A subset of patients evaluated for immune dysregulation presents with increased proportions of TCR γδ cells despite normal total lymphocyte counts. Corresponding to this phenotype, the authors report a case of a somatic TCR γδ–specific STAT5B mutation that is molecularly amenable to tailored immune modulation. This raises awareness of druggable TCR γδ–intrinsic, genetically determined immune dysregulation.

Within a prospective cohort of patients with immune dysregulation, we identified several individuals with chronically increased proportions of TCR γδ cells but normal peripheral lymphocyte counts. Among those, we identified one individual with a TCR γδ cell-specific heterozygous p.Y665F STAT5B gain-of-function mutation. Recurrent oral aphthous lesions, susceptibility to infection, arthralgia, and fatigue, were linked to relatively elevated numbers of γδ T cells expressing a Vγ9Vδ2 TCR, displaying hyperphosphorylation of STAT5 upon in vitro IL-2 stimulation. The TCR Vγ9Vδ2 cells exhibited enhanced proliferative response to (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate and dysregulated cytokine production. The TCR γδ cell transcriptome revealed the suppression of the default Th17 program, along with inhibition of RORC and MAF expression. The JAK inhibitor baricitinib improved clinical features of the observed immune dysregulation and reduced the frequency of peripheral TCR Vγ9Vδ2 cells. Thus, functionally altered TCR γδ cells may underlie chronic immune dysregulation of unknown molecular cause, demonstrated here to be amenable to tailored immune modulation.

Amoeboid cell migration is key to efficient T cell immunity. Spatial polarization of organelles within cells, including endo-lysosomes, is a prerequisite of migration. However, how ultrastructural polarization is linked to the signaling requirements governing T cell migration remains unknown. Here we show that signaling molecules generated by endo-lysosome-localized kinases regulate velocity of amoeboid migration. Specifically, imaging of T cells identifies accumulation of endo-lysosomes decorated with the lipid kinases VPS34-PIKfyve at the uropod of polarized cells. Activity of VPS34 and PIKfyve regulates speed, but not directedness, of migrating T cells. Mechanistically, PI(3,5)P2 generated by the sequential action of VPS34 and PIKfyve, mediates Ca2+ efflux from lysosomes via the mucolipin TRP cation channel 1 (TRPML1), thus controlling activity of myosin IIA and hence the generation of propulsive force through retrograde actin flow. The VPS34-PIKfyve kinases also regulate velocity of myeloid cells, as well as of the amoeba Dictyostelium discoideum - establishing the axis as an evolutionarily conserved speed control system of amoeboid cell migration.

Interleukin (IL)-7 promotes T cell expansion during lymphopenia. We studied the metabolic basis in CD4+ T cells, observing increased glucose usage for nucleotide synthesis and oxidation in the tricarboxylic acid (TCA) cycle. Unlike other TCA metabolites, glucose-derived citrate does not accumulate upon IL-7 exposure, indicating diversion into other processes. In agreement, IL-7 promotes glucose-dependent histone acetylation and chromatin accessibility, notable at the loci of the amino acid-sensing Ragulator complex. Consistently, the expression of its subunit late endosomal/lysosomal adaptor, MAPK and mTOR activator 5 (LAMTOR5) is promoted by IL-7 in a glucose-dependent manner, and glucose availability determines amino acid-dependent mechanistic target of rapamycin (mTOR) activation, confirming integrated nutrient sensing. LAMTOR5 deletion impairs IL-7-mediated T cell expansion, establishing that glycolysis in the absence of Ragulator activation is insufficient to support this. Clinically, CD4+ T cells from stem cell transplant recipients demonstrate coordinated upregulation of glycolytic and TCA cycle enzymes, amino acid-sensing machinery, and mTOR targets, highlighting the potential to therapeutically target this pathway to fine-tune lymphopenia-induced T cell proliferation.

Changes in cell fate are primarily attributed to the spatio-temporal influence of transcription factors, but the ultimate level of expression control remains translation. Some transcription factors (such as YB-1, RfaH and Bicoid) play complementary roles in translation, and we have recently reported that also the pluripotency-inducing transcription factor SOX2 has ribosomal affinity and modulates transcript selection (Schaefer et al., Cell Reports 2024). Although this post-transcriptional layer of regulation mainly reflects SOX2‘s C-terminal influence in the cytosol, we here present evidence for a further involvement also of N-terminal SOX2 in translation.Ribosomal affinity within N-terminal parts of SOX2 first showed in domain separation analyses in breast cancer-derived cell lines. However, although SOX2 fragments (1-119) and (1-179) co-sedimented with 60S ribosomes in sucrose density gradients, they imposed no translational fingerprint in polysome profiles as otherwise seen for full-length or C-terminal SOX2. Nonetheless, the synthesis of bulk protein (indicated by OPP incorporation into nascent polypeptides) did change and hundreds of mRNAs experienced a translational regulation upon SOX2 N-terminus induction. Among these, 65 differentially regulated factors stood out as co-regulated by full-length or N-terminal SOX2, but unaltered or counter-regulated in SOX2 C-terminus induced cells. Overrepresentation analyses within STRING and TISSUES databases indicated a preferential expression in the reproductive tract for 35 of these hits, and also under more stringent inclusion criteria, a functional assignment to the reactomes mitosis and reproduction was reconfirmed. In phenotypic correlation, we indeed noted a co-regulation of cell growth in full-length or N-terminus induced T47D and MDA-MB468 reporter cells, while the C-terminus recapitulated the proliferation rate of control cells. Real-life evidence for a SOX2 N-terminal contribution to translation, however, came from a disease-linked human mutant, SOX2(L97P), originally identified in the context of eye development. When expressed in reporter cells the L97P mutation severely impaired 60S binding, so that neither the polysome profile nor the phosphorylation status of RPS6 changed as otherwise seen for wild-type SOX2.Our study highlights that, despite decades of preceding research, the protein biochemistry of even key pluripotency factors remains underexplored and still holds unforeseen learning. In summary, we present here extended evidence for a translational significance of SOX2 that (i) involves N-terminal contributions, (ii) arises in physical contact with ribosomes, and (iii) takes influence on cell proliferation. A better understanding of the underlying molecular principles may thus pave the way to a targeted control of cell division, selectively in SOX2-driven reprogramming and cancer. Meric Ataman, Nitish Mittal, Hui Wang, Sergiy Velychko, Tata Nageswara Rao, Jordan Löliger, Jonas Lötscher, Sarah Roffeis, Christoph Hess, Hans R. Schöler, Ed Hurt, Matthias P. Wymann, Mihaela Zavolan, Claudia Lengerke, Thorsten Schaefer. A disease-linked mutant reveals a critical N-terminal influence of SOX2 on translation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 13.

Autocrine engagement of the human-specific complement receptor CD46, driven by T cell receptor (TCR) activation on human CD4+ T cells, is critical for human Th1 induction: Processing of the intracellular CD46 domain CYT-1 by g-secretase mediates mTORC activation and metabolic adaptation required for cell growth, expansion and effector function. How, at the molecular level, CYT-1 enables this fundamental cellular adaptation remains unknown. Identifying the CYT-1 protein interactome in T cells via co-immunoprecipitation with antibodies recognizing cleaved-CYT-1 followed by protein mass spectrometry, we observed that CYT-1 associates with five of the ten metabolic enzymes mediating glycolysis.Focusing on the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) we used ELISAs, Microscale Thermophoresis and Proximity Ligation Assays to confirm a direct interaction between GAPDH and CYT-1. Functionally, CYT-1 directly increased GAPDH’s classic enzymatic activity allowing it to meet the heightened energetic demand that T cell activation requires. Unexpectedly, CYT-1-augmented GAPDH glycolytic activity was accompanied by a concurrent increase in a non-canonical key moonlighting function of GAPDH: the ability of GAPDH to stabilize mRNAs selectively associated with metabolic states underlying Th1 differentiation. Accordingly, both classical and non-classical GAPDH functions were abrogated in in vitro-activated Jurkat and primary human CD4+ T cells with selective CYT-1-deficieny induced by CRISPR/Cas9 deletion. Consequently, CYT-1 deficient T cells exhibited reduced GAPDH enzymatic activity, reduced glycolytic flux and impaired cell proliferation. Employment of a xenogeneic Graft-versus-host disease model (GvHD) confirmed reduced T cell activation, activity and poor engraftment of CYT-1-deficient primary human CD4+ T cells in vivo, while engineered CYT-1 deficiency in Jurkat cells significantly reduced Jurkat cell expansion in a xenogeneic leukemia mouse model. CYT-1 binding to aldolase or enolase also augmented the glycolytic and moonlighting functions of these proteins, suggesting a more generalized effect of CYT-1 on CYT-1-intercating enzymes of the glycolytic pathway.These data identify the CD46 CYT-1–glycolytic enzyme interaction as a direct facilitator of classic and non-classic glycolytic enzyme activities, solidify the notion that autocrine complement is a critical regulator of cell physiology, and suggest that the CYT-1-GAPDH axis may be a potential target in CD4+ T cell-associated disease states including autoimmunity and leukemia.

Amoeboid cell migration is key to efficient T cell immunity. Spatial polarization of organelles within cells, including endo-lysosomes, is a prerequisite of migration. However, how ultrastructural polarization is linked to the signaling requirements governing T cell migration, remains unknown. Here we show that signaling molecules generated by endo-lysosome-localized kinases regulate velocity of amoeboid migration. Specifically, imaging of T cells identified accumulation of endo-lysosomes decorated with the lipid kinases VPS34–PIKfyve at the uropod of polarized cells. Activity of VPS34 and PIKfyve regulated speed, but not directedness, of migrating T cells. Mechanistically, PI(3,5)P2 generated by the sequential action of VPS34 and PIKfyve mediated Ca2+ efflux from lysosomes via the mucolipin TRP cation channel 1 (TRPML1), thus controlling activity of myosin IIA and hence the generation of propulsive force through retrograde actin flow. The VPS34–PIKfyve kinases also regulated velocity of myeloid cells, as well as of the amoeba Dictyostelium discoideum – establishing the axis as an evolutionary conserved speed control system of amoeboid cell migration. Graphical Abstract ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. [1]: pending:yes

Inflammatory bowel disease (IBD) occurring following allogeneic stem cell transplantation (aSCT) is a very rare condition. The underlying pathogenesis needs to be better defined. There is currently no systematic effort to exclude loss- or gain-of-function mutations in immune-related genes in stem cell donors. This is despite the fact that more than 100 inborn errors of immunity may cause or contribute to IBD. We have molecularly characterized a patient who developed fulminant inflammatory bowel disease following aSCT with stable 100% donor-derived hematopoiesis. A pathogenic c.A291G; p.I97M HAVCR2 mutation encoding the immune checkpoint protein TIM-3 was identified in the patient's blood-derived DNA, while being absent in DNA derived from the skin. TIM-3 expression was much decreased in the patient's serum, and in vitro-activated patient-derived T cells expressed reduced TIM-3 levels. In contrast, T cell-intrinsic CD25 expression and production of inflammatory cytokines were preserved. TIM-3 expression was barely detectable in the immune cells of the patient's intestinal mucosa, while being detected unambiguously in the inflamed and non-inflamed colon from unrelated individuals. In conclusion, we report the first case of acquired, "transplanted" insufficiency of the regulatory TIM-3 checkpoint linked to post-aSCT IBD.

Abstract The synthesis of complement component C3 within the tumor microenvironment has been implicated as a pivotal modulator in oncogenesis and is emerging as an attractive therapeutic target. Historically, tumor-infiltrating immune cells have been recognized as principal contributors to intra-tumoral C3, with resultant activation fragments primarily facilitating tumor progression via immunosuppression and induction of angiogenesis. Despite the ubiquity of C3 expression in neoplastic tissues, the implications of cancer cell autonomous C3 during oncogenesis remain inadequately characterized. Here we show that loss of steady-state, endogenous C3 expression, C3a generation, and C3a receptor engagement in human prostate epithelial cells (PECs) mark a salient transition towards malignancy. We reveal that tonic intrinsic C3a-C3aR engagement in non-transformed PECs serves to restrain phosphoinositide 3-kinase delta activity, which inhibits the oncogenic MYC cascade and MYC-driven ribosomal biogenesis and nucleolar dynamics to maintain normal cell homeostasis. Further, comprehensive analyses show that C3 transcript and C3 protein levels are widely suppressed across human prostate cancers. Collectively, these findings ascribe a non-traditional, tumor-suppressor function to cell intrinsic C3 and advocate for dissection of the context-specific roles of complement, a strategy that may inform the development of targeted cancer therapies.

When B cells engage in an immune response, metabolic reprogramming is key to meeting cellular energetic and biosynthetic demands. Epstein-Barr virus (EBV) is a highly prevalent gamma-herpesvirus, latently infecting B cells for the human host's lifetime. By hijacking signaling pathways of T cell-dependent humoral immunity, EBV activates B cells in a T cell-independent manner, forcing lymphoblastoid transformation. Interlinked with this coercion of signaling pathways, EBV has also evolved strategies to manipulate B cell metabolism. In this opinion article we integrate recent findings from studies of B cell metabolic reprogramming after EBV infection and during antigen-specific activation, respectively. We hypothesize that defining EBV host-cell metabolic vulnerabilities that differ from pathways required for B cell immunity might uncover novel therapeutic targets against EBV-related diseases.

Persistent symptoms following SARS-CoV-2 infection are increasingly reported, although the drivers of post-acute sequelae (PASC) of COVID-19 are unclear. Here we assessed 214 individuals infected with SARS-CoV-2, with varying disease severity, for one year from COVID-19 symptom onset to determine the early correlates of PASC. A multivariate signature detected beyond two weeks of disease, encompassing unresolving inflammation, anemia, low serum iron, altered iron-homeostasis gene expression and emerging stress erythropoiesis; differentiated those who reported PASC months later, irrespective of COVID-19 severity. A whole-blood heme-metabolism signature, enriched in hospitalized patients at month 1–3 post onset, coincided with pronounced iron-deficient reticulocytosis. Lymphopenia and low numbers of dendritic cells persisted in those with PASC, and single-cell analysis reported iron maldistribution, suggesting monocyte iron loading and increased iron demand in proliferating lymphocytes. Thus, defects in iron homeostasis, dysregulated erythropoiesis and immune dysfunction due to COVID-19 possibly contribute to inefficient oxygen transport, inflammatory disequilibrium and persisting symptomatology, and may be therapeutically tractable.

After infection of B cells, Epstein-Barr virus (EBV) engages host pathways that mediate cell proliferation and transformation, contributing to the propensity of the virus to drive immune dysregulation and lymphomagenesis. We found that the EBV protein EBNA2 initiates nicotinamide adenine dinucleotide (NAD) de novo biosynthesis by driving expression of the metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) in infected B cells. Virus-enforced NAD production sustained mitochondrial complex I activity, to match adenosine triphosphate (ATP) production with bioenergetic requirements of proliferation and transformation. In transplant patients, IDO1 expression in EBV-infected B cells, and a serum signature of increased IDO1 activity, preceded development of lymphoma. In humanized mice infected with EBV, IDO1 inhibition reduced both viremia and lymphomagenesis. Virus-orchestrated NAD biosynthesis is therefore a druggable metabolic vulnerability of EBV-driven B cell transformation, opening therapeutic possibilities for EBV-related diseases.

Tumor cells undergo uncontrolled proliferation driven by enhanced anabolic metabolism including glycolysis and glutaminolysis. Targeting these pathways to inhibit cancer growth is a strategy for cancer treatment. Critically, however, tumor-responsive T cells share metabolic features with cancer cells, making them susceptible to these treatments as well. Here, we assess the impact on anti-tumor T cell immunity and T cell exhaustion by genetic ablation of lactate dehydrogenase A (LDHA) and glutaminase1 (GLS1), key enzymes in aerobic glycolysis and glutaminolysis. Loss of LDHA severely impairs expansion of T cells in response to tumors and chronic infection. In contrast, T cells lacking GLS1 can compensate for impaired glutaminolysis by engaging alternative pathways, including upregulation of asparagine synthetase, and thus efficiently respond to tumor challenge and chronic infection as well as immune checkpoint blockade. Targeting GLS1-dependent glutaminolysis, but not aerobic glycolysis, may therefore be a successful strategy in cancer treatment, particularly in combination with immunotherapy.

BACKGROUND:The use of assays detecting cytomegalovirus (CMV)-specific T cell-mediated immunity may individualize the duration of antiviral prophylaxis after transplantation.METHODS:In this randomized trial, kidney and liver transplant recipients from 6 centers in Switzerland were enrolled if they were CMV-seronegative with seropositive donors or CMV-seropositive receiving antithymocyte globulins. Patients were randomized to a duration of antiviral prophylaxis based on immune monitoring (intervention) or a fixed duration (control). Patients in the control group were planned to receive 180 days (CMV-seronegative) or 90 days (CMV-seropositive) of valganciclovir. Patients were assessed monthly with a CMV ELISpot assay (T-Track CMV); prophylaxis in the intervention group was stopped if the assay was positive. The co-primary outcomes were the proportion of patients with clinically significant CMV infection and reduction in days of prophylaxis. Between-group differences were adjusted for CMV serostatus.RESULTS:Overall, 193 patients were randomized (92 in the immune-monitoring group and 101 in the control group), of whom 185 had evaluation of the primary outcome (87 and 98 patients). CMV infection occurred in 26 of 87 (adjusted percentage, 30.9%) in the immune-monitoring group and in 32 of 98 (adjusted percentage, 31.1%) in the control group (adjusted risk difference, -0.1; 95% confidence interval [CI], -13.0% to 12.7%; P = .064). The duration of prophylaxis was shorter in the immune-monitoring group (adjusted difference, -26.0 days; 95%, CI, -41.1 to -10.8 days; P < .001).CONCLUSIONS:Immune monitoring resulted in a significant reduction of antiviral prophylaxis, but we were unable to establish noninferiority of this approach on the co-primary outcome of CMV infection.CLINICAL TRIALS REGISTRATION:NCT02538172.

Our increased understanding of how key metabolic pathways are activated and regulated in malignant cells has identified metabolic vulnerabilities of cancers. Translating this insight to the clinics, however, has proved challenging. Roadblocks limiting efficacy of drugs targeting cancer metabolism may lie in the nature of the metabolic ecosystem of tumors. The exchange of metabolites and growth factors between cancer cells and nonmalignant tumor-resident cells is essential for tumor growth and evolution, as well as the development of an immunosuppressive microenvironment. In this Review, we will examine the metabolic interplay between tumor-resident cells and how targeted inhibition of specific metabolic enzymes in malignant cells could elicit pro-tumorigenic effects in non-transformed tumor-resident cells and inhibit the function of tumor-specific T cells. To improve the efficacy of metabolism-targeted anticancer strategies, a holistic approach that considers the effect of metabolic inhibitors on major tumor-resident cell populations is needed.

Abstract Intracellularly active complement C3 and C3a emerged as central regulators of normal immune cell function and proliferation via control of mTOR and glycolysis. Because increased glycolysis is a hallmark of many cancer cells, we hypothesized that augmented cell-intrinsic C3 activity may contribute to epithelial cell malignancy. However, while benign prostate epithelial cells (PECs) harbored expected intracellular C3/C3a storages, cancerous PECs, surprisingly, exhibited loss of C3/C3a. Further, C3/C3a reduction levels in PECs correlated inversely with worsening Gleason scores in patients, silencing of C3 in healthy PECs induced uncontrolled proliferation, and reconstitution of intracellular C3a in prostate cancer cell line DU145 normalized their hyper-proliferation. In line with an unexpected anti-proliferative role for C3a in PECs, C3ar−/− mice developed spontaneous hyperplasia of prostate tubular cells with age, treatment of DU145 tumors, implanted subcutaneously into the flanks of athymic mice, with C3a-expressing adenovirus significantly reduced tumor growth in vivo, and augmented C3 levels are associated with a better prognosis in patients with prostate and other types of epithelial cell cancers. RNA-sequencing of C3 or C3aR-deficient human PECs identified intrinsic C3a as novel controller of several known PEC oncogenes, likely via up-stream impact on the c-MYC pathway. In sum, while intracellular C3 drives proliferation in immune cells, in (prostate) epithelial cells, cell-autonomous C3/C3a is a negative regulator of growths and, thus, represses oncogenic transformation. Such cell-specific intracellular C3/C3a activities should be taken into consideration when targeting this system therapeutically.

Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. We here report on a human antigen-specific ex vivo model to explore new therapeutic options for T cell immunotherapies. T cells generated with this model resemble tumor-infiltrating exhausted T cells on a phenotypic and transcriptional level. Using a targeted pooled CRISPR-Cas9 screen and individual gene knockout validation experiments, we uncover sorting nexin-9 (SNX9) as a mediator of T cell exhaustion. Upon TCR/CD28 stimulation, deletion of SNX9 in CD8 T cells decreases PLCγ1, Ca2+, and NFATc2-mediated T cell signaling and reduces expression of NR4A1/3 and TOX. SNX9 knockout enhances memory differentiation and IFNγ secretion of adoptively transferred T cells and results in improved anti-tumor efficacy of human chimeric antigen receptor T cells in vivo. Our findings highlight that targeting SNX9 is a strategy to prevent T cell exhaustion and enhance anti-tumor immunity.

BACKGROUND:Biallelic mutations in LIG4 encoding DNA-ligase 4 cause a rare immunodeficiency syndrome manifesting as infant-onset life-threatening and/or opportunistic infections, skeletal malformations, radiosensitivity and neoplasia. LIG4 is pivotal during DNA repair and during V(D)J recombination as it performs the final DNA-break sealing step. OBJECTIVES:This study explored whether monoallelic LIG4 missense mutations may underlie immunodeficiency and autoimmunity with autosomal dominant inheritance. METHODS:Extensive flow-cytometric immune-phenotyping was performed. Rare variants of immune system genes were analyzed by whole exome sequencing. DNA repair functionality and T-cell-intrinsic DNA damage tolerance was tested with an ensemble of in vitro and in silico tools. Antigen-receptor diversity and autoimmune features were characterized by high-throughput sequencing and autoantibody arrays. Reconstitution of wild-type versus mutant LIG4 were performed in LIG4 knockout Jurkat T cells, and DNA damage tolerance was subsequently assessed. RESULTS:A novel heterozygous LIG4 loss-of-function mutation (p.R580Q), associated with a dominantly inherited familial immune-dysregulation consisting of autoimmune cytopenias, and in the index patient with lymphoproliferation, agammaglobulinemia, and adaptive immune cell infiltration into nonlymphoid organs. Immunophenotyping revealed reduced naive CD4+ T cells and low TCR-Vα7.2+ T cells, while T-/B-cell receptor repertoires showed only mild alterations. Cohort screening identified 2 other nonrelated patients with the monoallelic LIG4 mutation p.A842D recapitulating clinical and immune-phenotypic dysregulations observed in the index family and displaying T-cell-intrinsic DNA damage intolerance. Reconstitution experiments and molecular dynamics simulations categorize both missense mutations as loss-of-function and haploinsufficient. CONCLUSIONS:This study provides evidence that certain monoallelic LIG4 mutations may cause human immune dysregulation via haploinsufficiency.

Mutations in CD46 predispose to atypical hemolytic uremic syndrome (aHUS) with low penetrance. Factors driving immune-dysregulatory disease in individual mutation carriers have remained ill-understood. In addition to its role as a negative regulator of the complement system, CD46 modifies T cell-intrinsic metabolic adaptation and cytokine production. Comparative immunologic analysis of diseased vs . healthy CD46 mutation carriers has not been performed in detail yet. In this study, we comprehensively analyzed clinical, molecular, immune-phenotypic, cytokine secretion, immune-metabolic, and genetic profiles in healthy vs . diseased individuals carrying a rare, heterozygous CD46 mutation identified within a large single family. Five out of six studied individuals carried a CD46 gene splice-site mutation causing an in-frame deletion of 21 base pairs. One child suffered from aHUS and his paternal uncle manifested with adult-onset systemic lupus erythematosus (SLE). Three mutation carriers had no clinical evidence of CD46-related disease to date. CD4 + T cell-intrinsic CD46 expression was uniformly 50%-reduced but was comparable in diseased vs . healthy mutation carriers. Reconstitution experiments defined the 21-base pair-deleted CD46 variant as intracellularly—but not surface-expressed and haploinsufficient. Both healthy and diseased mutation carriers displayed reduced CD46-dependent T cell mitochondrial adaptation. Diseased mutation carriers had lower peripheral regulatory T cell (Treg) frequencies and carried potentially epistatic, private rare variants in other inborn errors of immunity (IEI)-associated proinflammatory genes, not found in healthy mutation carriers. In conclusion, low Treg and rare non- CD46 immune-gene variants may contribute to clinically manifest CD46 haploinsufficiency-associated immune-dysregulation.