Did the stability of the transcriptome be affected by factors such as pathological conditions, diet?

Question

[GrantS]

Dear all, We plan to conduct a population-based study with the main method being transcriptomic analysis of human peripheral blood.

Would the stability of the transcriptome be affected by factors such as physical activity, diet, pathological conditions, and environmental factors?

If this is indeed the case, are there any feasible solutions available? If this problem cannot be resolved, is it even necessary to conduct transcriptomic analysis?

Are there any omics fields, such as genomics, transcriptomics, metabolomics, epigenomics, proteomics, gut microbiomics, single-cell omics, immunomics, and peptidomics, that may be less influenced by factors such as physical activity, diet, pathological conditions, environmental factors, among others?

Thank you for your help!

[Yogi]

This is such a fundamentally great question that many folks don't even think to ask.

The very fact that you think deeply enough about this shows that you're trying to be systematic.

It most definitely does have an effect.

The best way I can think to control for this is to literally CONTROL or, if the aforementioned is not possible, RECORD all these different metrics to be used as covariates.

[GrantS]

Thank you, we are also learning and exploring through communication with you and other knowledgeable researchers, represented by you, hoping to make progress.

The two methods you mentioned: literally CONTROL and RECORD all these different metrics to be used as covariates, are very inspiring. In addition, we have also seen some literature such as: Bowyer JF, Tranter KM, Hanig JP, et al (2015) Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood. PLoS ONE 10(7): e0133315. doi:10.1371/journal.pone.0133315.

Unfortunately, this paper also does not provide a clear discussion on the mentioned issues. Do you have any recommended literature that discusses or researches the above issues? Thank you.

[Yogi]

Sadly nothing that I know of.

Answer 1

[roberto.bonnellya]

Yes, the transcriptome is indeed affected by these factors, as the expression of certain genes is enhanced or silenced depending on external stimulus, something you can do is divide your population in sub-groups depending on these conditions, so that these groups are as homogene as possible. Another approach is to work with the genome instead, but that could demand higher resources.

Best Regards and Good Luck!

[GrantS]

Thank you. Is it true that, as you mentioned, we collaborate with the genome? For example, during the process of peripheral blood testing, do we conduct simultaneous transcriptome and genome analysis. If so, would this method be considered a form of joint analysis? We are also hearing about this approach for the first time. Do you have any specific methods or examples that you could provide? Thank you for your help!

Answer 2

[Kevin]

The whole-blood transcriptome is gonna be highly enriched with globin transcripts from all the erythrocytes. Remove the globin transcripts and sure, you'll see some effect from diet, exercise, etc on relative abundances of different transcripts of interest.

The serum/plasma transcriptome is gonna be even more responsive to external factors. You can get a substantial change in the amount of total RNA that's extractable from a given volume of plasma, just by varying the time of day at which the patient donated blood.

[GrantS]

Thank you. We are interested in the globin transcripts you mentioned. However, I am not sure if they are related to the paper you mentioned: Bowyer JF, Tranter KM, Hanig JP, et al (2015) Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood. PLoS ONE 10(7): e0133315. doi:10.1371/journal.pone.0133315.

Furthermore, you mentioned that " You can get a substantial change in the amount of total RNA that's extractable from a given volume of plasma, just by varying the time of day at which the patient donated blood." How should we understand the idea of changing the time mentioned here? Or how should we implement it? Do we need to first investigate the physiological and pathological status as well as the environmental conditions of the subjects to be included, and then collect peripheral blood during a time period considered stable or with minimal impact?

We understand that it may be challenging to maintain consistent physiological and pathological conditions, as well as environmental exposures, in a population-based cohort study. As a result, the feasibility of implementing such an approach may be limited. We would like to receive your professional advice again. Thank you.