Immunological and hematological outcomes following protracted low dose/low dose rate ionizing radiation and simulated microgravity

Using a ground-based model to simulate spaceflight [21-days of single-housed, hindlimb unloading (HLU) combined with continuous low-dose gamma irradiation (LDR, total dose of 0.04 Gy)], an in-depth survey of the immune and hematological systems of mice at 7-days post-exposure was performed. Collected blood was profiled with a hematology analyzer and spleens were analyzed by whole transcriptome shotgun sequencing (RNA-sequencing). The results revealed negligible differences in immune differentials. However, hematological system analyses of whole blood indicated large disparities in red blood cell differentials and morphology, suggestive of anemia. Murine Reactome networks indicated majority of spleen cells displayed differentially expressed genes (DEG) involved in signal transduction, metabolism, cell cycle, chromatin organization, and DNA repair. Although immune differentials were not changed, DEG analysis of the spleen revealed expression profiles associated with inflammation and dysregulated immune function persist to 1-week post-simulated spaceflight. Additionally, specific regulation pathways associated with human blood disease gene orthologs, such as blood pressure regulation, transforming growth factor-β receptor signaling, and B cell differentiation were noted. Collectively, this study revealed differential immune and hematological outcomes 1-week post-simulated spaceflight conditions, suggesting recovery from spaceflight is an unremitting process.


Results
Seven-days post-simulated spaceflight conditions result in distinct gene expression profiles. Principal component analysis (PCA) plots were generated with each cohort (Fig. 1A). Venn diagrams revealed no overlap of downregulated ( Fig. 1B) nor upregulated (Fig. 1C) DEG. However, 33 genes were downregulated and 95 genes were upregulated in simulated spaceflight (simSpace) conditions combining LDR and HLU at 7-days post-exposure (Fig. 1B,C). In addition, the calculated coefficient of gene expression variation was determined for each experimental condition, which identified elevated variance in simSpace conditions (Fig. 1D).
As a secondary lymphoid organ, the spleen stores RNA-containing whole blood cells including white blood cells (WBC) or leukocytes, reticulated platelet and reticulocyte RBC, acting as a filter for circulating blood cells. Using NASA GeneLab's volcano plot visualization tool with a maximum adjusted p-value of 0.05, statistically significant Log 2 fold change of DEG (simSpace versus control) were plotted 23 (Fig. 2A). Downregulated and upregulated genes associated with whole blood cell types include, CD19, H2-DMb2, Alox5, and RhD (Fig. 2B). The proportion of upregulated : downregulated DEG is approximately three : one (Fig. 2B). Collectively, 7-days post-simulated spaceflight conditions resulted in dysregulated immune and hematological system. Seven-days post-simulated spaceflight conditions reveal multiple Reactome pathway involvement. Murine Reactome pathway analysis was performed, which displayed pathways involved in signal transduction, metabolism, cell cycle, DNA repair, and chromatin organization at 7-days post-simSpace exposure (Fig. 3). The majority of DEG fall within the signal transduction pathway including multiple solute carrier family, Slc genes involved in transporter signaling of sodium/potassium and cation elimination. Metabolism-related genes involved in liposome and glycoprotein formation were also highly upregulated, including Igf2r, B4galt2, and B4galt3 and the ubiquitin-pathways, including Ubap1, Fbxl22, and Ube2d2b. Cell cycle genes were also induced, including DEG associated with mitosis, such as Sssca1 and Kif24 and cytokinesis, such as Myh10 and Tor1aip1. Induction of DNA damage repair genes were also noted including, recombination repair genes, Swsap1 and Ippk and downregulation of DNA double stranded break repair gene, Ppp4r2.
Marginal immune modifications at 7-days post-simulated spaceflight. Blood was collected 7-days post-simulated spaceflight and WBC were counted with an automated analyzer, which displayed no significant differences between control and simSpace for immune differentials including, platelets (Fig. 4A), mean platelet volume (MPV, Fig. 4B), WBC, lymphocytes, monocytes, granulocytes, and granulocyte-to-lymphocyte ratio (GLR, Fig. 4C). Spleen DEG were categorized to specific leukocyte subtypes (monocyte, granulocyte, or lymphocyte) by their known functional output (Fig. 4D). Collectively, the results showed although there were no significant differences in population distributions, there were significantly different DEG between controls and post-simSpace cohorts with functional associations to leukocyte subtype. Alterations in hematological system at 7-days post-simulated spaceflight conditions. CBC differentials were characterized by an automated hematological analyzer between control and post-simSpace cohorts. The results displayed significant reductions in RBC and hemoglobin (HGB) in post-simSpace cohorts, compared to controls (Fig. 5A,B). Significant increases in mean corpuscular hemoglobin (MCH), RBC distribution width (RDW), and MCV levels were revealed (Fig. 5C-E). No differences were noted between mean corpuscular hemoglobin concentration (MCHC) and hematocrit (HCT) levels (Fig. 5F,G). Murine spleen DEG that were orthologous to human blood disease/disorders markers, as defined by GeneCards Human Gene Database and MalaCards Human Disease Databases, were identified (Fig. 5H). Using the Network Analyst Global EnrichNetwork tool, blood disease/disorder markers were mapped to determine common pathways. The results showed three genes Bcl11a, Nedd4l, and Aspn had common pathways involved in regulation of blood pressure, protein modifications, transforming growth factor-β signaling, anatomical structure regulation, and negative regulation of developmental processes (Fig. 5I).

Discussion
Recovery post-spaceflight is systemically taxing and often leaves a lasting impression on human health. Circulating RBC and WBC interact with all physiological systems; therefore, a systems biology approach was applied to assess the effects of the immune and hematological outcomes post-simulated spaceflight (simSpace). Since astronaut collections are difficult to acquire, ground-based animal models are a useful alternative that provides valuable insight into these outcomes. Therefore, spleens and blood of mice were analyzed by RNAseq and hematological analyses, respectively, at 7-days post-simSpace. Previous studies in our lab have developed a simSpace model of low-dose radiation (LDR, 0.04 Gy) and hindlimb unloading (HLU) that mimics astronauts in-orbit on the International Space Station (ISS) 18 . Analyses at 7-days post-simSpace provide insight into the immediate early responses similarly experienced by crew during Earth readaptation, a critical time point of equalizing www.nature.com/scientificreports/ homeostasis. Hematological profiling revealed minimal disparities in WBC differentials, however RBC displayed a wide variation in morphology and disrupted function, including reduced overall numbers and hemoglobin levels, suggestive of anemia. Transcriptomic analysis of the spleen, which is the filter for circulating blood cells and a secondary lymphoid organ, displayed genes involved in signal transduction, metabolism, cell cycle, chromatin organization and DNA repair pathways are altered. These analyses also revealed pathways connected to dysfunctional immunity and inflammation, including Cd19, Alox5, Trem1, and H2-DMb2 expression. Genes also  www.nature.com/scientificreports/ implicated in blood disorders, including Bcl11a, Nedd4l, and Aspn, with common pathways involved in regulation of blood pressure, protein modifications, transforming growth factor regulation, and negative regulation of developmental pathways were identified. Thus, understanding immediate early immune and hematological pathways engaged post-simulated spaceflight sheds light on suitable timepoints for therapeutic intervention to promote homeostasis and restoration. DEG from spleens collected at 7-days post-simSpace were compared to single exposures of post-LDR or -HLU alone, which showed negligible overlap in genes ( Fig. 1A-C), indicating distinct transcriptomic profiles are generated following each condition. Similar outcomes were also observed in our previous report that analyzed brain tissues at 4-months post-exposure 18 , indicating LDR, HLU, and simSpace independently trigger divergent pathways post-exposure. Interestingly, post-HLU appears to produce a large number of transcriptional changes compared to post-LDR alone, indicating altered gravity may cause pronounced physiological impairments. However, different doses and types of irradiation experienced on deep space missions would also cause distinct www.nature.com/scientificreports/ results 24 ; therefore, future studies are aimed to delineate these transcriptional profiles as well. In addition, combined exposures of post-simSpace (HLU + LDR) compared to single exposures of post-HLU or post-LDR alone also created increased expression profile variability, which may account for reduced DEG observed in post-simSpace (Fig. 1D). A complete list of DEG for each condition is provided in supplemental information. We next wanted to determine DEG induced post-simSpace and found 33 genes were downregulated and 95 genes were upregulated, compared to controls (Fig. 2). Of note, no significant differences in overall body 18 or spleen tissue weights (data not shown) were observed, supporting either minimal physiological effects occurred during simSpace or recovery post-simSpace has reached homeostasis. Reactome analysis identified five major functional pathways that were affected, including metabolism, cell cycle, chromatin organization, DNA repair, and signal transduction (independent pathways from metabolism, cell cycle, chromatin organization, and DNA repair) (Fig. 3). The majority of DEG were grouped as signal transduction genes, including a large fold upregulation of the cation transporter, Slc22a4. In fact, multiple Slc genes were upregulated post-simSpace, which are transporters of small molecules, including sodium/potassium and cation elimination, suggesting systemic electrolyte imbalance and potential dehydration. Of note, these ion channels are also mechanosensitive and regulate signaling pathways via physical forces they receive 25 . Therefore, more studies are required to better understand the contribution of these mechanosensitive transporter signaling pathways during-and post-simSpace.
We and others have identified the oxidative stress response as a major pathway engaged during spaceflight 26-28 , while metabolic syndromes and ageing are also linked to oxidative stress 29 . In this study, multiple genes involved in metabolism were upregulated, including the insulin signaling receptor, Igf2r. Additionally, glycoprotein forming genes, B4galt2 and B4galt3 were both upregulated, suggesting heightened glycoprotein synthesis. Cell cycle pathways were also altered, including upregulation of genes Sccca1, Kif24, Myh10, and Tor1aip1. These DEG are involved in mitosis and meiosis via microtubule formation and cytokinesis, suggesting increased cellular turnover and division post-simSpace. Chromatin organization and remodeling genes Chd3 and Ncoa3 downregulation were also identified. Furthermore, Swsap1, Ift57, and Ippk genes were upregulated, indicating DNA repair mechanisms occur post-simSpace. Collectively, multiple DEG pathways were actively engaged at 7-days post-simSpace, indicating a dynamic and constant healing process seeking homeostasis.
Immune-related genes were grouped according to their cellular function. Myeloid cell (monocyte and granulocyte)-related genes included downregulation of Card11, Sf3b1, H2-DMb2, Vps39, Ccdc50, and Pcm1; while SphK1, Trem1, and Alox5 were upregulated (Fig. 4D). H2-DMb2 is part of the MHC complex involved in antigen presentation to lymphocytes 30 . Downregulation of this gene would imply impaired antigen presentation and deficient immunological activation; however, this may be an important mechanism post-simSpace to dull the immune response, as recovery should be devoid of self-antigenic stimulation. Furthermore, downregulation of Vps39 (involved in fusion of endosomes/lysosomes) suggests phagocytosis impairment 31 . In line with this, impairment of neutrophil phagocytosis is observed up to 3-days post-spaceflight 32,33 , suggesting a possible role for downregulated Vps39 in this process. The transcription factor NFκB activates a wide variety of signaling pathways involved in immune activation, inflammation, and cytokine production 34 . Card11 and Ccdc50 are both regulators of NFκB signaling. Their expression levels are downregulated, indicating dysregulated immunity. In addition, Alox5 is typically upregulated by the proinflammatory cytokine, GM-CSF, involved in the generation of emergency myelopoiesis and activates matured myeloid cells into a pro-inflammatory state 35 . Therefore, Alox5 upregulation suggests a proinflammatory environment predominates post-simSpace. In line with this, Trem1 is upregulated and is involved in amplifying inflammation of neutrophils and monocytes 36 . Indeed, Trem1 inhibition has been successfully shown to prevent mir-155-driven lung inflammation and injury 37 , septic shock 38 , and neuroinflammation 39 . Trem1 is expressed in neutrophils, which are granulocytes 40 . Elevated granulocytes and granulocyte-to-lymphocyte ratio (GLR) has been identified as a biomarker for inflight immune monitoring 26,41 , therefore, it is plausible that Trem1 induction may also be a determinant for inflight inflammation. Acute inflammation is beneficial in the face of immunological challenges, such as infections or tumors, yet chronic persistence, specifically post-exposures can be detrimental to the host. Resolution of inflammation does not appear to occur at 7-days post-simSpace, suggesting the potential disease development 42 . Furthermore, although correlation of Alox5 and Trem1 expression levels and severity of inflammation is not clear, monitoring Alox5 and Trem1 upregulation may be useful biomarkers to measure chronic inflammation in future spaceflight studies.
Lymphocytes play an important role in cell-mediated and humoral immunity. Notable DEG altered post-simSpace, included downregulation of Sla, Cd19, Pikap1, Kbtbd8, Pcm1, Card11, and Cccdc50; and upregulation of Sphk1 and Zfp341 (Fig. 4D). Of note, Sla negatively regulates TcR signaling, which may contribute to issues during positive selection and non-specific antigen-immunity 43 . Indeed, T cell function is impaired during-and post-spaceflight 44,45 , therefore supporting identification of gene pathways involved in this process for future studies. Additionally, Cd19 and Pik3ap1, are involved in B cell phenotypes, including development and BcR signaling 46,47 , therefore downregulation suggests deficiency in humoral immunity. Certainly, B cells are impacted by ground-based deep space simulation models 24 and post-spaceflight 48 . Further, activation of splenocytes collected 3-days post-flight produced a robust elevation of the inflammatory chemokine MIP-1α, further supporting a proinflammatory state post-spaceflight 44 . Yet, the overall contribution of immune responses on wholeorganism physiology cannot be fully concluded until longitudinal phenotypic studies are performed, as mission timeframes vary, ground-model conditions and exposure timeframes are non-standardized, and post-mission/ model tissue collections differ, which can all result in different interpretations. Nonetheless, altered immunity is recognized across multiple in-flight, at readaptation, and in ground-based models of spaceflight, suggesting a need to delineate all potential mechanisms involved, and strongly supports the need for personalized medicine for future crewmembers.
CBC indicated no differences in WBC counts, which may be due to either group-housing effects on cell distribution 49  www.nature.com/scientificreports/ reductions in overall RBC numbers and HGB levels (Fig. 5A,B). These results suggest at 7-days post-sim-Space anemic conditions persist, which may explain post-flight etiology during return to Earth's gravity in crewmembers [9][10][11] . Other parameters showed no significant differences including, MCHC and HCT (Fig. 5D,E). However, significantly increased levels of mean corpuscular hemoglobin (MCH), RBC distribution width (RDW), and MCV (Fig. 5C,F,G). Collectively, abnormal RBC shape suggest anemic outcomes occurred post-simSpace. Furthermore, both elevated or reduced values of MCH, RDW, and MCV indicate abnormal size and volume of RBC, which impacts hemoglobin function and oxygen carrying capacity, contributing to anemic states 50,51 . An elevated RDW can also contribute to cardiovascular and cancer risk 52 , highlighting the necessity to normalize these biomarkers during post-flight readaptation. Interestingly, elevated RDW may be caused by elevated inflammation 53 , which is also observed in our model, therefore targeting inflammation early post-flight may avert cardiovascular-or cancer-related risks. In line with this, RDW was the only hematological marker that remained elevated at 30-days post-simSpace, while reaching homeostasis at 270-days post-simSpace (data not shown), suggesting the importance of regulating this biomarker in particular for future spaceflight studies. Since RBC do not contain a nucleus and thus genetic material, the majority of blood disease/disorder genes are likely pooled from DNA-containing immature RBC or reticulocytes, immature platelets or reticulated platelets, WBC, and other cells of the spleen, including mesothelial cells and smooth muscle cells 54 . Using Malacards Human Disease Database, outstanding blood disease/disorder orthologs including, upregulated Tmem184a, Daam2, Ippk, Aspn, RhD, and Igf2r; and downregulated Nedd4l and Bcl11a were identified (Fig. 5H). For one, an elevated RhD (Rh factor antigen) was noted post-simSpace, which may have been induced due to RBC loss, as Rh(null) phenotypes are associated with hemolytic anemia 55 . As it is unclear if anemia was induced during-or post-simSpace in our model, and due to the complex definition of space/post-flight anemia, more studies are required. Nonetheless, while determining the timeframe of anemia onset is important, we propose the potential for prolonged and pronounced anemia manifestation in astronauts on partial gravity surfaces of the Moon and Mars, following long duration, deep space travel. Therefore, identifying biomarkers to assist with future countermeasure developments to help safeguard astronauts on future deep space missions is critical. Interestingly, pathway analysis implicated Bcl11a, Aspn, and Nedd4l are interconnected and regulate a wide variety of pathways including, blood pressure, B cell differentiation, and TGF-βR signaling (Fig. 5I). Due to fluidic shifting and reduced normal loading in spaceflight, astronauts returned to Earth are at an increased risk of low blood pressure when standing 12 and arterial stiffening 56 . Therefore, targeting these interconnected genes may provide a robust countermeasure suited to reverse both immune and cardiovascular disparities during readaptation. We recognize complex pathways depend on multiple genes for function. Therefore, differential gene expression of a few may not disrupt biological phenotypes, and as such additional studies are required to assess functional consequences. Furthermore, physiological responses depend on multiple gene expressions within collective pathways; therefore, a thorough survey of the pan-transcriptomic landscape is required to construct reliable countermeasures.
In brief, this study identified key DEG and DEG pathways engaged in systemic blood circulation via spleen transcriptome and CBC differential analyses at 7-days post-simSpace. Primary responses include persistent inflammation and anemia are protracted up to 7-days post-simSpace. Limitations of this study include restricted cross-translation to humans, lack of baseline and longitudinal results, and absence of galactic cosmic ray radiation testing parameters. Nonetheless, future space biology queries can be generated from this study. Furthermore, this study highlights the requisite of systemic homeostasis upon return to Earth's gravity and describes options for recourse during reduced gravity experiences. In brief, comprehensive and dynamic outcomes of the immune and hematological systems occur 7-days post-protracted simulated spaceflight.

Methods
Experimental conditions. Six-month-old, female C57BL/6J mice (Jackson Laboratory) were acclimatized in standard habitats at 20 °C with a 12 h:12 h light:dark cycle for 7 days. Following acclimatization, animals were housed one per cage and assigned to one of four groups: (1) control (n = 6); (2) hindlimb unloaded (HLU) (n = 3); (3) low-dose irradiated (LDR, total dose 0.04 Gy) (n = 6); and (4) simSpace, combination of hindlimb unloaded and low-dose irradiated (HLU + LDR) (n = 6) for 21 days. Low-dose/low-dose rate was delivered using 57 Co plates (a total dose of 0.04 Gy at 0.01 cGy/h) placed 7 cm below the cages, with 1 plate per 2 cages for whole-body irradiation. Uniformity of dose was ± 5%, as previously described [18][19][20][21][22] . Post-exposure animals were group housed (3 per cage) for 7-days. Commercial pellet chow (5LG4, LabDiet R ) and hydrogel were available ad libitum. Health status, water and food intake were daily monitored. After 7-day post-simSpace, mice were CO 2 euthanized and spleens were collected and frozen. RNA was isolated from whole, frozen spleens and samples were subjected to whole transcriptome shotgun sequencing (RNA-sequencing) 18 . Datasets were deposited to the NASA GeneLab Data Systems (GLDS)-211 and were analyzed using the NASA pipeline for determination of differentially expressed genes (DEG) 23 . All methods were performed in accordance with the guidelines recommended in the Guide for the Care and Use of Laboratory Animals 57 and was approved by the Institutional Animal Care and Use Committee (IACUC) at Loma Linda University (Protocol number 8130028). This study is reported in accordance with ARRIVE guidelines 58 .
Complete blood count differential analysis. Mice were euthanized with 100% CO 2 at day seven after the simulated spaceflight period of 21-days. Whole blood was collected via cardiac punch in [K2]-ethylenediaminetetraacetic acid (EDTA) coated syringes immediately following euthanasia and evaluated using the ABC Vet Hematology Analyzer (Heska Corp., Waukesha, WI, USA). Parameters characterized include red blood cell (RBC), platelet (PLT), and white blood cell (WBC) counts, hemoglobin concentration (HGB) and hematocrit (HCT, percentage of whole blood consisting of RBC www.nature.com/scientificreports/ concentration (MCHC; concentration of hemoglobin per RBC), RBC distribution width (RDW; width of the RBC histogram produced by cell number x cell size), and the mean platelet volume (MPV; volume per cell) were also reported, along with absolute counts of granulocytes, monocytes, and lymphocytes (× 10 6 cells/ml).
Tissue collection and nucleic acid extraction. Mice were humanely CO 2 euthanized followed by immediate exsanguination by cardiac puncture. Spleens were isolated and placed in a sterile cryovial, snap frozen in liquid nitrogen and kept at − 80 °C. Spleens were homogenized with CKMix (Bertin Instruments, Montigny-le-Bretonneux, France) and a Minilys homogenizer (Bertin Instruments). AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) extracted RNA and DNA according to the manufacturer's instructions. RNA and DNA concentrations were measured using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and stored at − 80 °C.

RNA sequencing.
To construct RNA-sequencing libraries, an Ovation Mouse RNA-Seq System 1-96 (NuGEN Technologies, Redwood City, CA, USA) was used per manufacturer's instructions. RNA integrity was determined using a 2100 Bioanalyzer (Agilent) with RIN values > 8. 100 ng of total RNA was used as input. cDNA (first and second strands) was synthesized from total RNA spiked with ERCC ExFold RNA Spike-In Mix 1 (Life Technologies, Carlsbad, CA, USA) at the appropriate ratio. Products were sheared using Covaris S220 Focused-ultrasonicator (Covaris Inc., Woburn, MA, USA) to obtain fragment sizes between 150-200 bp. Followed by end-repair, adaptor index ligation and strand selection. For multiplexing, barcodes with unique indices out of 96, were used per sample. Custom InDA-C primer mixture SS5 Version5 for mice (NuGEN Technologies) was used for strand selection. Libraries were amplified by PCR (17 cycles) on a Mastercycler Pro (Eppendorf) and purified with RNAClean XP Agencourt beads (Beckman Coulter, Pasadena, CA, USA). Libraries were sequenced on a HiSeq 4000 (Illumina, Mira Loma, CA, USA) to generate 15-30 M 75-bp single end reads per sample. Raw data are available at NASA GeneLab (genelab.nasa.gov, accession GLDS-211) 23 .
Differential expression and pathway enrichment analysis. With Cutadapt 59 using the Trim Galore! wrapper, sequencing reads were trimmed. All reads were mapped with STAR 60 and expressions were quantified and imported with RSEM 61 and tximport 62 respectively, into DESeq2 (R Bioconductor) 63 . Log 2 fold-change (0.263) and adjusted p-value cutoffs (0.05) were used. All groups were compared using the Wald test and the likelihood ratio test was used to generate the F statistic p-value. Reactome version 67 64 was used to detect enriched murine pathways. Volcano plots were generated using NASA's GeneLab tool 23 . Murine spleen DEG that were orthologous to human blood gene-related diseases, as defined by GeneCards Human Gene Database and MalaCards Human Disease Databases, were identified. Using the Network Analyst Global EnrichNetwork tool, with parameters including the gene ontology: biological process (GO:BP) enrichment analysis database, large graph layout, and single node display (https:// www. netwo rkana lyst. ca/ Netwo rkAna lyst/ Secure/ vis/ ListE nrich ment. xhtml), the blood gene-related gene list was mapped to determine common pathways. www.nature.com/scientificreports/