Category Archives: Genes

Macrophages Like IL-10 and DNA Methylation Regulates Tregs

This week on TIBDI, we see a plethora of interesting articles including a parallel publication about the necessity of IL-10 conditioning for gut macrophages and the ways that DNA methylation influences colon Treg proliferation.

IL10 Crystal Structure.rsh
IL-10 is an important conditioning factor for gut macrophages.
Intestinal Macrophages Need IL-10 Conditioning: Parallel Publication

Macrophages are an important immune cell of the intestines. For instance, CX3CR1hi macrophages capture antigens from the lumen by extending dendrites up through the epithelial layer and into the mucus to interact with passing bacteria. In the latest set of publications by the journal Immunity, parallel articles examine the relationship between macrophages and the anti-inflammatory cytokine interleukin (IL)-10. Using two different approaches, Dr. Ehud Zigmond of the Weizmann Institute of Science in Israel and Dr. Dror S. Shouval of Harvard Medical School in the United States were able to make similar conclusions.

Dr. Zigmond, using macrophage-restricted Il-10-/- and Il-10ra-/- mice, determined that macrophages with deficient IL-10 secretion were not nearly so harmful to the gut as macrophages not being able to respond to IL-10. Losing the ability to be conditioned by IL-10 made the macrophages more pro-inflammatory and led to spontaneous colitis. Dr. Shouval approached his research by creating bone-marrow chimeras with Rag2-/-Il-10rb-/- bone marrow and using the T cell transfer model of colitis. He found that loss of IL-10 signaling in innate immune cells led to colitis development. His work, unlike that of Dr. Zigmond, revealed that IL-10 conditioned macrophages are needed for proper regulatory T cell (Treg) development, and mucosal immune tolerance. He also found that pediatric inflammatory bowel disease (IBD) patients with mutations in their IL-10 receptors also had more pro-inflammatory macrophages. This work may lead to insights about why IBD develops.

Colonic Treg Proliferation Needs Uhrf1

Finding the ways that epigenetic mechanisms control T cell function and numbers is an exciting new field of research. One of the latest Nature Immunology articles adds fuel to the fire by publishing the work of Dr. Yuuki Obata of the University of Tokyo in Japan. She found that the DNA-methylation adaptor Uhrf1 was needed for Treg proliferation in the colon. This was determined by profiling genes activated in proliferating Treg after colonization with bacteria. This was then confirmed using T cell-specific Uhrf1-/- mice. Loss of Uhrf1 led to hypomethylation of a cell-cycle gene and a loss of Treg division in the colon. As a consequence of the low Treg numbers, Uhrf1-/- mice developed spontaneous colitis. It will be interesting to see if the same results can be found in the human setting.


Anti-CD3 Control of T Cells and Milk for Immune Development

Mansion Becomes Maternity Home- Life at Brocket Hall, Welwyn, Hertfordshire, 1942 D9026
Breast milk sugars are crucial for regulating the intestinal immune responses in newborns.
This week on TIBDI! Gene expression signatures of anti-TNFα non-responders are investigated, breast milk oligosaccharides regulate developing immune responses, and an anti-CD3 antibody offers hope for T cell regulation in the gut.

Inflammatory Signatures of Anti-TNFα Non-Responders

Even though anti-TNFα therapy for Crohn’s disease (CD) patients is very effective, up to 40% of patients are or become non-responders. To find out if there were differences in gene expression between these groups of patients, Dr. Raquel Franco Leal of the Hospital Clinic in Barcelona Spain examined mRNA levels of inflammatory genes in these two populations. She found that treatment with anti-TNFα effectively regulated many cytokines and chemokine genes despite the clinical outcome. However, those that achieved a clinical remission also had a number of changes in many other genes including IL1B, S100A8 and CXCL1. In contrast, refractory patients continued to have deregulated genes associated with pathways inducing IL17A. Besides introducing new drugs targets, these results reemphasize the importance of IL-17 pathways in CD.

Developing Immune Systems Need Milk

The complex immunoregulatory mechanisms needed to protect and control the human gut are developed early after birth, and are catalyzed by the colonization of the intestinal tract with bacteria. Suspecting that breast milk may protect the early intestinal tract from unwanted inflammatory responses, Dr. Y. He and colleagues investigated human milk oligosaccharides from colostrum (cHMOSs). Using human fetal intestine explants, they were able to determine that cHMOSs significantly altered immune gene expression. Their model suggests that cHMOSs attenuate pathogen-associated receptor signaling, simultaneously lowering immune cell activation and enhancing pathways needed for clearance, regulation and tissue repair.

Anti-Inflammatory Anti-CD3

T cells likely play an important role in inflammatory bowel disease (IBD) by maintaining inflammatory responses. Finding a way to specifically reduce or deactivate these cells in IBD patients could be a possible therapy. Dr. Anna Vossenkämper, together her colleagues, experimented with this idea using a special anti-CD3 antibody called otelixizumab, which is known to induce tolerance. Using mucosal biopsies from IBD patients, she was able to determine that otelixizumab could decrease pro-inflammatory cytokine production and lower the activity of multiple immune pathways. The antibody’s effects were determined to be dependent on IL-10 expression.



New and Exciting Ways to Control Th17 Differentiation

The basic unit of chromatin organization is the nucleosome, which comprises 147 bp of DNA wrapped ar
Controlling DNA packing could be a future way to alter T cell differentiation for IBD.
This week on TIBDI we get an overload on new Th17 research including Th17 induction via segmented filamentous bacteria and dendritic cells, the role of methyltransferases during T cell differentiation, and, my own article describing how TLR6 stimulation in the gut leads to increased Th17.

Segmented Filamentous Bacteria, DCs and Th17

It is already well described that segmented filamentous bacteria (SFB) are associated with the induction of Th17 cells in the gut, and that Th17 is associated with inflammatory bowel disease (IBD). However, the mechanisms behind the induction were not entirely clear. Yoshiyuki Goto and Casandra Panea of Columbia University Medical Center worked together to answer these questions, and found that dendritic cells (DCs) were the missing link. They determined that DCs presented SFB via MHC class II molecules to T cells, and induced SFB-directed Th17 cells. These interactions were not limited to areas of lymphoid tissue, but also happened in the small intestinal lamina propria. Interestingly, RORγt+ innate lymphoid cells simultaneously played an inhibiting role also via MHC class II molecules.

TLR6 Involved with Intestinal Inflammation

Pattern recognition receptors, like those from the Toll-like Receptor (TLR) family, alert the immune system when pathogens enter areas of the body. While this system is essential for fighting infection, the same receptors also induce inflammation during IBD. To learn more about TLR6 in intestinal inflammation, Dr. M.E. Morgan of Utrecht University in the Netherlands and her colleagues looked at immune responses induced in the gut both in vitro and in vivo. They found that stimulation of TLR6 in the gastrointestinal-associated lymphoid tissue supported the induction of Th1 and Th17 cells, and oral feeding of TLR6 ligands induced Th17 cells. Mice deficient in TLR6 had lower numbers of Th1 and Th17 cells, and were also protected from experimental colitis suggesting that TLR6 could be an interesting candidate for future IBD therapeutics.

Chromatin Control of T Cell Differentiation

Histone methyltransferases modify histones (by adding methyl groups to lysine residues) to control DNA packing and gene accessibility. These kinds changes could impact IBD. Recent research has indicated that the methyltransferase G9A controls a repressive modification called H3K9me2 that influences T cell differentiation. Dr. Frann Antignano of the University of British Columbia in Canada now sheds more light on this process. She found that G9A dynamically inhibited the differentiation of regulatory T cells and Th17, and that loss of G9A specifically led to more activity of the Foxp3 and Rorγt genes, which are the master transcription factor of regulatory T cells and Th17 cells respectively. Specifically eliminating G9A from T cells transferred during the T cell transfer colitis model increased regulatory T differentiation and lowered disease. This could mean that targeting histone methyltransferases could be a potential IBD therapy.


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.


Regulatory T cell Development and Crohn’s Disease Siblings

Albert Anker Schreibender Knabe mit Schwesterchen I 1875
Siblings of Crohn’s disease patients have signs of inflammation.
This week on TIBDI: A gene behind very early onset inflammatory bowel disease (IBD) is uncovered, the receptor needed for colon regulatory T cell development is found and siblings of Crohn’s disease (CD) patients have signs of nascent intestinal inflammation.

Gene Behind Early Onset IBD

While many IBD cases are diagnosed during young adulthood and middle age, there is subset of patients that develop the disease before the age of six. To determine if there were certain mutated genes behind this early disease presentation, scientists from a multitude of institutions examined the DNA of children with very early onset IBD. They found that the children had loss of function mutations in the gene for tetratricopeptide repeat domain 7 (TTC7A). TTC7A is involved with phosphatidylinositol-4 kinase signaling. When the researchers specifically knocked down this gene in intestinal cell lines, they found that the cells lost adhesion and had increased apoptosis. This supported the clinical presentation in the children studied, which was marked by apoptotic enterocolitis.

Regulatory T cell development with GPR109A

Butyrate, a short chain fatty acid (SCFA) produced by intestinal bacteria, was recently shown to induce regulatory T cells in the colon. Scientists from Georgia Regents University have now clarified this effect even further by discovering the butyrate receptor behind increased regulatory T cells. This receptor is GPR109A, and it is also the receptor for the B vitamin niacin. They found that both butyrate and niacin gave anti-inflammatory properties to dendritic cells and macrophages via GPR109A, which encouraged Foxp3 and IL-10 expression in T cells. In colitis models, loss of the receptor led to severe disease. Studies using germ-free mice suggested that regulatory T cell defects caused by the loss of microbiota-derived butyrate could potentially be replaced by pharmacological doses of niacin.

CD Siblings As CD Models

Sisters and brothers of CD patients have an increased risk of developing disease. Initial studies of these potential patients show that they have some signs of intestinal inflammation like increased fecal calprotectin and intestinal permeability. Scientists from the United Kingdom have now investigated further and found that CD patients and their siblings have other striking similarities, such as abnormal changes in the intestinal microbiota and T cell phenotypes. The siblings were significantly different from control healthy populations, making them an unique “at risk” group. The researchers feel that studies of patient siblings could lead to new insights about the immune processes that lead to full blown CD.