Category Archives: Autophagy

X-linked and Autophagy Genes Support Crohn’s Disease Development

Caspase 3 subunits
Caspase-3 is the missing link between an autophagy gene mutation and heightened inflammation.
This week on TIBDI: Impressive results in Nature show how gene mutations cause reduced autophagy, and mutations in the XIAP gene lead to early-onset CD in male patients.

From an Autophagy Gene to Crohn’s Disease

Genome wide association scans confirmed the importance of ATG16L1 mutations in Crohn’s disease (CD), especially a variant consisting of an Alanine to Threonine exchange at the 300th amino acid. Despite an abundance of literature, the precise mechanism linking the mutation to reduced autophagy was unknown. Dr. Aditya Murthy from Genentech, Inc. has now found an answer. The mutation is located in a cleavage site for the enzyme caspase-3, and it makes the protein more susceptible to cleavage. Caspase-3 is well known for its role in initiating apoptosis during cellular trauma, for instance during metabolic stress or intestinal infection. Without proper autophagy, macrophages are unable to neither regulate their energy consumption nor properly eliminate pathogens, and have an heightened inflammatory response.

XIAP Mutations in Early Onset CD

Variants in the gene encoding for the X-linked inhibitor of apoptosis protein (XIAP) can sometimes lead to intestinal inflammation. XIAP is involved with a multitude of processes including NOD signaling, apoptosis and NKT cell development. To investigate XIAP’s possible role in CD, Dr. Yvonne Zeissig and her colleagues at the University Medical Center Schleswig-Holstein in Germany, looked at CD patient samples to find if there were clear associations between XIAP and immune cell function. She found that approximately 4% of male early-onset CD patients had unique mutations in their XIAP genes. Experiments with patient primary cells revealed that loss of XIAP function caused defects in NOD1/2 signaling.

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Macrophages Encourage Autophagy and Are Hindered by IL-10

Macrophage
Macrophages could play a key role in the initiation of IBD.
This week on TIBDI: Macrophages are reined in via their IL-10 receptors, Macrophage derived Wnt1 encourages epithelial autophagy, and γδ T cells are controlled by BTLA and IL-7.

Continue reading Macrophages Encourage Autophagy and Are Hindered by IL-10

Th9 Clears Parasites and Aluminum Worsens IBD

Aluminium
Aluminum could be one of the causes of IBD.
This week we find new ways that bacteria interact with the gut, aluminum looks like a deadly suspect in inflammatory bowel disease and parasitic worms seem to have their own T helper subset.

Bacteria Escapism in Crohn’s Disease Revealed

Adherent-invasive Escherichia coli (AIEC) are found in Crohn’s disease (CD) patients and are able to aggravate inflammation. Control of these kinds of bacteria requires functional autophagy, which destroys intracellular pathogens. Researchers from the University of Auvergne in France have now discovered that AIEC protect themselves from destruction by manipulating the genes needed to control autophagy.  This was achieved by an upregulation of microRNAs designed to inhibit ATG5 and ATG16L1 expression. Blocking the microRNAs restored autophagy and reduced inflammatory responses. This mainly in vitro study suggests that restoring autophagy in CD may lead to lowered inflammation.

Aluminum: New Culprit in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) incidence has risen simultaneously with industrialization and the emergence of modern society. This suggests that environmental pollutants may cause IBD. One possible guilty suspect is aluminum, which is known to be associated with abnormal immune function. To determine if aluminum was involved with intestinal inflammation, scientists from France administered aluminum to three types of murine IBD models. They found that aluminum worsened disease severity in each model, impaired intestinal barrier function and directly increased cellular immune responses.

Parasitic Worms Get Their Own T Cell Subset

Parasitic worms are now being investigated in clinical trials as a possible way to treat IBD. Research investigating the immune response generated by parasitic worms would be helpful for refining these studies. A current publication in Immunity does just this by examining T cell responses and the clearance of Nippostrongylus brasiliensis, a worm similar to Necator americanus used in the mouse IBD studies. They found that interleukin-9 producing T cells (Th9) were essential for worm clearance and the induction of T helper 2 cytokines. An interesting research question would be to determine if Th9 is involved in the therapeutic effect of parasitic worms in IBD.

Pathogens Plunder the Gut after Antibiotic Treatment

Antibiotic treatment is associated with IBD development. In general, this is likely associated with the resultant changes in the microbiota and also the entrance of enteric pathogens. Finding ways to use antibiotics safely could prevent some cases of IBD. A research team from Stanford has brought us one step closer by clarifying how some enteric pathogens thrive after antibiotic treatment. They found that the availability of bacterial sugars after antibiotics is part of the problem. Normal microbiota “harvest” sugars attached to the mucus for food. However when antibiotics are applied, surviving Salmonella typhimurium and Clostridium difficile quickly utilize the free sugars to grow and thrive.

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Insight: What is Autophagy?

Mycobacterium tuberculosis Ziehl-Neelsen stain 02
Autophagy is also responsible for the destruction of Mycobacterium tuberculosis.
After genome wide association scans discovered that autophagy genes were involved in Crohn’s disease (CD), autophagy suddenly became an interesting research topic. Autophagy, however, actually is a somewhat general term that encompasses a wide variety of processes. Below is a short overview of the basics and what you need know to understand its involvement in CD.

Autophagy, which means “self-eating” in Greek, refers to when cells digest cytoplasmic contents in lysosomes. Those of you who are familiar with lysosomes will probably realize that autophagy must be occurring in a wide variety of situations ranging from simple protein recycling to the destruction of internal pathogens. This is correct, and this, most basic, form of autophagy is referred to as macroautophagy and requires the specialized autophagy-related proteins (ATGs), which include the famous, CD-related ATG16L1.

Simple Autophagy:

During the first steps of autophagy, ATGs and other proteins drive the formation of the initial structure called the phagophore. The phagophore looks like a crescent moon and is derived from internal membranes from various sources (mainly the endoplasmic reticulum). Key proteins to remember that drive this process are Beclin 1, the kinase ULK1, LC3 proteins and γ-aminobutyric acid receptor-associated proteins (GABARAPs). The phagophore scoops up cytoplasm and closes forming a completed autophagosome. Degradation happens when the autophagosome fuses to a lysosome.

But what signals initiate autophagy? The signals are diverse and often related to the detection of danger. They can include loss of nutrients (a sign of infection), signaling through internal pattern recognition receptors (NOD-like receptors, TLR4), danger signals (HMGB1), pro-inflammatory cytokines (IL-1β and IFNγ), reactive oxygen species and even signals via co-stimulatory molecules (CD40). Important downstream molecules that need to be activated include Beclin 1 and TRAF6.

Autophagy and the Immune Response

Autophagy has the potential to modulate immune reactions at multiple levels besides simply providing a means for the destruction of invading internal pathogens like mycobacteria and viruses. It also controls the clean up of organelles and modulates the destruction of internal proteins. Autophagy plays such a basic role in the cells that numerous changes arise when it becomes deregulated. In particular, various immune consequences could arise like changes in protein presentation or even the increase of important microRNAs. Autophagy machinery is also involved in the secretion of stored cytokines and other mediators.

Autophagy and Crohn’s Disease

Individuals with mutations in NOD2 and ATG16L1 have a much greater chance to develop CD. One reason appears to be that these patients have a decreased ability to induce autophagy in response from signals from NOD2. NOD2, besides being a receptor for bacterial muramyl peptides in the cytoplasm, also has the job of recruiting ATG16L1 and allowing autophagy protein complexes to be initiated at the plasma membrane near bacterial entry. The most common CD-associated mutation truncates NOD2 so that it is unable to localize ATG16L1 to the membrane. This would make cells more susceptible to mycobacterial infections.

There is an overlap of susceptibility between mycobacterial infections and inflammatory bowel disease, and there was a time when it was widely believed that CD could be related to a mycobacterial infection similarly to Johne’s disease in cows. Seeing that the mutations in NOD2 and ATG16L1 could be detrimental to the proper elimination of mycobacteria could be another reason to resurrect the hypothesis.

However, there is another interesting option as well. These same mutations also impact the ability of Paneth cells to secrete anti-microbial peptides in response to intestinal bacteria. This was also mentioned in last weeks post. It could also be that these mutations are also upsetting the relationship between the gut and the neutral microorganisms that inhabit them.

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Controlling Intestinal Lymphocytes and Abnormal Paneth Cells

Complete intestinal metaplasia in a case of chronic gastritis, HE 3
Paneth cells, the red cells in the crypts, become abnormal in Crohn’s patients with NOD2 and ATG16L1 mutations.
This week, there are interesting insights about intestinal lymphocyte population maintenance with exciting functions for TGFβ and NOD2. Also a unique perspective uncovers relationships between Crohn’s disease mutations and Paneth cell function.

TGFβ-directed Memory Retention

Memory; it’s the characteristic of the adaptive immune system that allows it to react quickly and specifically. Resident memory CD8+ T cells (Trm) found in the intestines are a valuable subset of cytotoxic T cells that defends against intestinal viral pathogens. However, the signals that mediate this population were unclear. The recent article by Zhang and Bevan sheds some light on how this works. To do this, they created a transgenic mouse with TCRs specific for a model virus and lacking a transforming growth factor (TGF)-β receptor. With this unique tool, they were able to determine that TGFβ plays two important roles for Trm during inflammation. 1) It inhibits the migration of dividing CD8+ T cells from the secondary lymphoid organs during the beginning of inflammation, and 2) it helps retain the same cells in the intestines during the later stages of inflammation.

NOD2 Maintains Intraepithelial Lymphocytes

Despite the association between NOD2 and Crohn’s disease being known for more than ten years, how NOD2 functions in the gut is only now be unraveled. In a recent article in the Journal of Experimental Medicine, it was found that Nod2 deficient mice lack intraepithelial lymphocytes (IELs). IELs are mainly CD8+ T cells and γδ+ T cells and appear to have a protective role in inflammatory bowel diseases. The loss was mediated largely by deficiencies in proliferation and survival. Further investigation revealed that Nod2-microflora interactions were required along with Nod2 signaling on antigen presenting cells and interleukin-15 production to have optimal populations of IELs and protection from colitis.

Crohn’s Mutations and Paneth Cell Phenotypes

Genome wide association scans are an interesting way to learn more about diseases like Crohn’s disease. However, they provide an enormous amount of data. To gain a clearer view of the possible effects of associated mutations, VanDussen et al decided to narrow their scope and focus only on the function of Paneth cells. Paneth cells are the gatekeepers of the intestinal crypts and produce anti-microbial peptides to control bacteria infiltration. The researchers observed that high numbers of defect alleles for NOD2 and ATG16L1 led to high amounts of abnormal Paneth cells in Crohn’s disease patients. This was also associated with altered immune activation, changes in granuloma numbers and disease recurrence.

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