Gene expressions/Cost sharing and research products

This resource summarizes those descriptions requested as part of the Step 2 submission for the proposal.

Title: Gene expressions in human exploration beyond low earth orbits.

Number: 15-15Omni1-0008.

Solicitation: NNJ15ZSA001N-OMNIBUS.

Due date and time of submission are 5:00PM ET on November 23, 2015.

Table of Contents

1. Project description

The Project narrative already submitted for Step 1 (which we were asked not to change) serves as the Scientific Project Description. This Project narrative is included with additions per Step 2 at the end.

Project summary

The objective of this proposal is to explore each avenue of the Human Research Roadmap to determine gene suites that may be contributing to or causing these effects or increasing risks of these effects sufficiently to impair astronaut functioning. Even normal (Earth-based) gene expression may be producing physiological and performance effects from the hazards mentioned. Under, or over expression, of genes in each suite may alter gene expression sufficiently to add to adverse effects.

Altered expression of genes from each suite during spaceflight and in preparation for return to normal (Earth-based) environments may reduce hazards during the mission or before return to Earth.

Human Research Roadmap

Starting with each entry in the roadmap, a concept search of the National Institutes of Health NCBI gene database (http://www.ncbi.nlm.nih.gov/gene/) may provide possible initial genes (and associated isoforms and variants) participating in each risk.

For example, from the first risk statement in the roadmap, entering "adverse cognitive condition" + "human" yields a list of 52 genes, of which 37 are for humans and 15 are for mouse and rat analogs. For this research, the mouse and rat analogs will be examined where applicable.

An edit search of the site for the first gene "APOE" reveals the following references:
 * 1) "APOE epsilon4 carriers with self-assessed cognitive concerns appear to have worse memory, and possibly accelerated memory decline."
 * 2) "APOE E4 carrier status is associated with a steeper cognitive decline in a Korean population."
 * 3) "A genome-wide scan for common variants affecting the rate of age-related cognitive decline. [...] NHGRI GWA Catalog, PubMed".

The first gene is GeneID: 348 APOE apolipoprotein E. It has only one isoform expressing the gene itself for all conditions: "The protein encoded by this gene is a major apoprotein of the chylomicron. It binds to a specific liver and peripheral cell receptor, and is essential for the normal catabolism of triglyceride-rich lipoprotein constituents." per NCBI entry.

Although Alzheimer's and vascular dementia types would be unexpected in a healthy astronaut, "Given the extended duration of current and future missions and the isolated, confined and extreme environments, there is a possibility that (a) adverse cognitive or behavioral conditions will occur affecting crew health and performance; and (b) mental disorders could develop should adverse behavioral conditions be undetected and unmitigated." from this first roadmap's risk statement. As such GeneID: 348 APOE would be added to the resource, https://en.wikiversity.org/wiki/Genes/Expressions, Gene expressions at Wikiversity.

NASA databases The next step is to check potentially applicable NASA databases for more information to possibly indicate that expressions of this gene are producing or contributing to any "adverse cognitive condition".

For example, a brief scan of the Report for this risk, "Risk of Behavioral and Psychiatric Conditions" by Kelley J. Slack, et al. suggests that GeneID: 348 APOE apolipoprotein E may not be involved. A much more extensive literature search needs to be performed before GeneID: 348 APOE apolipoprotein E can be eliminated from the list as a direct actor or as an associated expression from gene interactions with other genes.

In addition to working through the risks, there will be separate investigations of NASA databases. For example, "How Long Does It Take to Rebuild Bone Lost During Space Flight?" from url=http://www.nasa.gov/mission_pages/station/research/subregional_bone.html.

The image on the right shows the loss of bone mass apparently due to long-term microgravity on the International Space Station. "[A]stronauts, on average, lost roughly 11 percent of their total hip bone mass over the course of their mission." from this report.

"The success of human exploration missions depends on finding countermeasures to overcome such effects on crew members. There are important synergies between osteoporosis research on Earth, and studies of bone loss and recovery in healthy astronauts in space. Each area of study complements the other." by Julie Robinson, International Space Station program scientist at NASA's Johnson Space Center in Houston, from the same report.

Submitting "osteoporosis" and "human" to the NCBI gene database, produces GeneID: 348 APOE as the first one on the list of some 264 of which about 40 are from mouse or rat analogs. Each of these would also need to be investigated for inclusion.

Google Scholar web search

A search of literature with Google Scholar using the concepts "spaceflight" and "apolipoprotein E" result in about 160 literature results including "In contrast, work overload increased the expression of genes like apolipoprotein E (7-fold) and stearyl-CoA desaturase (29.2-fold)." and "They should help in determining the mechanisms regulating skeletal muscle mass, which may lead to strategies to combat muscle atrophy in at-risk individuals: those in spaceflight as well as the bedridden and aged." from Differential gene expression in the rat soleus muscle during early work overload-induced hypertrophy by JA CARSON, DAN Nettleton, JM REECY published in The FASEB Journal in 2002.

Literature results such as this indicate that GeneID: 348 APOE apolipoprotein E should be included in any gene suite likely to be expressed adversely during spaceflight.

Gene clusters

GeneID: 348 APOE apolipoprotein E description also contains this: "This gene maps to chromosome 19 in a cluster with the related apolipoprotein C1 and C2 genes." These two genes are not included in the initial 52 genes returned by NCBI search. A second search using "apolipoprotein C1" returns 59 genes with
 * 1) GeneID: 341 APOC1 on chromosome 19,
 * 2) GeneID: 344 APOC2 on chromosome 19,
 * 3) GeneID: 346 APOC4 on chromosome 19,
 * 4) GeneID: 348 APOE, already found above, on chromosome 19,
 * 5) GeneID: 718 C3 on chromosome 19,
 * 6) GeneID: 3949 LDLR on chromosome 19,
 * 7) GeneID: 23526 HMHA1 on chromosome 19, and
 * 8) GeneID: 282617 IFNL3 on chromosome 19. A third search using "apolipoprotein C1" returns 51 genes and most of the above list on chromosome 19.

Although these genes on chromosome 19 may not be expressed when APOE is expressed, they may be close enough or part of the cluster that is activated. Each of these would then be checked against the NASA database and the open literature searchable with Google Scholar or other search engines.

Gene regulations

Each gene, or its isoforms, is likely to have upregulation and downregulation transcription factors. As each gene is investigated, these enhancers and inhibitors are noted as discovered.

For example, submitting "gene regulation" APOE human to the NCBI gene database returns 28 genes and 21 mouse analogs. The first on the list is GeneID: 2099 ESR1 estrogen receptor 1. "This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. [...] Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis." from the page url=http://www.ncbi.nlm.nih.gov/gene/2099. The database also maintains the DNA sequence upstream, downstream, and through the entire gene locus so that analysis of "Alternative promoter usage and alternative splicing result in dozens of transcript variants, but the full-length nature of many of these variants has not been determined. [provided by RefSeq, Mar 2014]" can be attempted. The site lists gene interactions and six variants for three isoforms (1, 2, and 3) and ten experimental transcriptions. Each of these sixteen isoforms or potential transcripts, may be investigated for specific involvement in osteoporosis or bone effects due to microgravity.

Gene similarities

There are genes on other chromosomes that are similar to each gene being considered. For example, GeneID: 338, Apolipoprotein B, is on chromosome 2. Yet it has been included in studies of rat models for predicting skeletal changes during spaceflight.

Human DNA

"[H]uman DNA has millions of on-off switches and complex networks that control the genes' activities. ... [A]t least 80% of the human genome is active, which opposed the previously held idea that most of the DNA are useless." By Bryan McBournie (September 6, 2012) "Human genome study could unlock the biology of disease", American Scientist.

"DNA contains genes, which hold the instructions for [life. But, these] take up only about 2 percent of the genome ... The human genome is made up of about 3 billion “letters” along strands that make up the familiar double helix structure of DNA. Particular sequences of these letters form genes, which tell cells how to make proteins. People have about 20,000 genes, but the vast majority of DNA lies outside of genes. ... [A]t least three-quarters of the genome is involved in making RNA [...] it appears to help regulate gene activity." By Malcolm Ritter (September 6, 2012) "Far from being mostly junk, human DNA is ‘a jungle’ of complex activity, huge project shows", The Washington Post.

There are "more than 4 million sites where proteins bind to DNA to regulate genetic function, sort of like a switch." Ritter, ibid.

Over 50% of human DNA consists of non-coding repetitive sequences, from T. Wolfsberg, J. McEntyre, and G. Schuler "Guide to the draft human genome" Nature 409 (6822) 824–6 (2001).

Some DNA sequences may encode functional non-coding RNA molecules, which are involved in the regulation of gene expression, from The ENCODE Project Consortium, "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project", Nature 447 (7146) 799–816 (2007).

About 2700 formerly active genes are now pseudogenes. Additional DNA is used in introns and for centromeres and telomeres.

Some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules, by D. Rearick, A. Prakash, A. McSweeny, S.S. Shepard, L. Fedorova, and A. Fedorov, "Critical association of ncRNA with introns", Nucleic Acids Research 39 (6) 2357–66 (March 2011).

Epigenome

Inside each eukaryote nucleus is genetic material (DNA) surrounded by protective and regulatory proteins. These protective and regulatory proteins and the dynamic changes to them that occur during the course of a eukaryote's existence are the epigenome.

There are "nearly 50,000 acetylated sites [punctate sites of modified histones] in the human genome that correlate with active transcription start sites and CpG islands and tend to cluster within gene-rich loci." by Bradley E. Bernstein, Alexander Meissner, and Eric S. Lander, "The Mammalian Epigenome", Cell, (February 23, 2007) 128 (4) 669–81.

Any of the epigenome sites may be influenced during or before transcription to modify gene expressions.

Entering "APOE human epigenome" into the NCBI gene database returns GeneID: 7157 TP53, url=http://www.ncbi.nlm.nih.gov/gene/7157, and one mouse analog GeneID: 93759 sirtuin 1. An associated condition for GeneID: 7157 per the page is osteosarcoma (a malignant tumor of bone in which there is a proliferation of osteoblasts). "This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism." per the page. The gene locus contains twelve isoforms and eight variants for apparently at least seven unique transcripts. For example, variants 1, 2, and 8 encode isoform g, per the page.

Gene transcriptions

Gene transcription involves gene promoters that may lie upstream of the gene or downstream. The number and variety of gene promoters, enhancers and inhibitors, and other triggers for each gene can by quite large, but each may be an opportunity to alter gene expression as needed.

There are at least 60 specific transcription factors, such as the TATA box, that initiate or contribute to transcription.

Entering "APOE human promoters" into the NCBI gene database returns forty-three genes and forty-one analogs. The first gene after APOE is GeneID: 4023 LPL lipoprotein lipase which in turn describes a rare variant of APOE and diseases with splenomegaly (abnormal enlargement of the spleen) and dyslipidemia such as Gaucher disease (glucocerebrosidase deficiency) where Type 1 involves bone erosion and anemia. While mutations in GeneID: 2629 GBA glucosidase, beta, acid, cause Gaucher disease, perhaps expression of this gene can reduce bone erosion. As such these may be included in the collection of risk related genes.

Schedule

Each of the Human Research Roadmap entries should be researchable within a month or less so that all have been studied by year's end.

Major milestones

Each entry in the Human Research Roadmap corresponds to the Major milestones. Researching each of these is likely to uncover common genes to many of the entries in the Human Research Roadmap.

Statistical section

Each gene suite may have statistical significance and studies should include these. Any gene enhancers or inhibiters examined may require statistical analysis. This will be presented as needed.

Research strategy

The research strategy is described in the Project description or Project narrative using a specific example.

2. References and Citations

These are already included in the Project narrative submitted in Step 1.

3. Management Approach

This is described in the Business data already submitted.

4. PI Curriculum Vita

Downloaded offline.

5. Current and Pending Support, Section D.3

At present no substantial compensating benefits for the performance of this work are likely or planned. Any updates to computer hardware or necessary software for accessing Wikiversity resources such as Gene expressions (for this proposal) or the on-going Gene project (sponsored by the commercial organization) will be supplied by the commercial organization. Compensating benefits are supplied for the on-going gene transcription portion of the gene project. Information from this endeavor will be used to guide inquiries into various databases including those of NASA to obtain necessary information for the successful completion of the proposal.

6. Facilities and Equipment

These are already available and upgrades will be through the commercial organization.

7. Research Products, Section E.2

The research products from this proposal are likely to fall in research product type 1. These may consist of:
 * 1) gene suites that may be contributing to or causing the effects or increasing risks of the effects listed in the Human Research Roadmap sufficiently to impair astronaut functioning,
 * 2) documentation of under, or over expression, of genes in each suite that may alter gene expression sufficiently to add to adverse effects,
 * 3) documentation of or suggested altered expression of genes from each suite during spaceflight and in preparation for return to normal (Earth-based) environments that may reduce hazards during the mission or before return to Earth, and where possibly applicable,
 * 4) those mouse and rat analogs that have been examined or could be examined to indicate or suggest alterations to reduce these hazards. In addition, should the literature present such
 * 5) upregulation and downregulation transcription factors including enhancers and inhibitors for specific genes,
 * 6) analysis of alternative promoter usage, alternative splicings, additional transcript variants, and alternate transcription options such as using the coding strand or the opposite transcription direction that may, have or can be attempted.
 * 7) RNA that appears to help regulate the activity of any genes in each suite. Further,
 * 8) any epigenome sites that may influence during or before transcription to modify gene expressions. Lastly,
 * 9) specific transcription factors, such as the TATA box, that initiate or contribute to transcription of genes in the suites.

8. Budget Justification of Proposed Costs

As most of the proposed effort involves direct literature searching and interpretation by the PI, this is the Salary of the PI for these efforts.

Travel includes any conference presentations and/or publication costs for research results or research products.