A ratiometric catalog of protein isoform shifts in the cardiac fetal gene program

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Abstract

Pathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the heart’s fetal gene program and its impact on proteome compositions remain incompletely understood. Here, using a new proteome-wide protein ratio quantification strategy with mass spectrometry, we identify pervasive isoform usage shifts in fetal and postnatal mouse hearts, involving 145 pairs of highly homologous paralogs and alternative splicing-derived isoform proteins. Proteome-wide ratio comparisons readily rediscover hallmark fetal gene signatures in muscle contraction and glucose metabolism pathways, while revealing novel isoform usage in mitochondrial and gene expression proteins, including PPA1/PPA2, ANT1/ANT2, and PCBP1/PCBP2 switches. Paralogs with differential fetal usage tend to be evolutionarily recent, consistent with functional diversification. Alternative splicing adds another rich source of fetal isoform usage differences, involving PKM M1/M2, GLS-1 KGA/GAC, PDLIM5 long/short, and other spliceoforms. When comparing absolute protein proportions, we observe a partial reversion toward fetal gene usage in pathological hearts. In summary, we present a ratiometric catalog of paralogs and spliceoform pairs in the cardiac fetal gene program. More generally, the results demonstrate the potential of applying the proteome-wide ratio test concept to discover new regulatory modalities beyond differential gene expression.

Authors

Yu Han, Shaonil Binti, Sara A. Wennersten, Boomathi Pandi, Dominic C.M. Ng, Edward Lau, Maggie P.Y. Lam

Transgenic augmentation of erythroferrone in mice ameliorates anemia in adenine-induced chronic kidney disease

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Abstract

Anemia is a common and disabling complication of chronic kidney disease (CKD). Current therapies can be burdensome, and full correction of anemia is limited by cardiovascular side effects. New approaches that may offer additional therapeutic options are needed. We explored the anti-anemic effects of erythroferrone, an erythroid hormone that induces iron mobilization by suppressing the master iron-regulatory hormone hepcidin. In a preclinical murine model of adenine-induced CKD, transgenic augmentation of erythroferrone mobilized iron, increased hemoglobin concentrations by approximately 2 g/dl, and modestly improved renal function without affecting systemic or renal inflammation, fibrosis, or markers of mineral metabolism. This study supports the concept that therapeutic augmentation of erythroferrone is a promising approach for alleviating CKD-associated anemia.

Authors

Brian Czaya, Joseph D. Olivera, Moya Zhang, Amber Lundin, Christian D. Castro Andrade, Grace Jung, Mark R. Hanudel, Elizabeta Nemeth, Tomas Ganz

BLIMP-1 and CEACAM1 cooperatively regulate human Treg homeostasis and function to control xenogeneic GVHD

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Abstract

Regulatory T cells (Tregs) are essential for peripheral tolerance and depend on TCR and IL-2R signaling for their homeostasis and function. In mice, IL-2-dependent BLIMP-1 contributes to Treg homeostasis. BLIMP-1 is a major transcriptional hub in human Tregs, but its mechanisms of action remain undefined. Here, using CRISPR/Cas9 ablation, we show that BLIMP-1 limits human Treg proliferation, but supports IL-10, CTLA4, several immune checkpoints, including CEACAM1, and Treg functional activity. BLIMP-1 restrains Treg expansion to IL-2 by downregulating CD25 and IL-2R signaling, and by enhancing CEACAM1 expression, which in turn inhibits responsiveness to CD3/CD28 signaling and activation of mTOR. Prolonged IL-2R signaling optimizes BLIMP-1 expression, supporting chromosomal opening of CEACAM1 to increased CEACAM1 expression through STAT5- and BLIMP-1-driven enhancers. Correspondingly, CEACAM1 is highly induced on Tregs from autoimmune patients undergoing low-dose IL-2 therapy, and these Tregs showed reduced proliferation. A humanized mouse model of xenogeneic graft versus host disease demonstrates that BLIMP-1 normally promotes, while CEACAM1 restrains, Treg suppressive activity. Collectively, our findings reveal that BLIMP-1 and CEACAM1 function in an IL-2-dependent feedback loop to restrain Treg proliferation and affect suppressive function. CEACAM1 also acts as a highly selective biomarker of IL-2R signaling in human T cells.

Authors

Ying Ding, Aixin Yu, Milos Vujanac, Sabrina N. Copsel, Alejandro Moro, Luis Nivelo, Molly Dalzell, Nicolas Tchitchek, Michelle Rosenzwajg, Alejandro V. Villarino, Robert B. Levy, David Klatzmann, Thomas R. Malek

p53 maintains lineage fidelity during lung capillary injury-repair in neonatal hyperoxia

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Abstract

Bronchopulmonary dysplasia (BPD), a prevalent and chronic lung disease affecting premature newborns, results in vascular rarefaction and alveolar simplification. Although the vasculature has been recognized as a main player in this disease, the recently found capillary heterogeneity and cellular dynamics of endothelial subpopulations in BPD remain unclear. Here, we show Cap2 cells are damaged during neonatal hyperoxic injury, leading to their replacement by Cap1 cells which, in turn, significantly decline. Single cell RNA-seq identifies the activation of numerous p53 target genes in endothelial cells (ECs), including Cdkn1a (p21). While global deletion of p53 results in worsened vasculature, endothelial-specific deletion of p53 reverses the vascular phenotype and improves alveolar simplification during hyperoxia. This recovery is associated with the emergence of a transitional EC state, enriched for oxidative stress response genes and growth factors. Notably, this transitional EC gene signature is conserved in an aberrant capillary population identified in human BPD with pulmonary hypertension, underscoring the biological and clinical relevance of our findings. These results reveal a key role for p53 in maintaining endothelial lineage fidelity during pulmonary capillary repair following hyperoxic injury and highlight the critical contribution of the endothelium to BPD pathogenesis.

Authors

Lisandra Vila Ellis, Jonathan D. Bywaters, Amanda Ceas, Yun Liu, Jennifer M.S. Sucre, Jichao Chen

Altered Cardiac Excitability and Arrhythmia in Models of SCN1B-Linked Developmental and Epileptic Encephalopathy

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Abstract

Biallelic variants in SCN1B, encoding the voltage-gated sodium channel β1/β1B subunits, are linked to DEE52, a developmental and epileptic encephalopathy with a high risk of Sudden Unexpected Death in Epilepsy (SUDEP). DEE52 patients present clinically with Dravet syndrome or the more severe early infantile DEE. SCN1B is expressed in brain and heart in humans and in mice. Thus, we have proposed that, in addition to generalized seizures, cardiac arrhythmia may play a role in SUDEP. Mice with homozygous expression of the DEE52 variant Scn1b-c.265C>T, predicting p.R89C, have spontaneous and hyperthermia-induced generalized seizures and SUDEP. Here we conducted cardiac characterization of Scn1b-c.265C>T mice and studied induced pluripotent stem cell cardiomyocytes (iPSC-CMs) derived from two SCN1B-c.265C>T DEE52 patients. Scn1bC89/C89 mouse CMs showed increased transient outward potassium current (Ito) density and heart sections revealed ventricular fibrosis. Scn1bC89/C89 mice were susceptible to pacing-induced cardiac arrhythmias. Patient-derived iPSC-CMs with biallelic SCN1B-c.265C>T variant expression showed increased sodium current (INa), late INaL, and Ito current densities. We conclude that, while mouse and human cardiac AP waveforms have critical differences, increased Ito is common to both models of DEE52. Overall, our data suggest that electrical and structural substrates may lead to arrhythmias and contribute to SUDEP in DEE52.

Authors

Roberto Ramos-Mondragon, Shuyun Wang, Nnamdi Edokobi, Qinghua Liu, Xiaotan Qiao, Maya Shih, Louis T. Dang, Yao-Chang Tsan, Katalin Štěrbová, Adam S. Helms, Sarah Weckhuysen, Luis F. Lopez-Santiago, Jack M. Parent, Lori L. Isom

Hyperosmotic stimuli activate polycystin proteins to aid in urine concentration

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Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1 or PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2) respectively. These proteins are thought to form a signaling complex that can flux cations including calcium. One of the earliest symptoms in ADPKD is a decline in the concentrating ability of the kidneys, occurring prior to cyst formation. We reasoned that hyperosmolality stimulates the polycystin complex, and that the loss of this function impairs water reabsorption. We found that hyperosmolality resulted in the phosphorylation of a microtubule associated protein 4 (MAP4) in a PC1-dependent manner which then elicited ER-localized PC2 calcium signals. ER-localized PC2 hyperosmotic calcium signals were required for trafficking of the water channel aquaporin (AQP2). Pre-cystic PC1-KO and PC2-KO murine kidneys had cytosolic localized AQP2, and diluted urine compared to their respective controls. Kidney tissue sections from ADPKD patients showed decreased AQP2 apical membrane localization in cystic and non-cystic tubules. Our study demonstrates that osmolality is a physiological stimulus of the polycystin complex, and loss of polycystin osmosensing results in impaired water reabsorption via AQP2. This likely contributes to the declined concentrating ability of the kidneys and high circulating vasopressin levels in ADPKD patients.

Authors

Karla M. Márquez-Nogueras, Ryne M. Knutila, Virdjinija Vuchkovska, Charlie Yang, Patricia Outeda, Darren P. Wallace, Ivana Y. Kuo

Delineating the short- and long-term impact of ionizing radiation on antigen-inexperienced CD8⁺ T cell subsets

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Abstract

Radiation-induced lymphopenia (RIL) remains a challenging side effect of radiation therapy, often associated with poor prognosis and reduced overall survival. Although CD8+ T cells are highly radiosensitive, the dynamics of quantitative and qualitative changes to the CD8 T cell pool following exposure to high doses of ionizing radiation (IR) remains understudied. Herein, we sought to determine the long-term impact of sublethal whole body irradiation (WBI) on antigen (Ag)-inexperienced CD8 T cell pool, comprised of naïve (TN) and virtual memory (TVM) CD8+ T cells. We show that although both TN and TVM cells gradually regenerate after WBI-induced loss, TN recovery only occurs through de novo thymic production. Despite the numerical restoration, the subset and phenotypic composition of post-recovery Ag-inexperienced CD8+ T cells do not qualitatively recapitulate the pre-WBI state. Specifically, the frequency of TVM cells is increased, especially during the early stages of recovery. Within the TN subset, a lasting overrepresentation of Ly6C+CD122+ cells and an altered TCR clonotype diversity are also observed. Overall, our data highlight the dynamic changes to the Ag-inexperienced CD8+ T cell pool upon recovery from RIL.

Authors

Mohammad Heidarian, Shravan K. Kannan, Whitney Swanson, Thomas S. Griffith, John T. Harty, Vladimir P. Badovinac

GATA2 mutation is associated with immune dysfunction and increased Mycobacterium haemophilum susceptibility in immunocompromised individuals

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Abstract

Infections with non-tuberculous mycobacterium (NTM) are on the rise. Here, we investigated an uncommon NTM infection, by M. haemophilum (Mh, n = 3), from a shared geographic location in the USA. All patients had underlying immunosuppressive conditions or treatments. We identified that all these individuals had a non-synonymous mutation in GATA2 gene, which was absent in Healthy controls (HCs, n = 4) from the same geographic area (Missouri, USA). Whole blood from these individuals had attenuated cytokine responses to Mh stimulation for IL1β, IL-6, IL-8, MIP-1α and β, but not to Phytohemagglutinin (PHA) or another NTM, M. abscessus. Impaired whole blood transcriptional responses in individuals with GATA2 mutation, included heightened Ras-homolog (Rho) guanosine triphosphate hydrolases (GTPase) and lowered Transforming growth factor (TGF)-β responses among others. Our results highlight that comparatively, M. abscessus and Mh elicit differential immune responses in humans, and we identify a 23-gene signature that distinguishes host response to Mh and M. abscessus and show that in vitro GATA2 siRNA knockdown indeed attenuates cytokine responses to Mh. Thus, we provide new evidence that links GATA2 mutation and immune dysfunction in individuals with compromised immunity to Mh infection in humans and outline host factors associated with the immune response of this clinically relevant NTM.

Authors

Ananya Gupta, Shail B. Mehta, Abhimanyu A, Bruce A. Rosa, John Martin, Mushtaq Ahmed, Shyamala Thirunavukkarasu, Farheen Fatma, Gaya Amarsinghe, Makedonka Mitreva, Thomas C. Bailey, David B. Clifford, Shabaana A. Khader

PRDM16 acts as a therapeutic downstream target of TGF-β signaling in chronic kidney disease

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Abstract

Transforming growth factor beta (TGF-β) signaling is the master modulator of renal fibrosis. However, targeting drugs have failed to prevent the progression of chronic kidney disease (CKD) in clinical trials due to the extensive biological regulation of TGF-β signaling. It is necessary to investigate the precise downstream mechanisms of TGF-β signaling that regulate renal fibrosis. In this study, we found that PR-domain containing 16 (PRDM16) expression in human renal tubular epithelial cells was markedly reduced by TGF-β. Mechanistically, activated Smad3 induced by TGF-β interacted with the cofactor H-Ras and bound to the promoter of PRDM16, downregulating its transcription. Tubular-specific knockout of PRDM16 promoted renal fibrosis in models of unilateral ureteral occlusion (UUO) and unilateral ischemia-reperfusion injury (UIRI) by exacerbating mitochondrial dysfunction. In vitro, PRDM16 blocked TGF-β-induced mitochondrial injury and lipid deposition by upregulating Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1α (PGC-1α). Delivery of the exogenous PRDM16 gene preserved renal function and ameliorated the progression of renal fibrosis by protecting mitochondrial function. We report PRDM16 as a novel downstream target of TGF-β signaling that attenuates renal fibrosis by safeguarding tubular mitochondrial function.

Authors

Qian Yuan, Ben Tang, Yuting Zhu, Chao Wan, Yaru Xie, Yajuan Xie, Cheng Wan, Hua Su, Youhua Liu, Chun Zhang

Pro-inflammatory macrophages transporting gut-derived bacterial DNA drive autoimmune arthritis in spondyloarthropathy

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Abstract

Spondyloarthritis (SpA) is an inflammatory arthritis of the spine and joints associated with intestinal inflammation, in which it is hypothesized that innate immune exposure to entero-invasive species is followed by self/bacterial peptide presentation. However, the mechanisms underlying loss of tolerance to gut bacteria in genetically at-risk individuals are unclear. Curdlan (β-1,3-glucan, dectin-1 ligand)-treated ZAP-70W163C (SKG) mice develop autoimmune arthritis and ileitis associated with Gram-negative faecal dysbiosis. Using gnotobiotic mice, we show that curdlan-treated SKG mice mono-associated with Parabacteroides goldsteinii or Lactobacillus murinus developed ileitis, arthritis and enthesitis, while BALB/c mice were tolerant. Gnotobiotic SKG ileum upregulated Il23a and ER stress genes and lost goblet cells. Whereas bacterial DNA co-localised with neutrophils and inflammatory macrophages in SKG lamina propria, peri-articular bone marrow, entheses and spleen, in BALB/c bacterial DNA co-localised with resident macrophages in lamina propria and spleen. Human psoriatic-arthritis synovial tissue also contained cell-associated peri-vascular bacterial DNA. Curdlan-treated SKG spleen/bone marrow macrophages transferred severe arthritis and expanded Th17 cells in naïve SKG recipients, while BALB/c or germ free-SKG macrophages transferred mild arthritis and regulated Th17 cells. Thus, bacterial DNA and myeloid cells in the gut and their subsequent traffic regulate or enforce T cell pathogenicity in SpA.

Authors

Benjamin Cai, Rabina Giri, Amy J. Cameron, M. Arifur Rahman, Annabelle Small, Christopher Altmann, Yenkai Lim, Linda M. Rehaume, Mark Morrison, Mihir D. Wechalekar, Jakob Begun, Anne-Sophie Bergot, Ranjeny Thomas