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The COVID pandemic has refreshed and expanded recognition of the vital role that sustained antibody (Ab) secretion plays in our immune defenses against microbes and of the importance of vaccines that elicit Ab protection against infection. With this backdrop, it is especially timely to review aspects of the molecular programming that govern how the cells that secrete Abs arise, persist, and meet the challenge of secreting vast amounts of these glycoproteins. Whereas plasmablasts and plasma cells (PCs) are the primary sources of secreted Abs, the process leading to the existence of these cell types starts with naive B lymphocytes that proliferate and differentiate toward several potential fates. At each step, cells reside in specific microenvironments in which they not only receive signals from cytokines and other cell surface receptors but also draw on the interstitium for nutrients. Nutrients in turn influence flux through intermediary metabolism and sensor enzymes that regulate gene transcription, translation, and metabolism. This review will focus on nutrient supply and how sensor mechanisms influence distinct cellular stages that lead to PCs and their adaptations as factories dedicated to Ab secretion. Salient findings of this group and others, sometimes exhibiting differences, will be summarized with regard to the journey to a distinctive metabolic program in PCs.

Naive T cells are actively maintained in a quiescent state that promotes their survival and persistence. On antigen stimulation, T cells exit quiescence to initiate clonal expansion and effector differentiation. Initial studies focused on the immune receptors and transcriptional regulators involved in T cell quiescence and activation, but recent findings highlight cell metabolism as a crucial regulator of these processes. Here we summarize these intrinsic metabolic programmes and also describe how cell-extrinsic factors, such as nutrients and regulatory T cells, directly and indirectly balance quiescence and activation programmes in conventional T cells. We propose that immunological cues and nutrients license and tune metabolic programmes and signalling networks that communicate in a bidirectional manner to promote quiescence exit. Understanding the programmes that regulate T cell quiescence will be key for developing novel approaches to modulate protective and pathological T cell responses in human diseases.

Germinal center (GC) formation, which is an integrant part of humoral immunity, involves energy-consuming metabolic reprogramming. Rag-GTPases are known to signal amino acid availability to cellular pathways that regulate nutrient distribution such as the mechanistic target of rapamycin complex 1 (mTORC1) pathway and the transcription factors TFEB and TFE3. However, the contribution of these factors to humoral immunity remains undefined. Here, we show that B cell-intrinsic Rag-GTPases are critical for the development and activation of B cells. RagA/RagB deficient B cells fail to form GCs, produce antibodies, and to generate plasmablasts during both T-dependent (TD) and T-independent (TI) humoral immune responses. Deletion of RagA/RagB in GC B cells leads to abnormal dark zone (DZ) to light zone (LZ) ratio and reduced affinity maturation. Mechanistically, the Rag-GTPase complex constrains TFEB/TFE3 activity to prevent mitophagy dysregulation and maintain mitochondrial fitness in B cells, which are independent of canonical mTORC1 activation. TFEB/TFE3 deletion restores B cell development, GC formation in Peyer’s patches and TI humoral immunity, but not TD humoral immunity in the absence of Rag-GTPases. Collectively, our data establish the Rag GTPase-TFEB/TFE3 pathway as a likely mTORC1 independent mechanism to coordinating nutrient sensing and mitochondrial metabolism in B cells. Rag-GTPases play roles in sensing nutrient availability, and it is not fully known how they contribute to energy-consuming immunological processes such as the B cell response. Here authors show that genomic deletion fo RagA/RagB distrupts both T-dependent and T-independent humoral immune responses, independent of mechanistic target of rapamycin complex 1 but involving the transcription factors TFEB and TFE3.

Cancers reprogram macrophages (MΦs) to a tumor-growth-promoting TAM (tumor-associated MΦ) phenotype that is similar to the anti-inflammatory M2 phenotype. Poly(ADP-ribose) polymerase (PARP) enzymes regulate various aspects of MΦ biology, but their role in the development of TAM phenotype has not yet been investigated. Here, we show that the multispectral PARP inhibitor (PARPi) PJ34 and the PARP14 specific inhibitor MCD113 suppress the expression of M2 marker genes in IL-4-polarized primary murine MΦs, in THP-1 monocytic human MΦs, and in primary human monocyte-derived MΦs. MΦs isolated from PARP14 knockout mice showed a limited ability to differentiate to M2 cells. In a murine model of TAM polarization (4T1 breast carcinoma cell supernatant transfer to primary MΦs) and in a human TAM model (spheroids formed from JIMT-1 breast carcinoma cells and THP-1-MΦs), both PARPis and the PARP14 KO phenotype caused weaker TAM polarization. Increased JIMT-1 cell apoptosis in co-culture spheroids treated with PARPis suggested reduced functional TAM reprogramming. Protein profiling arrays identified lipocalin-2, macrophage migration inhibitory factor, and plasminogen activator inhibitor-1 as potential (ADP-ribosyl)ation-dependent mediators of TAM differentiation. Our data suggest that PARP14 inhibition might be a viable anticancer strategy with a potential to boost anticancer immune responses by reprogramming TAMs.

Accumulating evidence suggests that many immune responses are influenced by local nutrient concentrations in addition to the programming of intermediary metabolism within immune cells. Humoral immunity and germinal centers (GC) are settings in which these factors are under active investigation. Hypoxia is an example of how a particular nutrient is distributed in lymphoid follicles during an antibody response, and how oxygen sensors may impact the qualities of antibody output after immunization. Using exclusively a bio-informatic analysis of mRNA levels in GC and other B cells, recent work challenged the concept that there is any hypoxia or that it has any influence. To explore this proposition, we performed new analyses of published genomics data, explored potential sources of disparity, and elucidated aspects of the apparently conflicting conclusions. Specifically, replicability and variance among data sets derived from different naïve as well as GC B cells were considered. The results highlight broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. Based on these analyses, a standard is proposed under which the relationship of new data sets should be compared to prior “fingerprints” of cell types and reported transparently to referees and readers. In light of independent evidence of diversity within and among GC elicited by protein immunization, avoidance of overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features also is warranted.

Cytokines are inflammatory mediators important in responding to pathogens and other foreign challenges. Interleukin-4 (IL-4) and IL-13 are two cytokines produced by T helper type 2 cells, mast cells, and basophils. In addition to their physiological roles, these cytokines are also implicated in pathological conditions such as asthma and allergy. IL-4 can stimulate two receptors, type I and type II, whereas IL-13 signaling is mediated only by the type II receptor. These cytokines activate the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling cascades, which may contribute to allergic responses. In addition, stimulation of the phosphatidylinositol 3-kinase (PI3K) pathway through recruitment of members of the insulin receptor substrate family may contribute to survival and proliferation.

Background Systemic lupus erythematosus (SLE) is a spontaneous systemic auto-immune condition for which the inciting factors and genetic basis are generally unknown. Although heterogeneous in its manifestations and severity, SLE involves chronic inflammation along with sustained autoantibody production. The root causes and pathophysiology of the inflammation and breaches of tolerance are incompletely understood, but neutrophils are thought to be important elements of the pathophysiology. Type I interferons (IFN) in the bloodstream and an IFN-stimulated gene (ISG) signature in circulating leukocytes, including neutrophils, are common features in many patients. Earlier work has provided evidence of increased levels of transcripts derived from transposable elements (TEs) in peripheral blood cells of SLE patients. Using six leukocyte types, including neutrophils, we tested the correlation of TE expression with disease severity and explored the relationships between increased ISG and TE expression with attention to the genomic locations of the expressed TEs. Results We reanalysed previously published data from neutrophils and other leukocytes of SLE patients sub-divided into ISG-high (termed IFNpos, n  = 12) and ISG-low (termed IFNneg, n  = 11) patients in the original study, examining RNA-seq data from B and T lymphocytes, conventional and plasmacytoid dendritic cells (DC), monocytes and PMN of IFNpos and IFNneg SLE patients compared to healthy controls. SLE patients pre-stratified as IFNneg showed no significant increase in TE expression. All IFNpos cell types had similar amounts of total TE-encoded RNA, but among the 6 cell types, PMN had the highest number of differentially expressed TEs and ISGs in IFNpos SLE patients compared to healthy controls. There was a strong correlation between expression of several specific TE families and disease activity assessed at the time of the visit. Although most upregulated TEs (∼ 80%) were present in introns of upregulated genes, a substantial portion (∼ 20%) were not. Of the upregulated genes linked to upregulated TEs, approximately 1/3 were not ISGs whereas ∼ 67% were ISGs. By mapping expressed TEs in ISGs, we found that high intronic TE expression correlated strongly with increased ISG expression as well as with splicing alterations in annotated exons flanking expressed TEs. Consistent with autonomous TE expression, upregulated TEs were also observed at intergenic sites distant from annotated genes, perhaps due to weakening of heterochromatin integrity. Conclusions Here we describe a strong association between increased TE expression and an ISG-based gene network signature in multiple types of leukocytes centrally involved in SLE pathogenesis. The subset of SLE patients with higher ISG expression also showed high TE expression, compared to healthy donors and SLE patients with low ISG expression. Our data do not offer mechanistic insights into how TE expression might be linked to SLE pathogenesis or ISG expression. Rather, they emphasize the need for long-reads sequencing to understand the causes and consequences of high TE expression in SLE and other autoimmune/inflammatory disorders. Important questions for future study include whether TE expression in introns of ISGs and other genes is independently regulated or reflects exonization or partial intron retention, and how frequently TE expression correlates with splicing variations in adjacent exons. Although limited by short-read RNA-seq technology, our analyses support selective regulation of many TEs independent from the regulation of conventional genes, thereby suggesting (but not directly demonstrating) that an autonomous mechanism of TE de-repression as well as altered splicing patterns may each be factors in SLE pathogenesis. Important questions for future study include whether TE expression in introns of ISGs and other genes is independently regulated or reflects exonization or partial intron retention, and how frequently TE expression correlates with splicing variations in adjacent exons.

Rapidly proliferating tumor and immune cells need metabolic programs that support energy and biomass production. The amino acid glutamine is consumed by effector T cells and glutamine-addicted triple-negative breast cancer (TNBC) cells, suggesting that a metabolic competition for glutamine may exist within the tumor microenvironment, potentially serving as a therapeutic intervention strategy. Here, we report that there is an inverse correlation between glutamine metabolic genes and markers of T cell-mediated cytotoxicity in human basal-like breast cancer (BLBC) patient data sets, with increased glutamine metabolism and decreased T cell cytotoxicity associated with poor survival. We found that tumor cell-specific loss of glutaminase (GLS), a key enzyme for glutamine metabolism, improved antitumor T cell activation in both a spontaneous mouse TNBC model and orthotopic grafts. The glutamine transporter inhibitor V-9302 selectively blocked glutamine uptake by TNBC cells but not CD8+ T cells, driving synthesis of glutathione, a major cellular antioxidant, to improve CD8+ T cell effector function. We propose a \"glutamine steal\" scenario, in which cancer cells deprive tumor-infiltrating lymphocytes of needed glutamine, thus impairing antitumor immune responses. Therefore, tumor-selective targeting of glutamine metabolism may be a promising therapeutic strategy in TNBC.

Metastatic outgrowth in distant microscopic niches requires sufficient nutrients, including fatty acids (FAs), to support tumor growth and to generate an immunosuppressive tumor microenvironment (TME). However, despite the important role of FAs in metastasis, the regulation of FA supply in metastatic niches has not been defined. In this report, we show that tumor endothelium actively promotes outgrowth and restricts antitumor cytolysis by transferring FAs into developing metastatic tumors. We describe a process of transendothelial FA delivery via endosomes that requires mTORC1 activity. Thus, endothelial cell-specific targeted deletion of Raptor (RptorECKO), a unique component of the mTORC1 complex, significantly reduced metastatic tumor burden that was associated with improved markers of T cell cytotoxicity. Low-dose everolimus that selectively inhibited endothelial mTORC1 improves immune checkpoint responses in metastatic disease models. This work reveals the importance of transendothelial nutrient delivery to the TME, highlighting a future target for therapeutic development.