Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells

The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+ T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.

Next generation of astronauts or ESA astronaut 2.0 concept and spotlight on immunity

Although we have sent humans into space for more than 50 years, crucial questions regarding immune response in space conditions remain unanswered. There are many complex interactions between the immune system and other physiological systems in the human body. This makes it difficult to study the combined long-term effects of space stressors such as radiation and microgravity. In particular, exposure to microgravity and cosmic radiation may produce changes in the performance of the immune system at the cellular and molecular levels and in the major physiological systems of the body. Consequently, abnormal immune responses induced in the space environment may have serious health consequences, especially in future long-term space missions. In particular, radiation-induced immune effects pose significant health challenges for long-duration space exploration missions with potential risks to reduce the organism's ability to respond to injuries, infections, and vaccines, and predispose astronauts to the onset of chronic diseases (e.g., immunosuppression, cardiovascular and metabolic diseases, gut dysbiosis). Other deleterious effects encountered by radiation may include cancer and premature aging, induced by dysregulated redox and metabolic processes, microbiota, immune cell function, endotoxin, and pro-inflammatory signal production^1,2. In this review, we summarize and highlight the current understanding of the effects of microgravity and radiation on the immune system and discuss knowledge gaps that future studies should address.

Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation

mRNA translation plays a critical role in determining proteome composition. In health, regulation of mRNA translation facilitates rapid gene expression responses to intra- and extracellular signals. Moreover, dysregulated mRNA translation is a common feature in disease states, including neurological disorders and cancer. Yet, most studies of gene expression focus on analysis of mRNA levels, leaving variations in translational efficiencies largely uncharacterized. Here, we outline procedures to identify mRNA-selective alterations in translational efficiencies on a transcriptome-wide scale using the anota2seq package. Anota2seq compares expression data originating from translated mRNA to data from matched total mRNA to identify changes in translated mRNA not paralleled by corresponding changes in total mRNA (interpreted as changes in translational efficiencies impacting protein levels), congruent changes in total and translated mRNA (interpreted as changes in transcription and/or mRNA stability), and changes in total mRNA not paralleled by corresponding alterations in translated mRNA (interpreted as translational buffering). To illustrate the functionality of the anota2seq analysis package, we demonstrate a detailed analysis using a polysome-profiling data set quantified by RNA sequencing, revealing that estrogen receptor α modulates gene expression via a type of translational buffering termed offsetting. Notably, this anota2seq analysis procedure is also applicable to ribosome-profiling (RiboSeq) data sets and can be adapted to a variety of other data types and experimental contexts. Finally, we provide guidance for extending anota2seq analysis to examine associations between untranslated regions and altered translational efficiencies as well as targeted cellular functions to gain insights into mechanisms and phenotypic consequences of altered mRNA translation. Thus, this step-by-step manual allows users to interrogate selective changes in mRNA translation on a transcriptome-wide scale using the Bioconductor package anota2seq.

Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation

Protein synthesis and degradation determine the relationship between mRNA and corresponding protein amounts. This relationship can change in a dynamic and selective fashion when translational efficiencies of transcript subsets are altered downstream of, for example, translation factors and/or RNA binding proteins. Notably, even transcription factors such as estrogen receptor alpha (ERα) can modulate mRNA translation in a transcript-selective manner. Yet, despite ample evidence suggesting a key role for mRNA translation in shaping the proteome in health and disease, it remains largely unexplored. Here, we present a guide for the extraction of mRNA engaged in translation using polysome fractionation with linear and optimized sucrose gradients. The isolated polysome-associated RNA is then quantified, in parallel with total mRNA from the same conditions, using methods such as RNA sequencing; and the resulting data set is analyzed to derive transcriptome-wide insights into how mRNA translation is modulated. The methods we describe are applicable to cultured cells, small numbers of FACS-isolated primary cells, and small tissue samples from biobanks or animal studies. Accordingly, this approach can be applied to study in detail how ERα and other factors control gene expression by selectively modulating mRNA translation both in vitro and in vivo.

Abstract 2439: Transcriptome-wide polysome profiling of glioblastomas identifies molecular subgroups with impact in survival and treatment

Glioblastoma (GBM) is the most common primary brain malignancy in adults and one of the most aggressive cancers. While the genetic landscape of glioblastomas has been characterized, the identified molecular subgroups have so far had limited impact on prognosis and clinical practice. Translation of mRNA into proteins is a key mechanism governing gene expression and a node for convergence of signaling pathways frequently dysregulated in cancer. For example, in vitro, mTORC1 activity has been linked to selective translation of a subset of mRNAs including those encoding pro-proliferative and pro-survival proteins, commonly referred to mTORC1 sensitive translation. Thus, cancer may be associated with altered mRNA translation, leading to differences between the transcriptome and the proteome, which could underlie tumor-associated properties. Transcriptome-wide quantification of efficiently translated mRNAs, or the translatome can, in addition to increasing the knowledge on post-transcriptional dysregulation of gene expression, provide a better approximation of the tumor proteome, as compared to studies of transcriptomes, and identify patient subsets defined by altered mRNA translation. Herein, we used a recently developed transcriptome-wide polysome profiling for small samples approach to quantify efficiently translated mRNA from 37 human GBM samples. The resulting translatomes allowed classification into three molecular subgroups differing in survival. Group 1, which had a median survival of 5 months, was characterized by increased translation of mRNAs encoding components of the mTORC2 pathway, mitochondria and cilia. Group 2, with a median survival of 6.3 months, was characterized by augmented mTORC1 dependent translation despite low translation of mRNAs encoding mitochondria associated proteins together with increased translation of mRNAs encoding angiogenesis related proteins. In contrast, group 3 showed a relatively longer median survival of 21.1 months and was characterized by high translation of mRNAs encoding mitochondria associated proteins despite low mTORC1 dependent translation, as well as low translation of mRNAs encoding cilia and mTORC2 pathway associated proteins. Strikingly, these groups could not be defined using corresponding data originating from total RNA and thus do not match previous molecular classifications. These translation profiles suggest that distinct treatment regimens employing e.g. mitochondria inhibitors, mTOR inhibitors or anti-angiogenic agents may be effective in patient subsets defined by translation. In conclusion, although this study is limited in terms of the number of studied patients, our data support that that translatomes may define molecular subgroups of GBMs amendable to distinct therapeutic approaches. Funding support: FAPESP 2018/17796-6

Citation Format: Glaucia N. Hajj, Fernanda C. Lupinacci, Martin Roffe, Hermano M. Bellaro, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Rui M. Reis, Christian Oertlin, Laia M. Sanz, Vilma R. Martins, Ola Larsson. Transcriptome-wide polysome profiling of glioblastomas identifies molecular subgroups with impact in survival and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2439.

Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR

In response to disturbed mitochondrial gene expression and protein synthesis, an adaptive transcriptional response sharing a signature of the integrated stress response (ISR) is activated. We report an intricate interplay between three transcription factors regulating the mitochondrial stress response: CHOP, C/EBPβ, and ATF4. We show that CHOP acts as a rheostat that attenuates prolonged ISR, prevents unfavorable metabolic alterations, and postpones the onset of mitochondrial cardiomyopathy. Upon mitochondrial dysfunction, CHOP interaction with C/EBPβ is needed to adjust ATF4 levels, thus preventing overactivation of the ATF4-regulated transcriptional program. Failure of this interaction switches ISR from an acute to a chronic state, leading to early respiratory chain deficiency, energy crisis, and premature death. Therefore, contrary to its previously proposed role as a transcriptional activator of mitochondrial unfolded protein response, our results highlight a role of CHOP in the fine-tuning of mitochondrial ISR in mammals.

Abstract IA13: Targeting redox dependencies in pancreatic cancer

Dysregulation of mRNA translation is a common feature of human cancers. As such, therapeutic agents that target components of the protein synthesis apparatus hold promise as anticancer drugs. We previously showed that protein synthesis is upregulated in Kras mutant pancreatic cancer cells in a manner that is redox-dependent (1). By modulating formation of the eIF4F complex, the PI3K/AKT and mTOR signaling pathways act as major regulators of global and mRNA-specific translation. Consistently, we observed that protein synthesis and the viability of pancreatic tumor organoids are selectively decreased by the pan-AKT inhibitor MK2206, an effect that was potentiated by co-treatment with the pro-oxidant BSO1. Treatment of KrasG12D;p53R172H;PdxCre (KPC) mice with this drug combination resulted in suppressed tumor kinetics and modest improvement in survival. Inhibition of AKT/mTOR blunts cap-dependent translation initiation but also perturbs a plethora of other cellular functions. We thus investigated more selective means of targeting the translation machinery that do not entail wholesale ablation of the AKT/mTOR pathway. The RNA helicase eIF4A initiates translation by unwinding highly structured 5′-untranslated regions (UTRs) in mRNAs. Using polysome profiling followed by deep sequencing, we found that the translation of eIF4A-sensitive mRNAs was selectively increased in Kras-mutant tumor versus normal organoids. The rocaglate, CR-13-1b, is a compound that selectively inhibits the eIF4A helicase and displayed high toxicity in Kras mutant tumor organoids, but not in normal organoids. Polysome sequencing revealed that CR131b selectively modulates translational efficiencies in tumor but not normal organoids. Interestingly, this included multiple mRNAs encoding proteins involved in mitochondrial activity and redox homeostasis. As a single agent, CR131b treatment in KPC mice effectively inhibited protein synthesis in vivo, resulting in a significant decrease in tumor kinetics in a short-term study and an improvement in survival in a longitudinal study.

Reference

1. Chio II et al. NRF2 promotes tumor maintenance by modulating mRNA translation in pancreatic cancer. Cell 2016;166:963-76, doi:10.1016/j.cell.2016.06.056.

Citation Format: Iok In Christine Chio, Christian Oertlin, Francis Robert, Karina Chan, Dana Kapellar Liberm, Abram Santana, Young Park, Ola Larsson, Jerry Pelletier, David Tuveson. Targeting redox dependencies in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr IA13.

Generally applicable transcriptome-wide analysis of translation using anota2seq

mRNA translation plays an evolutionarily conserved role in homeostasis and when dysregulated contributes to various disorders including metabolic and neurological diseases and cancer. Notwithstanding that optimal and universally applicable methods are critical for understanding the complex role of translational control under physiological and pathological conditions, approaches to analyze translatomes are largely underdeveloped. To address this, we developed the anota2seq algorithm which outperforms current methods for statistical identification of changes in translation. Notably, in contrast to available analytical methods, anota2seq also allows specific identification of an underappreciated mode of gene expression regulation whereby translation acts as a buffering mechanism which maintains protein levels despite fluctuations in corresponding mRNA abundance (‘translational buffering’). Thus, the universal anota2seq algorithm allows efficient and hitherto unprecedented interrogation of translatomes which is anticipated to advance knowledge regarding the role of translation in homeostasis and disease.

Enhanced translation expands the endo-lysosome size and promotes antigen presentation during phagocyte activation

The mechanisms that govern organelle adaptation and remodelling remain poorly defined. The endo-lysosomal system degrades cargo from various routes, including endocytosis, phagocytosis, and autophagy. For phagocytes, endosomes and lysosomes (endo-lysosomes) are kingpin organelles because they are essential to kill pathogens and process and present antigens. During phagocyte activation, endo-lysosomes undergo a morphological transformation, going from a collection of dozens of globular structures to a tubular network in a process that requires the phosphatidylinositol-3-kinase-AKT-mechanistic target of rapamycin (mTOR) signalling pathway. Here, we show that the endo-lysosomal system undergoes an expansion in volume and holding capacity during phagocyte activation within 2 h of lipopolysaccharides (LPS) stimulation. Endo-lysosomal expansion was paralleled by an increase in lysosomal protein levels, but this was unexpectedly largely independent of the transcription factor EB (TFEB) and transcription factor E3 (TFE3), which are known to scale up lysosome biogenesis. Instead, we demonstrate a hitherto unappreciated mechanism of acute organelle expansion via mTOR Complex 1 (mTORC1)-dependent increase in translation, which appears to be mediated by both S6Ks and 4E-BPs. Moreover, we show that stimulation of RAW 264.7 macrophage cell line with LPS alters translation of a subset but not all of mRNAs encoding endo-lysosomal proteins, thereby suggesting that endo-lysosome expansion is accompanied by functional remodelling. Importantly, mTORC1-dependent increase in translation activity was necessary for efficient and rapid antigen presentation by dendritic cells. Collectively, we identified a previously unknown and functionally relevant mechanism for endo-lysosome expansion that relies on mTORC1-dependent translation to stimulate endo-lysosome biogenesis in response to an infection signal.

Activation of phagocytes rapidly expands the endo-lysosomal system and promotes antigen presentation. Endo-lysosome expansion was driven by mTORC1-dependent enhanced translation, revealing regulated translation as a mechanism to remodel membrane organelles in response to external signals and stresses.

eIF4A supports an oncogenic translation program in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with limited treatment options. Although metabolic reprogramming is a hallmark of many cancers, including PDA, previous attempts to target metabolic changes therapeutically have been stymied by drug toxicity and tumour cell plasticity. Here, we show that PDA cells engage an eIF4F-dependent translation program that supports redox and central carbon metabolism. Inhibition of the eIF4F subunit, eIF4A, using the synthetic rocaglate CR-1-31-B (CR-31) reduced the viability of PDA organoids relative to their normal counterparts. In vivo, CR-31 suppresses tumour growth and extends survival of genetically-engineered murine models of PDA. Surprisingly, inhibition of eIF4A also induces glutamine reductive carboxylation. As a consequence, combined targeting of eIF4A and glutaminase activity more effectively inhibits PDA cell growth both in vitro and in vivo. Overall, our work demonstrates the importance of eIF4A in translational control of pancreatic tumour metabolism and as a therapeutic target against PDA.

Polysome-profiling in small tissue samples

Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.