AMED-funded projects

Why a cell doesn’t attack its own DNA

The long-standing puzzle of why the immune system is not activated by a cell’s own DNA has been solved by a molecular-structure study

A structural investigation of an enzyme that alerts the innate immune system to the presence of foreign DNA in a cell has revealed why the enzyme isn’t triggered by a cell’s own DNA. This finding will inform research into autoimmune disorders.

When foreign DNA enters a cell, an enzyme known as cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS) senses the DNA by binding to it, which triggers an innate immune response. But researchers have long puzzled over why cGAS doesn’t bind to the cell’s own DNA.

Recently, researchers have found that the binding of cGAS to a nucleosome, which is the structure that spools a cell’s DNA, inactivates the response of cGAS to the cell’s DNA, thereby avoiding an autoimmune response. However, the mechanism behind the inactivation of cGAS remained unclear.

Now, in an AMED-funded study, Hitoshi Kurumizaka of the University of Tokyo and his co-workers have used cryo-electron microscopy to investigate the molecular structure of cGAS and nucleosome complex. They found that the three sites that cGAS uses to bind to DNA are either blocked or repurposed when cGAS binds to the nucleosome.

“We discovered that all three cGAS–DNA binding and dimerization sites, which are required for cGAS activation, become inaccessible when cGAS binds to the nucleosome,” says Kurumizaka. “Surprisingly, we found that one site that binds to DNA was repurposed and instead it bound to histones [components of the nucleosome].”

“We believe these results are of great interest to the immunology community since they significantly advance our understanding of the cGAS mechanism. Surprisingly, in the same day, four other groups published the cGAS-nucleosome complex structures with quite similar conclusion,” says Kurumizaka. “They may contribute to our knowledge of autoimmune diseases and help the development of new therapeutic drugs.”

Intestinal inflammation alters clonal composition

Inflammation of the large intestine leads to the positive selection of specific gene mutations

Chronic inflammation of the intestines has been found to remodel the local cellular landscape and results in the proliferation of cells having certain mutations. This discovery could lead to new therapies for colorectal cancer.

Chronic inflammation involves accelerated destruction and repair of tissue and is associated with a higher risk of developing cancer. But it is not known how these recurring destroy-and-repair cycles affect the clonal composition of tissues and what role an altered clonal composition plays in the development of cancer.

In an AMED-funded study, Seishi Ogawa of Kyoto University and his co-workers have examined the clonal composition of people with ulcerative colitis—persistent inflammation of the large intestine, which is associated with an increased risk of cancer development. They found higher occurrences of certain gene mutations, but that these mutations differed from those that are positively selected in colitis-associated cancer.

This finding came as a surprise. “Unlike sun-exposed skin and esophageal epithelium in aged people, clonal expansion is rarely seen in the colorectal epithelium of healthy individuals, even in aged individuals,” says Ogawa. “Surprisingly, however, in ulcerative colitis patients, the colorectal epithelium underwent extensive remodelling by expansion of numerous independent clones, which are accompanied by several recurrent mutations and are thus positively selected.”

“Our finding provides insight into how our body responds to an inflammatory insult and also into how the positive-selection mechanism differs between inflammation and carcinogenesis,” adds Ogawa. This knowledge can be used to identify vulnerabilities in cancer development that could be exploited by new therapies.

Coffee drinking might be in your genes

Certain genetic variants exhibit associations with the eating and drinking habits of Japanese people

Nine gene locations that make a person more predisposed to consume certain foods (such as yogurt and fish) and beverages (including coffee and alcohol) have been identified in a genome-wide association study (GWAS).

GWAS have been extensively used to identify connections between gene variants and diseases. But until now they have not been used to determine the links between our genes and eating habits.

Now, in an AMED-funded study, Yukinori Okada of Osaka University and his co-workers have compared genetic data from more than 160,000 Japanese people with the consumption of 13 foods and drinks. From this comparison, they identified nine gene locations that had significant associations with the consumption of the foods and drinks. Ten of the associations they found had not been reported previously.

The researchers were surprised at how many gene variants were associated with consumption habits. “While some of these variants were previously known to be associated with drinking alcohol, we didn’t expect that so many of the variants would be associated with a wide range of dietary habits,” says Okada.

One gene variant was associated with many different food and drink preferences: people with a variation in a single DNA nucleotide at one specific gene were likely to consume more milk, yogurt, coffee and green tea but less alcohol, fish, tofu and fermented soybeans. “It was interesting that one variant at the ALDH2 gene affected so many dietary habits,” says Okada.

“Our study revealed that what we eat (in other words, our dietary habits) is defined by what we are (that is our, genetics),” he adds.

Antiviral-resistant influenza viruses are no less virulent

Resistance to an antiviral drug does not seem to put flu viruses at any disadvantage compared to their susceptible cousins

Influenza A viruses that are resistant to a new antiviral drug show no signs of being less active or transmissible than their non-resistant counterparts. This raises the spectre of the proliferation of antiviral-resistant strains of influenza A, unless multipronged strategies are employed.

The antiviral drug baloxavir marboxil (BXM) was approved for use in the USA and Japan in 2018. Unlike other antiviral drugs, BXM targets the polymerase acidic (PA) protein of influenza A and B viruses. However, influenza virus stains have been found that have reduced susceptibly to baloxavir acid (BXA), the active form of BXM, because they have a mutation in their PA gene. It was unclear how this mutation affects these mutant viruses’ pathogenicity and ability to spread.

Now, an AMED-funded study led by Yoshihiro Kawaoka and Masaki Imai, both of the University of Tokyo, has found that viruses with this mutation have similar pathogenicity and transmissibility as those without it.

The team isolated influenza A viruses with the mutation from patients in Japan and found that they grew just as well in cell culture as viruses lacking the mutation. The viruses also exhibited similar replicative abilities and pathogenicity in hamsters. Furthermore, they transmitted efficiently between ferrets via respiratory droplets.

These findings imply that the viruses with reduced susceptibility to BXA will not be at any significant disadvantage compared to BXA-susceptible viruses. “These findings suggest that the currently circulating seasonal influenza A viruses could maintain their viral fitness even though they have evolved to be less susceptible to BXA,” says Kawaoka. Combination treatments with multiple antiviral drugs may be needed.

Overcoming the final hurdle to bringing an eye treatment to patients

A procedure for repairing damage to the eyes is close to being cleared for use in Japan

Chie Sotozono of Kyoto Prefectural University of Medicine and her team really wanted patients to benefit from a procedure they had developed for regenerating damaged corneas. Since the eye conditions are relatively rare, it proved to be very challenging to find a pharmaceutical company willing to invest in the procedure. Instead, she opted to conduct an investigator-initiated clinical trial herself with all the challenges that involved. But before she could embark on the trial, she had to secure the needed funding.

That funding, along with other sources of support, came from AMED. The grant enabled Sotozono’s team to conduct a trial on seven patients. She says the results have been very encouraging, and she hopes the treatment will be approved by Japan’s Pharmaceuticals and Medical Devices Agency this fiscal year.

“Without AMED support, both financial and in other ways, we wouldn’t have been able to get this far,” says Sotozono.

The treatment, known as cultivated oral mucosal epithelial sheet transplantation (COMET), is for treating severe ocular-surface diseases. It involves taking cells from a person’s mouth, growing them in the lab and transplanting sheets of the cultivated cells onto the surface of the eye. COMET is unique in that both the mouth cells and the amniotic membrane they are cultivated on are grafted onto the patient’s eye. The membrane supplements loss of the existing membrane and its flexibility allows it to readily conform to the eye’s curved surface.