-Guerrero, L.F. et al. (2021): Massive expansion of human gut bacteriophage diversity. Resource, Vol. 184 (4)
Quote: “Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.”
#Liang, G. & Bushman, F. D. (2021): The human virome: assembly, composition and host interactions. Nature Reviews Microbiology (19)
https://www.nature.com/articles/s41579-021-00536-5
Quote: “A recent study constructed 33,242 viral species from 32 available public human virome studies, and >32,000 species were predicted to be phages, which is 12-fold higher than the phage number in the RefSeq database133. Thus, metagenomic sequencing boosts the discovery of novel viral genomes enormously.”
– At least a few trillion live in your gut, where also most of your resident bacteria are. At least 18 billion on your skin, 100 million in each drop of your saliva, dozens of millions in your urinary tract. Even in a single drop of the cerebrospinal fluid surrounding your nerves and brain, researchers found up to 10,000 viruses.
The abbreviation “VLP” stands for “virus-like particles” and indicates that in some cases it is not yet certain whether there are viruses that can replicate.
#Liang, G. & Bushman, F. D. (2021): The human virome: assembly, composition and host interactions. Nature Reviews Microbiology (19)
https://www.nature.com/articles/s41579-021-00536-5
Quote: “The discovery of so much dark matter is not surprising, given that seawater has ~107 virus-like particles (VLPs) per millilitre and faeces ~109 VLPs per gram. In these studies, particles that look like viral particles are not commonly verified as replication competent; thus, the term VLP is used to reflect the fact that we are uncertain that these particles are replication-competent viruses, although for many it seems likely. These vast populations, inferred to be mostly unstudied phages, are extremely diverse in the number of types as well as overall numbers of particles.”
Quote: “Gastrointestinal tract
The gastrointestinal tract is commonly the most abundant site of viral colonization, reaching ~109 VLPs per gram of intestinal contents. Analysis of virome sequence data suggests that phages are the most abundant identifiable members of this population (reviewed in refs9,10,35,36,37,38).
Quote: “Oral cavity
The human oral cavity contains diverse viral communities as well as complex microbial populations. To date, saliva samples have been the primary source of material to characterize the oral virome40,53, revealing abundant viral populations. Additional oral microenvironments, such as dental plaque54, have also been studied, revealing high diversity in these environments as well. Staining of particles with a fluorescent dye that binds DNA, followed by visualization under a fluorescent microscope, shows approximately 108 VLPs per millilitre of saliva in healthy humans55. The most abundant taxon of phages in the oral virome is the Caudovirales40,41,56.”
Quote: “Urogenital system
Urine samples from healthy humans have been reported to contain viruses in the region of 107 VLPs per millilitre72. Most of the identifiable viruses were phages; in addition, human papillomaviruses could be identified in >90% of subjects in some cohorts72,73. Virome analyses of healthy vaginal samples showed that the majority of identified viral sequences are derived from double-stranded DNA phages, with eukaryotic viruses contributing only 4% of total reads74. In seminal fluid, Anelloviridae, Herpesviridae and multiple genotypes of Papillomaviridae have been detected75. Thus, for these body sites we again see mixtures of viruses that replicate in human cells and viruses from the resident microbiota.”
Quote: “Nervous system
Little information is available on virome populations in the nervous system in healthy humans. A recent study estimated the VLP number at ~104 per millilitre of cerebrospinal fluid, with phages predominant, including Myoviridae, Siphoviridae and Podoviridae76. Herpesviridae were also detectable76. The clinical consequences of infection by herpesviruses in the nervous system have been well studied. Herpes simplex viruses, human cytomegalovirus and varicella zoster virus can establish latent infections in the central nervous system without symptoms77,78; these viruses can later be reactivated and produce viral particles78.”
For the bacteria on the skin, we took the average size of an adult man's skin and multiplied it by the number of bacteria per square centimeter. We have limited ourselves to the pure surface. If we were to include areas such as sweat glands, the figure would be even higher.
1 million bacteria per cm2 of skin x average 18,000 cm2 of skin on adult men = 18 billion
#Chen, Y.E .& Tsao,H. (2013): The skin microbiome: current perspectives and future challenges. Journal of the American Academy of Dermatology, Vol. 69 (1)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686918/#R1
Quote: “An estimated 1 million bacteria, with hundreds of distinct species, inhabit each square centimeter of skin1.”
#Richardson, M. (2003): Understanding the structure and function of the skin. Nursing times, Vol. 99(31)
https://pubmed.ncbi.nlm.nih.gov/13677123/
Quote: “The skin is the largest organ of the body and consists of an epidermis, dermis and subcutaneous adipose tissue. The skin surface area is often stated to be about 1.8 to 2m2 and represents our interface with the environment; however, when one considers that microorganisms live in the hair follicles and can enter sweat ducts, the area that interacts with this aspect of the environment becomes about 25–30 m2.”
– While this sounds like a horrible idea at first, at least in the gut, around 97% of them are bacteriophages, or phages, bizarre creatures that are specialised in hunting down and killing resident bacteria and are not able to infect your cells. Instead they kill trillions of bacteria every single day.
#Avellaneda-Franco, L. et al. (2023): The gut virome and the relevance of temperate phages in human health. Frontiers in Cellular and Infection Microbiology, Vol. 13
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10413269/
Quote: “While more than 60% of gut viral contigs cannot be assigned to a taxonomic level, upwards of 97% of the contigs that can be assigned represent bacteriophages (Shkoporov et al., 2019; Garmaeva et al., 2021).”
#Shkoporov, A. N. & Hill, C. (2019): Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome. Cell Host & Microbe, Vol. 25 (2)
Quote: “In a study with just 13 human donors, we were able to assemble 8,920 putative non-redundant complete and partial viral genomes, of which only 161 (1.8%) could be assigned to known viral taxa (with >50% identity over 90% of contig length). Of these, 157 were bacteriophages, two were human papillomaviruses, and one was a plant RNA virus (Shkoporov et al., 2018b).”
According to our experts, there are no specific calculations for this “kill count”. figure. You can only make a very rough estimate, for example by taking figures from other environments and applying them to the human body.
If we assume that almost 40 trillion bacteria live in the human body and we know figures that, for example, in marine environments viruses kill 20 to 40% of all bacteria every day, you get a small two-digit number of bacteria that could be killed by viruses every day.
#Sender, R. et al. (2016): Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, Vol. 14 (8)
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533&mod=article_inline
Quote: “We are now able to repeat the original calculation for the number of bacteria in the colon [3]. Given 0.9x1011 bacteria/g wet stool as derived in Box 2 and 0.4 L of colon, we find 3.8x1013 bacteria in the colon with a standard error uncertainty of 25% and a variation of 52% SD over a population of 70 kg males. Considering that the contribution to the total number of bacteria from other organs is at most 1012, we use 3.8x1013 as our estimate for the number of bacteria across the whole body of the "reference man.”
#Brown, T. L. et al. (2022): Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut. Current Opinion in Microbiology, Vol. 70
https://www.sciencedirect.com/science/article/pii/S1369527422001138
Quote: “The ocean encompasses a vast diversity of biomes, from shallow coastal waters to the darkness of the abyssalpelagic depths. Phages can contribute to ocean communities by regulating bacterial levels, as it is thought they lyse 20–40% of ocean bacteria every day, which is consistent with phages succeeding through KtW dynamics and cycling of dominant bacteria [1].”
– Together these viruses make up the human virome – a symbiotic virus ecosystem that is completely unique to you and that seems to be crucial for your health.
#Bai GH, Lin SC, Hsu YH, Chen SY. The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses. 2022
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876576/
Quote: “The human virome comprises the set of all viruses in the human body, including bacteriophages, eukaryotic viruses, and endogenous retroviruses (Figure 2) [15,22]. These viruses are present throughout the human body, in the gut, skin, and oral cavity, and can be found in various sample types, including blood, feces, and cerebrospinal fluid. Certain viruses can be acquired through birth and continue to be seeded from the maternal microbiome and shaped by dietary habits as well as intimate contact [12].”
#Liang, G. & Bushman, F. D. (2021): The human virome: assembly, composition and host interactions. Nature Reviews Microbiology (19)
https://www.nature.com/articles/s41579-021-00536-5
Quote: “Numerous factors have been reported to influence the human virome and, ultimately, affect health (Fig. 4), starting in infancy and extending throughout the life of the individual.”
– Inside your gut, a stealthy Lambda Phage floats through the buzzing crowds of bacteria, looking for a victim. It has six legs, a long thin body and a big head, made of geometric shapes, filled with genetic material. Each species is specialized in hunting one specific species of bacteria and ignores all others. Lambda is looking for Escherichia coli.
#Chatterjee, S. & Rothenberg, E. (2012): Interaction of Bacteriophage λ with Its E. coli Receptor, LamB. Viruses, Vol. 4 (11)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509688/
Quote: “Bacteriophage λ consists of an icosahedrally symmetric (5,3,2 rotational symmetries) head of diameter 60 nm encapsulating the 48,502 bp double strand DNA molecule and a flexible tail through which the viral DNA expel during infection (Figure 1) [28,29]. Following infection, the invading phage DNA can either replicate within the host, forming new phages and propagate by lysing the host cell (lytic pathway), or it can become a prophage by integrating its DNA into the host chromosome, which then replicate as a part of host chromosome (lysogenic pathway). However, a switch from lysogenic to lytic pathway can be induced where the prophages can replicate independently, assemble the head and tail, forming new viruses and promoting lysis for further propagation [10,11,12].
(...)
The adsorption of λ phages onto bacterial surface is the first step in the infection process [15]. At this stage, phages can either dissociate from the host cell, known as desorption or alternatively bind irreversibly to the host cell [14]. However, once the phage irreversibly bind to the cell surface it triggers a series of poorly understood events and finally delivers its DNA into the bacterial cytoplasm through the channel formed by its tail, leaving the phage protein capsid behind. The tail fibers of bacteriophages are also important to make specific contacts with receptor molecules on the surface of the bacterial cell.
– This versatile bacteria is numerous in your gut, usually a good boy synthesising vitamins for you. But it also has a dark side – some of them would much rather live inside your flesh and feast on your resources. If there are too many or if they manage to invade your tissue, they can cause serious diseases. So one of the most important jobs of the virome is to control the numbers of different bacteria populations. By killing them.
#Mueller, M. et al. (2023): Escherichia coli Infection. National Library of Medicine
https://www.ncbi.nlm.nih.gov/books/NBK564298/
Quote: “Escherichia coli (E. coli) is a gram-negative bacillus known to be a part of normal intestinal flora but can also be the cause of intestinal and extraintestinal illness in humans. There are hundreds of identified E. coli strains, resulting in a spectrum of disease from mild, self-limited gastroenteritis to renal failure and septic shock. Its virulence lends to E. coli’s ability to evade host defenses and develop resistance to common antibiotics.
(...)
E. coli is part of commensal intestinal flora and is also found on the floors of hospitals and long-term care facilities. E. coli is the most common gram-negative bacteria in the human gastrointestinal tract and lacks virulence in this setting. However, when found outside of the intestinal tract, E. coli can cause urinary tract infections (UTI), pneumonia, bacteremia, and peritonitis, among others.[2][3][4]”
(...)
Escherichia coli results in intestinal illness as well as infection outside of the intestine. Intestinal illness caused by E. coli is caused by one of five subtypes, and they are identified according to their O and H antigens.
(...)
Extraintestinal illness caused by E. coli results from a translocation of gut bacteria into other parts of the body or the environmental spread in hospitals and long term care facilities. E. coli is the predominant gram-negative bacteria to cause extraintestinal illness in humans and can cause urinary tract infection, abdominal and pelvic infection, pneumonia, bacteremia, and meningitis, among others.
– Lambda has found a victim. Spider-like legs get a hold of a bacteria and grip it hard. Like an angry syringe it violently rams its sharp bottom into the victim’s body and releases its DNA.
Once inside, the proteins disable the defenses of the bacterium It is now a factory under new management. It is forced to build new viruses until the victim is filled up and bursts open, releasing a horde of fresh Lambda viruses.
#Maffei, E. et al. (2021): Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection. PLoS biology, Vol. 19(11)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594841/#pbio.3001424.ref007
Quote: “Bacteriophages, the viruses infecting bacteria, are the most abundant biological entities on earth with key positions in all ecosystems and carry large part of our planet’s genetic diversity in their genomes [1–3]. Out of this diversity, a few phages infecting Escherichia coli became classical models of molecular biology with roles in many fundamental discoveries and are still major workhorses of research today [4]. The most prominent of these are the seven “T phages” T1 to T7 ([5]; reviewed in [6]) and bacteriophage lambda [7]. Like most known phages, these classical models are tailed phages or Caudovirales that use characteristic tail structures to bind host surface receptors and to eject their genomes from the virion head into the host cell. Three major virion morphotypes of Caudovirales are known, myoviruses with a contractile tail, siphoviruses with a long and flexible tail, and podoviruses with a very short, stubby tail [2]. While the T phages are all so-called virulent phages that kill their host to replicate at each infection event, lambda is a temperate phage and can either kill the host to directly replicate or decide to integrate into the host’s genome as a prophage for transient passive replication by vertical transmission in the so-called lysogen [2,8]. These 2 alternative lifestyles as obligately lytic or as temperate phages have major implications for viral ecology and evolution: While virulent phages have primarily been selected to overcome host defenses and maximize virus replication, temperate phages characteristically encode genes that increase the lysogens’ fitness, e.g., by providing additional bacterial immunity systems to fight other phages [8,9].”
– Phages need a healthy population of bacteria to survive. So sometimes they choose a way more sinister tactic. Instead of killing their victim, the virus integrates its DNA into the genome of the bacteria and goes to sleep. When the bacteria multiplies, the virus DNA is multiplied too. Until one day the viral DNA re-awakens and suddenly decides to kill its unsuspecting victim.
#Maffei, E. et al. (2021): Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection. PLoS biology, Vol. 19(11)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594841/#pbio.3001424.ref007
Quote: “While the T phages are all so-called virulent phages that kill their host to replicate at each infection event, lambda is a temperate phage and can either kill the host to directly replicate or decide to integrate into the host’s genome as a prophage for transient passive replication by vertical transmission in the so-called lysogen [2,8]. These 2 alternative lifestyles as obligately lytic or as temperate phages have major implications for viral ecology and evolution: While virulent phages have primarily been selected to overcome host defenses and maximize virus replication, temperate phages characteristically encode genes that increase the lysogens’ fitness, e.g., by providing additional bacterial immunity systems to fight other phages [8,9].”
This process in which the host produces new virus building blocks, assembles them, breaks them up and releases replicas of the phage is called lytic growth or cycle (see diagram below). The state in which the virus DNA lies “dormant” in the host is the lysogeny or lysogenic pathway.
#Liang, G. & Bushman, F. D. (2021): The human virome: assembly, composition and host interactions. Nature Reviews Microbiology (19)
https://www.nature.com/articles/s41579-021-00536-5
Quote: “Lytic phages inject their nucleic acid into cells, leading to the synthesis of new viral components, the assembly of particles and the lysis of host cells, thus releasing progeny phages. Another mode of replication, carried out by temperate phages, can spare the host initially. Phages inject DNA into cells, after which the DNA can then become integrated into the host cell chromosome, forming a prophage. Prophages are maintained in a quiescent state by repressor proteins23. However, should conditions become unfavourable in the host cell — for example, by damage to DNA — phage DNA can become excised from the cellular chromosome leading to lytic growth, resulting in cell lysis and the production of viral progeny. Phages can also have other relationships with their hosts — one is pseudolysogeny, in which phage genomes persist as episomes without integration. In another mode, phages can bud out of infected cells, sparing the host cell from lysis and death.”
#Ezzatpour, S. et al. (2023): The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases. Nutrients, Vol. 15 (4)
– And here things become exciting – your virome also needs you to thrive. It’s in its best interest that you are healthy. So some viruses inject genes into bacteria that actively make them support your body. Some force their bacteria hosts to support your gut’s mucus layer, break down complex carbohydrates from your food more efficiently, creating substances that protect against inflammation.
#Brown, E. M. et al. (2021): Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host and Microbe, Vol. 29 (9)
Quote: “Here, we show that ADPRTs are present, secreted, and enzymatically active in commensal isolates spanning the majority of prokaryotic taxa known to colonize the gut, including Archaea. These genes encode a unique protein class we named commensal-associated ribosyltransferase (crt) and are mostly found in bacteriophage elements. To better understand the functions of commensal ADPRTs, we characterized Bxa, one of the most abundant and prevalent ADPRTs in Bacteroides. Bxa is induced by oxidative stress and bile acids, binds to ganglioside lipids on the epithelial cell surface, and targets non-muscle myosin II proteins. Addition of Bxa to epithelial cells alters the actin cytoskeleton and induces secretion of inosine, which Bacteroides can use as a sole carbon source. Bxa also increases mucosal adherence of Bacteroides to epithelial cells in vitro and in vivo. Together, our data suggest that ADPRTs are prevalent in commensal bacteria and encode numerous functions that include conferring fitness advantages in the gut environment.
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The Bacteroides ADPRT Bxa is encoded by a functional phage and targets NMMII proteins to modify epithelial cell biology. Further, presence of bxa enhances colonization of the colonic epithelium and confers a competitive advantage in vivo. Our data suggest that phages transfer fitness factors in the form of ADPRTs, which are utilized by bacteria to promote survival of the strain and the lysogenic phage itself.
#Barr, J.J. et al. (2013): Bacteriophage adhering to mucus provide a non–host-derived immunity. Nutrients, Vol. 15(4)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696810/
Quote: “Also present in the mucus environment are bacteriophage (phage), the most common and diverse biological entities. As specific bacterial predators, they increase microbial diversity through Red Queen/kill-the-winner dynamics (32, 33). Many phages establish conditional symbiotic relationships with their bacterial hosts through lysogeny. As integrated prophages, they often express genes that increase host fitness or virulence (34– 36) and protect their host from lysis by related phages. As free phage, they aid their host strain by killing related competing strains (37–39). Phages participate, along with their bacterial hosts, in tripartite symbioses with metazoans that affect metazoan fitness (40–43). However, no direct symbiotic interactions between phage and metazoans are known.
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Currently, there is evidence that phages can stimulate and modulate the immune system of the host by various mechanisms. Indeed, phages can colonize the intestinal mucus layer, directly bind to mucin glycoproteins via their capsis, and provide the mammalian host with a defense mechanism against bacteria trying to breach the intestinal barrier [83]. Phages can also induce innate defenses from the host against bacterial colonization, stimulating the production of inflammatory cytokines and activating dendritic cells and innate lymphoid cells to produce interferons [20].
#Dikareva, E. et al. (2023): An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny. Frontiers in Microbiology, Vol. 14
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1254535/full
Quote: “Temperate phages have been shown to encode auxiliary metabolic genes (AMGs) that alter their bacterial host metabolism (Breitbart et al., 2007). These viral AMGs are not random but rather tuned to increase their hosts’ fitness in a specific environment (Hurwitz and U’Ren, 2016). Therefore, the characterization of viral AMGs can offer important insight into host fitness as well as the ecosystem’s nutritional constraints (Lindell et al., 2005; Hurwitz et al., 2014). In the recent years, metagenomic approaches have drastically expanded the diversity of known AMGs, including genes involved in carbon metabolism, sugar metabolism, lipid–fatty acid metabolism, signaling and stress responses, energy and nitrogen metabolism (Breitbart et al., 2018; Kieft et al., 2020; Shaffer et al., 2020; Fremin et al., 2022). In adult gut, a previous study suggested the presence of potential AMG (pAMG) encoding a large number of functions such as amino acid and carbohydrate transport and metabolism (Monaghan et al., 2019; Shaffer et al., 2020). In this study we observed a high prevalence of pAMGs encoding for amino acid metabolism as well as carbon and energy metabolisms, for both infant and adult pAMGs.”
– And they alter what signals bacteria send to your immune cells. Basically they’re letting them know: We have things under control, you can chill out. This may prevent allergic reactions or even protect you against autoimmune diseases.
#Górski, A. et al. (2018): Phage therapy in allergic disorders? Experimental biology and medicine, Vol. 243 (6)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882018/#bibr13-1535370218755658
Quote: “Phages present in mammalian organisms (endogenous phages, e.g. in the intestines) may exert immunomodulating action similar to probiotics2,3 and, by their ability to translocate from the gut to other tissues, they can mediate such activities, locally contributing to maintenance of immune homeostasis.4,5 Interestingly, phages have been shown to cause strong anti-inflammatory effects reducing levels of C-reactive protein and other indices of inflammation in patients receiving PT even though the infection has not been eliminated, thus suggesting that some phage effects are at least partly independent from their direct antibacterial action.6 The possible mechanisms of immunomodulating and anti-inflammatory activities of phages have recently been discussed in detail.7 Those observations have been confirmed and extended by other authors.8,9 Of particular interest are the recent data of van Belleghem et al.,10 who studied the effect of purified phages on immune responses of human peripheral blood mononuclear cells and showed that their prevailing effect is anti-inflammatory. Thus, phages were shown to induce the anti-inflammatory IL-1 receptor antagonist (IL-1RA) and strong upregulation of IL-10. This cytokine has been recognized as having anti-inflammatory properties blocking the expression of pro-inflammatory cytokines and inhibiting the activities of Th1 cells, NK cells and macrophages. Similar data were obtained by Sun and Feng,11 who showed that phage films downregulate the inflammatory response and induce high IL-10 expression. Van Belleghem’s group also showed a marked reduction of TLR4 expression on human mononuclears; TLR4 is known to induce pro-inflammatory cytokines and chemokines.10 Also of interest are data indicating that phages do not induce degranulation of human granulocytes and markedly decrease inflammation caused by the autoimmune reaction.12,13”
#Tzani-Tzanopoulou, P. et al. (2021): Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma. Frontiers in Allergy, Vol. 1
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8974763/
Quote: “Recently, we have proposed the possibility of controlling dysbiotic bacterial populations in asthma through phage interventions (162). New therapeutic modalities for asthma could potentially include targeted and customized re-colonization of the upper airway with lytic phages against key bacteria, including the ability of phages to act as anti-biofilm agents (76). Isolation and characterization of naturally occurring phages against M. catarrhalis, S. aureus, S. pneumoniae and H. influenzae may have prominent importance in this context.”
#Adiliaghdam, F. et al. (2022): Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Science Immunology, Vol. 7 (70)
https://www.science.org/doi/10.1126/sciimmunol.abn6660#sec-3
Quote: “IBDs affect more than 3.5 million people, with incidence increasing worldwide. These diseases, the most prevalent forms of which are CD and UC, are characterized by debilitating and chronic relapsing and remitting inflammation of the gastrointestinal tract (for CD) or the colon (in UC). These conditions result from a complex interplay between host, microbial, and environmental factors. Whereas disruption of the intestinal microbiome is an established contributor to IBD, the virome alterations observed in IBD by metagenomic analyses have been correlative findings. The interplay of the microbiota and virome is unsurprising given the dominance of bacteriophages. However, whether there is an autonomous functional role for the human intestinal virome in educating host immunity and IBD disease phenotype has remained elusive. To address this deficiency in knowledge of virome biology, in this study, we enriched viruses directly from colon surgical resections or ileostomy fluid of non-IBD, UC, or CD patients and assessed their immunomodulation by delivering them to human macrophages and IECs and creating mice with a humanized virome in vivo. We also identified the viruses that are present in colon tissue or ileostomy fluid of non-IBD, UC, or CD individuals by metagenomic analysis because only the fecal virome has been elucidated to date. Moreover, we established how genetic variation within IFIH1 that results in loss of function of the virus sensor MDA5 in IBD may contribute to disease in the context of the virome.
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Our data also show that viruses isolated from healthy colon tissues were capable of suppressing inflammatory responses invoked by UC or CD patient colon tissue viromes. Therefore, collective virus populations isolated from healthy individuals, and particularly from colon tissue, should be considered as a novel therapeutic approach to suppress inflammation in IBD.”
#Qv, L. et al. (2021): Roles of Gut Bacteriophages in the Pathogenesis and Treatment of Inflammatory Bowel Disease. Frontiers in Cellular and Infection Microbiology, Vol. 11
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8656360/
Quote: “Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, are chronic, relapsing intestinal inflammatory disorders. Although the molecular mechanisms governing the pathogenesis of IBD are not completely clear, the main factors are presumed to be a complex interaction between genetic predisposition, host immune response and environmental exposure, especially the intestinal microbiome. Currently, most studies have focused on the role of gut bacteria in the onset and development of IBD, whereas little attention has been paid to the enteroviruses. Among of them, viruses that infect prokaryotes, called bacteriophages (phages) occupy the majority (90%) in population. Moreover, several recent studies have reported the capability of regulating the bacterial population in the gut, and the direct and indirect influence on host immune response. The present review highlights the roles of gut phages in IBD pathogenesis and explores the potentiality of phages as a therapeutic target for IBD treatment.”
– Like the case of the Vibrio cholerae and the CTX phi bacteriophage hunting them. Most strains of the cholerae bacteria are harmless and billions of them may live in your gut right now. When CTX phi infect the bacteria, they gift it them genes for the cholera toxin, which permanently becomes part of their genetic lineage forever. It's like handing a house cat a shotgun.
#Boyd, E. F. (2010):Efficiency and specificity of CTXϕ chromosomal integration: dif makes all the difference. PNAS Vol. 107 (9)
https://www.pnas.org/doi/full/10.1073/pnas.1000310107
Quote: “Bacteriophage can convert their bacterial host from a nonpathogenic form to a pathogenic form by providing the bacterium with virulence genes, in a process called lysogenic phage conversion. Vibrio cholerae is a bacterium prevalent in marine environments that can infect humans to cause the devastating diarrheal disease cholera, which is endemic in much of Asia and Africa. Although the health and economic burdens of cholera are enormous, the disease is sometimes overshadowed by other diseases, but cholera's predilection for epidemic spread commands attention.
Cholera toxin, an A-B type exotoxin encoded by the ctxAB genes, is the main cause of the voluminous watery diarrhea that is characteristic of cholera (1–3). V. cholerae isolates that cause cholera encode the ctxAB genes in the genome of a filamentous bacteriophage CTXϕ (Fig. 1A) (4). CTXϕ is a small, positive, single-stranded DNA [(+) ssDNA)] virus that can be found either in a replicative form or, more commonly, integrated site-specifically in the host genome to form stable lysogens.”
#Safa, A. et al. (2020): Cholera toxin phage: structural and functional diversity between Vibrio cholerae biotypes. AIMS Microbiology, Vol. 6(2)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7326730/
Quote: “Vibrio cholerae is an ancient human pathogen that causes a severe form of diarrhea known as cholera. Humans are the only medically relevant living host of V. cholerae, and its transmission is mainly mediated by the consumption of V. cholerae-contaminated water and/or food. Endemic cholera in underdeveloped and developing countries frequently gives rise to explosive outbreaks that sometimes result in pandemics. During the course of recorded human history, V. cholerae has caused seven pandemics [1],[2].”
– Vibrio cholerae shower these toxins at the cells lining your gut, making them sick. They vomit large amounts of salt, which pulls out a flood of water into your intestines.
#Montero, D.A. et al. (2023): Vibrio cholerae, classification, pathogenesis, immune response, and trends in vaccine development. Frontiers in Medicine. Vol. 10
https://www.frontiersin.org/articles/10.3389/fmed.2023.1155751/full
Quote: “Figure 2. Pathogenesis of toxigenic V. cholerae. (A) Toxigenic V. cholerae produces several virulence factors that contribute to its pathogenesis. The precise pathogenic mechanism is not yet fully understood, but it is widely accepted that it involves the combination of these virulence factors and the ability to colonize and persist in the small intestine. (B) Upon ingestion, V. cholerae survives the low pH of the stomach via an acid tolerance response. In the small intestine, V. cholerae uses its flagellum to propel through the mucus layer and reach the epithelial surface. Meanwhile, V. cholerae must overcome host immunity and the colonization resistance mechanisms of the gut microbiota. To colonize the small intestine, it expresses virulence factors such as toxin-coregulated pilus (TCP) and cholera toxin (CTX). During infection, other factors such as HapA, GbpA, and NanH are also expressed. For more details on the roles of these virulence factors, please refer to the text. This figure was created using BioRender.com.”
Quote: “Figure 3. Mechanism of action of cholera toxin. (A) The crystal structure of CTX (PDB accession number 1XTC) was determined by Zhang et al. (136). CTX is composed of a heterodimeric CTX-A subunit, which consists of two polypeptide chains, CTX-A1 (22 kDa) and CTX-A2 (5 kDa), linked by a single disulfide bond. The CTX-A2 helical peptide links the CTX-A1 chain to the pentameric CTX-B subunit, which is composed of five identical polypeptide chains (11.6 kDa). (B) The CTX-B pentamer specifically binds to GM1 gangliosides (primary receptor) or histo-blood group antigens (HBGAs; secondary binding site) present on the apical side of intestinal epithelial cells, promoting the endocytosis of the toxin. (C) The internalization of CTX may occur through clathrin-dependent as well as caveolae- and clathrin-independent endocytosis. Regardless of the mechanism of endocytosis, the CTX is internalized to the early endosomal compartment, trafficked to the Golgi, and then onto the endoplasmic reticulum (ER), where it dissociates into a CTX-A1 and a CTX-A2/CTX-B complex. Next, the CTX-A1 is exported out of the ER to the cytosol, where it is activated by ADP ribosylation factor 6 (ARF6). The ARF6-bound, activated CT-A1 subunit, in turn, activates adenylyl cyclase (AC) by catalyzing ADP ribosylation of a G protein-coupled receptor (GPCR). The AC then catalyzes the conversion of ATP to cyclic adenosine monophosphate (cAMP), increasing the intracellular cAMP concentration. This leads to the activation of protein kinase A (PKA), which phosphorylates the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel proteins, ultimately resulting in the release of electrolytes (Cl−, HCO3−, Na+, K+) and water into the intestinal lumen, causing the secretory diarrhea characteristic of cholera (137, 138). The figure was created with BioRender.com.”
– Or the bacteria Staphylococcus aureus, which is hunted by the phage with the amazing name: φSa3ms.
#Tong, S.Y.C. et al (2015): Staphylococcus aureus Infections: Epidemiology, Pathophysiology, Clinical Manifestations, and Management. Clinical Microbiology Reviews, Vol. 28(3)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451395/
Quote: “Staphylococcus aureus is a leading cause of nosocomial and community-acquired infections worldwide (42). S. aureus causes a wide range of diseases that vary in severity from mild skin infections, such as boils and furuncles, to life-threatening diseases, like toxic shock syndrome and endocarditis. The ability of S. aureus to cause such a wide variety of diseases is thought to be due in part to its elaboration of a large number of secreted and cell-surface associated virulence factors (1, 5, 21, 36, 48).”
– But φSa3ms can change this quickly – it carries multiple dangerous genes, like giving a cat flamethrowers and grenades.
#Schelin, J. et al. (2011): The formation of Staphylococcus aureus enterotoxin in food environments and advances in risk assessment. Virulence, Vol. 2(6)
https://www.tandfonline.com/doi/full/10.4161/viru.2.6.18122
Quote: “Prophage-encoded enterotoxins (sea and see). The sea gene is carried by a polymorphic family of temperate bacteriophages.25 The bacteriophage is inserted into the bacterial chromosome as a prophage and behaves like part of the bacterial genome. However, under environmental stress conditions, such as mild food preservation conditions, the prophage can be induced to replicate the phage genome and release new bacteriophages.52 Today, at least six completely sequenced S. aureus strains containing different sea-carrying prophages, Φ252B, ΦMu3, ΦMu50A, ΦNM3, ΦSa3ms and ΦSa3mw, have been found, all of which frequently carry the genes for enterotoxin A, staphylokinase and the complement inhibitor.31,53,56”
– If such a modified Staphylococcus aureus bacteria gets into your body through a tiny cut, it becomes extremely dangerous.
Quote: “S. aureus does not normally cause infection on healthy skin; however, if it is allowed to enter the bloodstream or internal tissues, these bacteria may cause a variety of potentially serious infections.[1]
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S. aureus are one the most common bacterial infections in humans and are the causative agents of multiple human infections, including bacteremia, infective endocarditis, skin and soft tissue infections (e.g., impetigo, folliculitis, furuncles, carbuncles, cellulitis, scalded skin syndrome, and others), osteomyelitis, septic arthritis, prosthetic device infections, pulmonary infections (e.g., pneumonia and empyema), gastroenteritis, meningitis, toxic shock syndrome, and urinary tract infections.[6] Depending on the strains involved and the site of infection, these bacteria can cause invasive infections and/or toxin-mediated diseases.[6][7] The pathophysiology varies greatly depending on the type of S. aureus infection.[6] Mechanisms for evasion of the host immune response include the production of an antiphagocytic capsule, sequestering of host antibodies or antigen masking by Protein A, biofilm formation, intracellular survival, and blocking chemotaxis of leukocytes.[8][7] Binding of the bacteria to extracellular matrix proteins and fibronectin in infectious endocarditis is mediated by bacterial cell wall-associated proteins such as fibrinogen-binding proteins, clumping factors, and teichoic acids.[7] Also, Staphylococcal superantigens (TSST-1 or toxic shock syndrome toxin 1) are important virulence factors in infectious endocarditis, sepsis, as well as toxic shock syndrome.[9][10] Pneumonia infections are associated with the bacterial production of PVL (Panton-Valentine leukocidin), Protein A, and alpha-hemolysin, and infections are more common following influenza virus infection as well as a diagnosis of Cystic Fibrosis. Prosthetic device infections are often mediated by the ability of S. aureus strains to form biofilms as well as communicate using quorum sensing in a bacterial cell density-dependent manner. [11]”
– One of its new weapons are superantigens, which basically is like injecting your immune cells with cocaine. The toxin completely breaks your carefully fine tuned immune system. It activates all of your T Cells, all at once and makes them flip out. They release a tsunami of cytokines, activating all of your defenses at once. The infection is flooded with cells that can’t fight the bacteria and cause heavy inflammation.
#Sumby, P. & Waldor, M. K. (2003): Transcription of the Toxin Genes Present within the Staphylococcal Phage φSa3ms Is Intimately Linked with the Phage's Life Cycle. Journal of Bacteriology, Vol. 185 (23)
https://journals.asm.org/doi/10.1128/jb.185.23.6841-6851.2003
Quote: “The bacteriophages and pathogenicity islands of S. aureus encode many virulence factors (35). The known phage-encoded virulence factors include Panton-Valentine leukocidins (24, 33), exfoliative toxin type A (47), and staphylococcal enterotoxins (SEs) (3). The SEs constitute a family of related proteins whose activities are associated with staphylococcal food poisoning, toxic shock syndrome, and possibly several autoimmune disorders (17, 41). SEs are powerful superantigens that activate subsets of T lymphocytes to liberate various cytokines, including gamma interferon and tumor necrosis factor (41). In addition to these characterized phage-encoded virulence factors, a number of putative S. aureus virulence factors, such as staphylokinase (Sak), are also encoded in phage genomes (25). Staphylokinase, a potent plasminogen activator, has been hypothesized to aid in the dissemination of S. aureus from fibrinous clots and abscesses (1).”
– Your broken and confused immune cells have a really hard time fighting Staphylococcus aureus, which now invades, penetrating deep into your tissue. Your body is trying to seal the wounds and isolate the invader, but another new weapon it gained has the ability to just dissolve the barriers and penetrate even deeper. Before the onset of antibiotics an infection with Staphylococcus aureus was very deadly and we have φSa3ms to thank for making it even deadlier.
#Bokarewa, M. I. et al. (2006): Staphylococcus aureus: Staphylokinase. The International Journal of Biochemistry & Cell Biology 38
https://pubmed.ncbi.nlm.nih.gov/16111912/
Quote: “The role of staphylokinase as a virulence factor of staphylococci is assumed to be due to its interaction with plasminogen and -defensins. Binding of staphylokinase to plasminogen may affect bacterial invasion into the host tissues. Several models of staphylokinasemediated bacterial invasion are suggested (Christner & Boyle, 1996; Molkanen et al., 2002). The staphylokinase–plasmin(ogen) complex may bind to the fibrin net around the infectious focus or abscess and cleaves it, allowing staphylococci entry into the deeper host tissues. Plasmin is a serine protease with a broad-spectrum of substrates including matrix proteins such as fibrin, collagen and elastin. Plasmin is also recognized as an important activator of matrix metalloproteinases that enhance the lysing effects of plasmin on the surrounding tissues (reviewed by Lijnen, 2001). Staphylococci also express the plasminogen-binding sites on their surface -enolase and ribonucleotide reductase subunit 2 (Molkanen et al., 2002). Staphylococci carrying the staphylokinase–plasmin(ogen) complex on their surface may acquire the capacity to lyse and degrade extracellular matrix by further activating metalloproteinases of the host or the staphylococcal metalloproteinase, aureolysin.”
Cancer Killing Viruses
#Chaurasiya S. et al. (2021): Oncolytic Virotherapy for Cancer: Clinical Experience. Biomedicines, Vol. 9(4)
https://www.mdpi.com/2227-9059/9/4/419
Quote: “There has been an increasing interest in using viruses as potential therapeutics for different types of diseases. Two main ways in which viruses are being explored as therapeutics are (1) vectors for gene therapy and (2) oncolytic viruses. While viruses as vector for gene therapy are being studied for a wide range of diseases including cancer, “oncolytic viruses” are specific for cancer treatment. The major difference between viral vector for gene therapy and oncolytic virus is that viral vectors used in gene therapy are non-replicating viruses, whereas oncolytic viruses are replication-competent viruses. Oncolytic viruses (OV) are wild-type or engineered viruses that can selectively replicate in and kill cancer cells while leaving normal cells unharmed. OVs are a novel class of multi-mechanistic therapeutics for the treatment of cancer. Some of the mechanisms through which OVs exert their anti-cancer effect include direct lysis of cancer cells and activation of anti-tumor immunity (Figure 1)”
#Müller, L. et al. (2020): Past, Present and Future of Oncolytic Reovirus. Cancers, Vol. 12(11)
https://www.mdpi.com/2072-6694/12/11/3219
Quote: “Advancements in virology and molecular biology techniques over recent decades have allowed us to exploit the anti-tumour potential of oncolytic viruses (OVs) [1]. The unique ability of OVs to exploit oncogenic signalling pathways provides a significant advantage over traditional treatment modalities. OVs are specifically defined as viruses which: (i) preferentially infect and kill malignant cells through viral replication and oncolysis, and (ii) engage the immune system to promote anti-tumour immunity. Additional mechanisms of action have also been reported, including disruption of tumour-associated vasculature or stroma and modulation of the tumour microenvironment (TME) [2,3,4].
An array of OVs—naturally occurring, attenuated, and genetically modified—have been investigated in pre-clinical models and clinical trials but only two have received approval for clinical use: (i) a genetically engineered adenovirus H101, approved in China in 2005 [5], and (ii) the Food and Drug Administration (FDA)-approved talimogene laherparepvec (T-VEC)—a herpes simplex virus type 1 (HSV-1) genetically engineered to limit neurovirulence and promote an immunostimulatory environment [6,7]. This review will provide an overview of what we have learnt about oncolytic mammalian orthoreovirus since its rise as a clinically applicable agent, we will discuss areas of active pre-clinical and clinical research and consider the challenges that exist to harness its full therapeutic potential.”
– Oncolytic viruses specialize in hunting and killing cancer – like the Newcastle Disease virus or the Reovirus, who mostly ignore your healthy cells and instead hunt down tumors.
#Burman, B. et al. (2020): Newcastle Disease Virus at the Forefront of Cancer Immunotherapy. Cancers, Vol. 12(12)
https://www.mdpi.com/2072-6694/12/12/3552
Quote: “Preclinical and clinical studies dating back to the 1950s have demonstrated that Newcastle disease virus (NDV) has oncolytic properties and can potently stimulate antitumor immune responses. NDV selectively infects, replicates within, and lyses cancer cells by exploiting defective antiviral defenses in cancer cells. Inflammation within the tumor microenvironment in response to NDV leads to the recruitment of innate and adaptive immune effector cells, presentation of tumor antigens, and induction of immune checkpoints. In animal models, intratumoral injection of NDV results in T cell infiltration of both local and distant non-injected tumors, demonstrating the potential of NDV to activate systemic adaptive antitumor immunity. The combination of intratumoral NDV with systemic immune checkpoint blockade leads to regression of both injected and distant tumors, an effect further potentiated by introduction of immunomodulatory transgenes into the viral genome. Clinical trials with naturally occurring NDV administered intravenously demonstrated durable responses across numerous cancer types. Based on these studies, further exploration of NDV is warranted, and clinical studies using recombinant NDV in combination with immune checkpoint blockade have been initiated.
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Oncolytic properties of NDV derive primarily from deficient type I IFN signaling pathways and less sensitive type I IFN receptor-mediated signaling in tumor cells [19,20,21]. Mutations in genes related to the type I IFN pathway and the downstream Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway are associated with NDV susceptibility and cytotoxicity [19,22,23]. Tumor cell susceptibility to NDV infection may also be based on the presence of sialic acid-containing cell surface proteins. It was proposed that the combination of altered type I IFN-related gene expression and sialic acid content could act as a clinical biomarker for determining susceptible tumor types [24]. Finally, defects in apoptotic pathways such as the Fas-FasL interaction or overexpression of antiapoptotic genes such as Livin and BcL-xL, which are documented in many tumor types, may increase susceptibility to NDV allowing for viral persistence, increased replication, and spread to surrounding cells [25,26,27].
NDV has been shown to cause cell death by apoptosis, necrosis, or autophagy mechanisms [26,28,29,30]. Viral HN protein can directly trigger the release of type I IFN and upregulates tumor necrosis factor (TNF)-related apoptosis inducing ligand (TRAIL) [31]. In human peripheral blood mononuclear cells (PBMCs), TRAIL signaling in turn upregulates apoptotic genes (FasL, Bax, caspase-8, caspase-9, and caspase-3) [32]. HN gene expression alone has been reported to induce apoptosis in human breast cancer MCF-7 cells [33]. NDV can also induce apoptosis through interferon-independent mechanisms such as the intrinsic mitochondrial death pathway [34]. Finally, the formation of syncytia by some NDV strains (termed “fusogenic” strains) ultimately leads syncytium disintegration either through necrosis or apoptosis [35].”
Gong, J. & Mita, M.M. (2014): Activated Ras signaling pathways and reovirus oncolysis: an update on the mechanism of preferential reovirus replication in cancer cells. Frontiers in Oncology, Vol. 4
https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2014.00167/full
Quote: “Reovirus is a dsRNA virus whose mechanism of oncolysis remains unclear though activated Ras signaling, involving upstream and downstream mediators, appears important to permissiveness to reovirus replication. In promoting oncolysis, Ras-transformation affects multiple steps of the infectious life cycle including viral uncoating and disassembly, releasing PKR-induced translational inhibition, generation of viral progeny, release of progeny, and viral spread with reovirus-induced cancer cell death occurring through necrotic, apoptotic, and autophagic pathways. However, several studies have highlighted that reovirus oncolysis occurs independent of activated EGFR and Ras signaling pathways, while others have linked reovirus oncolysis to cell cycle phase (70–72). Undoubtedly, despite our progress in understanding reovirus oncolysis, further investigation into the mechanism of preferential replication in cancer cells is still warranted to enhance the antitumor efficacy of reovirus whose development has currently expanded to 32 clinical trials (both ongoing and completed) in the treatment of cancer.”
– A weakness to be exploited. Oncolytic viruses target the specific adaptations of cancer cells, hitting them where they are not ready to be hit.
#Huang, F. et al. (2022): Development of Molecular Mechanisms and Their Application on Oncolytic Newcastle Disease Virus in Cancer Therapy. Frontiers in Molecular Biosciences, Vol. 9
https://www.frontiersin.org/articles/10.3389/fmolb.2022.889403/full
Quote: “The NDV oncolytic properties originate from its capacity to proliferate in cancer cells (Shobana et al., 2013). Further research showed that it might be related to the deficiency of the interferon (IFN) system in tumors (Stojdl et al., 2000). H. Song et al. discovered that NDV enters the cell through a pH-independent direct fusion of its envelope to the host membrane via receptor-mediated endocytosis (Sánchez-Felipe et al., 2014). The process of NDV infection and replication in tumor cells is described as follows (Moliner et al., 2019). NDV binds to the sialic acid receptor on the surface of tumor cells through the HN protein, and then, protein F initiates the fusion of the viral and host cell membranes (Song et al., 2019; Xia et al., 2022). Viral RNA polymerase transcribes the viral negative single-stranded RNA into positive single-stranded RNA as a template for mRNA and protein synthesis (Burman et al., 2020; Sung et al., 2021). The rough endoplasmic reticulum processes surface proteins F and HN, assembled on the host cell membrane and mature to produce new virions that start a new round of tumor cell infection (Cuadrado-Castano et al., 2015). Importantly, virus-mediated direct oncolysis causes the release of tumor-associated antigens (TAAs), pathogen-associated molecular patterns (PAMPs), and danger-associated molecular patterns (DAMPs). These can activate antigen-presenting cells (APCs), including antigen-cross-presenting dendritic cells (DCs). Activated APCs then activate the immune cells, resulting in the generation of CD4+ T cells, CD8+ T cells, and NK cells directed toward tumor and viral antigens (Burman et al., 2020; Schirrmacher and Fournier, 2014) (Figure 2). It is worth mentioning that NDV does not replicate in the normal cells of non-avian hosts (Fiola et al., 2006).”
#Müller, L. et al. (2020): Past, Present and Future of Oncolytic Reovirus. Cancers, Vol. 12(11)
https://www.mdpi.com/2072-6694/12/11/3219
Quote: “The molecular features associated with the oncolytic capacity of reovirus have been the subject of decades of research. Initially, an association between reovirus permissiveness and epidermal growth factor receptor (EGFR) status was revealed [55,56], along with evidence that activation of downstream signalling pathways, induced after transfection with the oncogene v-erb, are important [57]. Subsequent transfection of cells with constitutively active elements of the RAS pathway, a group of small GTP-binding proteins that regulate cell fate and growth, identified a role for RAS in reovirus permissiveness [58]. Therefore, although JAM-A is important for host cell entry, gain-of-function mutations activating RAS signalling [59] could promote reovirus replication and the release of virus progeny [60]. RAS mutations are prevalent in cancer [61], supporting the use of reovirus as a potential therapeutic agent [58,62]. The link between reovirus and cellular RAS status was further strengthened by observations that tumour cell susceptibility could be influenced by modulating RAS and/or its downstream effectors using short-hairpin RNA or small-molecule inhibitors [63,64]. Mechanistically, modulation of RAS signalling may promote susceptibility via inhibition of PKR [58]. In healthy cells, binding of dsRNA by PKR results in its dimerization, autophosphorylation and activation. Activated PKR subsequently phosphorylates the translation initiation factor, eIF2, rendering it inactive, which prevents the translation of viral transcripts [65]; however, in RAS-transformed cells PKR remains inactive and viral replication can occur [58,66,67]. Currently, the mechanism that coordinates RAS-transformation and PKR inactivation remains unclear [68].
Although the RAS–PKR axis provides a plausible explanation for the susceptibility of cancer cells to reovirus, the true molecular mediator has been the subject of debate, with doubt being cast by the survival of some infected RAS-transformed cells [69,70]. Moreover, the absence of a correlation between total or phospho-PKR with RAS expression or cell death contradicts previous studies [71], as does the lack of association between oncolysis and EGFR signalling [72]. It has become increasingly apparent that viral replication and cell death are not inextricably linked. Indeed, it is possible that RAS activation does not underlie viral replication but rather sensitivity to apoptosis which can occur independently of replication [53,64]. Sensitivity to reovirus oncolysis is likely to be dependent on multiple cellular and molecular determinants, many of which may yet be undiscovered.”
– This death and destruction is not subtle, and one side effect is that it attracts immune cells that immediately begin attacking the tumor with full force.
#Russell, L. et al. (2019): Oncolytic Viruses: Priming Time for Cancer Immunotherapy. BioDrugs, Vol. 33 (5)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6790338/
Quote: “Subsequent to viral infection, host cells orchestrate diverse mechanisms directed to shut down replication and avoid pathogenicity. Initially, viral pathogen-associated molecular patterns (PAMPs) are recognized by surface or intracellular host pattern recognition receptors (PRRs) followed by the activation of several signaling pathways, resulting in the induction of chemokines and cytokines such as type I interferons (IFNs). Therefore, activated innate immune cells, including neutrophils, granulocytes, natural killer (NK) cells, and antigen-presenting cells (APCs), will be the first to arrive and respond at the site(s) of infection. To consolidate pathogen control, an antiviral adaptive immune response produced by B and T cells is subsequently established [17, 18]. Tumor cells and their microenvironment have evolved many mechanisms to suppress the generation of any local or systemic antitumoral immune effectors [19, 20]. Hence, OVs, due to their ability to selectively infect and replicate in tumor cells, as well as their capacity of attracting activated immune cells locally into the immunosuppressive tumor microenvironment, constitute an appealing strategy for cancer immunotherapy.
Different OVs kill tumor cells by triggering different cell death pathways with diverse degrees of immunogenicity. However, all of them will release PAMPs, which create an ‘acute inflamed’ environment consisting of activated de novo infiltrating and resident dendritic cells (DCs), macrophages, and NK cells, among others. These cells can destroy viral-infected tumor cells, release cytokines that can reduce tumor growth, and pick up viral and tumor antigens from dying tumor cells for presentation to, and activation of, T cells. However, at the same time, myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs) may also be recruited into the tumor microenvironment, serving to inhibit immune responses [17, 21]. OVs that can tilt the balance towards the generation of proinflammatory responses that cannot be counteracted by host/tumor immunosuppression would be appealing for further development.”
#Huang, F. et al. (2022): Development of Molecular Mechanisms and Their Application on Oncolytic Newcastle Disease Virus in Cancer Therapy. Frontiers in Molecular Biosciences, Vol. 9
https://www.frontiersin.org/articles/10.3389/fmolb.2022.889403/full
Quote: “As mentioned earlier, NDV selectively infects tumor cells and rapidly replicates in tumor cells to directly dissolve tumors (Fiola et al., 2006). Significantly, NDV oncolysis reshapes the tumor microenvironment (TME), transforming cold tumors into hot tumors (Burman et al., 2020). This process is beneficial for immune cells to infiltrate tumors. On the one hand, NDV induces the release of the risk-related molecular model of strong antitumor immunity after oncolysis, such as TAAs, PAMPs, and DAMPs (Figure 2). These key risk–related molecular models can activate not only some innate immune cells (NK cells) but also tumor-specific T cells (CD4+ and CD8+ T cells) and recruit APCs into the tumor to initiate an immune response (Schild et al., 1989; Ricca et al., 2018). Remarkably, upregulation of many immune checkpoint molecules (CTLA-4 and PD-1) has been observed on CD4+ and CD8+ T cells in recent years (Zamarin et al., 2014; Nakao et al., 2020). This suggests the possibility of combining NDV and immune checkpoint inhibitors to break immune resistance. On the other hand, the activated non-specific immune cells kill and devour infected tumor cells that are not lysed or resistant to viral oncolysis (Fuertes et al., 2011); when the inflammatory response to NDV infection helps the immune system clear tumors, it also causes immune cells to clear NDV, limiting antitumor effects (Buijs et al., 2014). As a result, developing NDV-based cancer regimens necessitates striking a balance between appropriate viral replication, tumor lysis, and immune response activation.”
#Müller, L. et al. (2020): Past, Present and Future of Oncolytic Reovirus. Cancers, Vol. 12(11)
https://www.mdpi.com/2072-6694/12/11/3219
Quote: “Immune cells and infected tumour cells secrete pro-inflammatory cytokines and chemokines in response to reovirus treatment [85,86,87,88]. This occurs via engagement of pathogen-associated molecular patterns (PAMPs; e.g., viral RNA, DNA or proteins) or damage-associated molecular patterns (DAMPs; e.g., heat-shock proteins, calreticulin, uric acid and ATP released from infected cells) with pattern recognition receptors (PRRs) [89]. As with most viral infections, the secretion of type I IFN is a key component of the innate response to reovirus [90].
(...)
The generation of a pro-inflammatory environment reverses the immunosuppressive state of the TME, induces cytotoxic bystander cytokine killing of tumour cells, activates and recruits innate immune effector cells to kill neoplastic cells, and facilitates the generation of an adaptive anti-tumour immune response [96,97,98,99]. Reciprocal cell-to-cell interactions between DCs and natural killer (NK) cells within the TME or tumour-draining lymph nodes, can stimulate both NK cell activation and DC maturation [85,100]; NK cell anti-tumour immunity within peripheral blood mononuclear cells (PBMCs) is mediated by type I IFN secretion from monocytes [35]. In addition to the recruitment and activation of NK cells, reovirus also activates innate T cells which are capable of eliminating tumour cells via the release of cytolytic granules [85,101]; this remains a poorly understood mechanism of action.”
– What is even more impressive, these viruses seem to disrupt the artificial environment that tumors create to keep your immune system at bay.
We have two videos on cancer where you can find information on this and many other things:
#Kurzgesagt (2023): Your Body Killed Cancer 5 Minutes Ago
https://www.youtube.com/watch?v=zFhYJRqz_xk&t=6s
#Kurzgesagt (2023): The Reason Why Cancer is so Hard to Beat
https://www.youtube.com/watch?v=uoJwt9l-XhQ&t=1s
– But they seem to go well together with chemotherapy or radiation.
#Müller, L. et al. (2020): Past, Present and Future of Oncolytic Reovirus. Cancers, Vol. 12(11)
https://www.mdpi.com/2072-6694/12/11/3219
Quote: “Multiple studies have investigated the combination of reovirus with chemotherapeutic agents, with synergy being frequently observed. As with radiotherapy, the enhanced treatment effect appeared to be due to increased oncolysis. For example, treatment of a range of prostate cancer cell lines with reovirus plus docetaxel, paclitaxel, vincristine, cisplatin or doxorubicin led to increased apoptosis/necrosis in vitro and reovirus improved docetaxel therapy in a xenograft prostate cancer model [152]. Increased apoptosis and/or necrosis has also been demonstrated by the combination of reovirus with: cisplatin in a melanoma model [153]; cisplatin, gemcitabine or vinblastine in non-small cell lung cancer cell lines [125]; and cisplatin plus paclitaxel in both in vitro and in vivo models of head and neck cancer [154]. Collectively, this evidence suggests that the beneficial outcomes resulting from combining reovirus with chemotherapy agents are generally mediated through oncolysis rather than immune-mediated mechanisms. However, Gujar et al. suggested that improved survival following reovirus plus gemcitabine treatment in an ovarian cancer model was at least partly immune-mediated, with reduced numbers of MDSC in tumours and improved anti-tumour CTL responses [155].”
#Schirrmacher, V. et al. (2019): Breaking Therapy Resistance: An Update on Oncolytic Newcastle Disease Virus for Improvements of Cancer Therapy. Biomedicines, Vol. 7(3)
https://www.mdpi.com/2227-9059/7/3/66
Quote: “That oncolytic NDV has the potential to break resistance of cancer cells to a variety of therapies has been suggested in 2015 [102]. Because this is of great importance, this update, four years later, appears to be justified.
Breaking resistance to chemotherapy (CT) or radiotherapy (RT): These therapies require cells to be in a proliferating state. Non-proliferating cells such as cancer stem cells or dormant tumor cells are not affected by CT or conventional photon radiotherapy using X-rays and gamma rays. In contrast to cytostatic drugs and RT, oncolysis by NDV does not depend on cell proliferation. Since NDV replicates in the cytoplasm of cells, it is independent from DNA replication. The virus is capable to replicate in X-irradiated cells such as ATV-NDV vaccine cells [103]. There is thus a potential of oncolytic NDV to target cancer stem cells and dormant tumor cells. In addition, NDV has the potential to break drug-resistance of cancer cells: (i) NDV was reported to induce apoptosis in cisplatin resistant human lung adenocarcinoma cells in vitro and in vivo [104]. Apoptosis was induced via the caspase pathway, particularly involving caspase-9. (ii) In another study, treatment with autophagy modulators was found an effective strategy to augment the therapeutic activity of oncolytic NDV against drug-resistant lung cancers [105]. (iii) Multidrug resistance, particularly resistance to temozolomide (TMZ), is a challenge in the treatment of GBM. NDV was found to enhance the growth-inhibiting and proapoptotic effects of TMZ on GBM cells in vitro and in vivo [106].”