Secretome, Microbiome/Hologenome, Proteome, Epigenome, Exome and Genome

Biologists clearly like "–omes".

A full understanding of all the –omes would lead to an understanding of pretty much all disease, including autism.  Science is still a long way from such an understanding.

More questions than answers

Even a partial understanding of the "-omes does help to see how things fit together and also it helps understand where the research is going and why. It also makes you realize how little we currently know, and that includes all those clever scientists. This is why we keep coming back to stumbled-upon and trial error as valid discovery methods.

You can also see why researchers and those who fund them, like Mr Simons, easily get lost in the detail. Behind the 5% of the detail they fully understand is another 95% that will take a hundred years to fully understand. 

Microbiome & Hologenome/Holobiont

The intestinal microbiome is currently very fashionable.

The intestinal microbiome describes the microorganisms that reside in your intestines/gut.  It includes bacteria, fungi, viruses and archaea/protists (single cell organisms). Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host.

The microbiome and host emerged together during evolution as a synergistic unit from epigenetic and genetic characteristics, called a holobiont.  The hologenome concept of evolution, considers a human as a community, or a holobiont - the host plus all of its symbiotic microbes. The collective genomes of the holobiont form a hologenome.

This becomes very relevant in human disease because in modern life humans have become separated from part of their evolutional holobiont (symbiotic microbes).  As a result all kinds on immune disease have become more prevalent.

It became accepted that all dirt is bad and daily contact with other living non-human animals is bad.

Humans are colonized by many microorganisms and surprisingly your body contains more  types of non-human cells than human cells. Some estimates suggest it is many times more; food for thought.

Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host.

Bacteria are transferred from mother to child through different pathways. As the newborn’s microbiome is established, bacteria quickly populate the gut, prompting a range of immune responses and programming the immune system with long-lasting effects.

Having pets at home during and after pregnancy has been shown to have beneficial health effects on the child. Your pet dog and his bugs are part of your holobiont. If you make drastic changes in your holobiont, do not be surprised if strange things happen; a case in point are the so-called Somali Autism Clusters. When Somali refugees moved to Sweden and the US, they produced children with a high incidence of autism and all the researchers wondered why.

Secretome

This was a new "–ome" to me, that we came across in a recent post.

The secretome is the totality of secreted organic molecules and inorganic elements by biological cells, tissues, organs, and organisms.

It turned out that human fat cells secrete over 600 different different proteins/hormones.  None of this was even known 25 years ago.

So your endocrinologist knows all about the usual endocrine glands: pineal gland, thymus gland, pituitary gland, thyroid/parathyroid gland, and adrenal glands; but what about the largest endocrine gland of all, your body fat (adipose tissue)?

Genome

I did write a post about genetics, more for completeness than in the expectation that many people would read it.

The genome includes a small part of so-called “coding DNA” that contains the instructions to make proteins, this is called the exome.  The remaining 98% is made up of non-coding DNA.  This 98% used to be called junk DNA, but it is not. It is suggested that 80% of human genomic DNA has biochemical activity, not just the 2% that is the coding DNA in the exome. 

Exome

The exome is the 2% of the genome that holds the codes to make the proteins that make up your body.

Epigenome

The epigenome are all the so-called epigenetic markers that you accumulate from the environment and that you inherited from your ancestors.  You could think about this as bruises and scars on your body.  Imagine if you inherited your Grandma’s appendix scar and Grandad’s scar from a skiing accident.  In epigenetics the fact that Grandad was a heavy smoker may have marked your genes that relate to oxidative stress.

Your personal epigenome is a record of all these markers and it would show which genes are likely miss-expressed.  It would be used to determine personalized medical therapies.

This would be very relevant to autism.  

Proteome

I rather like the proteome, because it would tell you what is happening right now, rather than what might happen (as in the genome, exome and epigenome).

Most people do not realize just how much in your body is changing all the time and is not fixed at all.

The proteome is the entire set of proteins expressed by the coding DNA (the exome part of the genome), at a certain time.

So it would tell you exactly what is happening in a specific part of your body at a specific time.

This would be invaluable in understanding autism, if it could be done in real time in different parts of the brain. This is not possible with today’s technology.