bims-nimamd 2022-03-06 papers

bims-nimamd

Biomed News

on Neuroimmunity and neuroinflammation in ageing and metabolic disease

Issue of 2022–03–06
twenty-six papers selected by
Fawaz Alzaïd, Sorbonne Université

Nicotinamide breaks effector CD8 T cell responses by targeting mTOR signaling.
Establishment of fetomaternal tolerance through glycan-mediated B cell suppression.
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.
Intact mitochondrial substrate efflux is essential to prevent tubular injury in a sex-dependent manner.
Creatine transport and creatine kinase activity is required for CD8+ T cell immunity.
A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement.
Single-cell profiling of human CD127+ innate lymphoid cells reveals diverse immune phenotypes in hepatocellular carcinoma.
Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis.
Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.
Designing sensitive viral diagnostics with machine learning.
ADAP1 promotes latent HIV-1 reactivation by selectively tuning KRAS-ERK-AP-1 T cell signaling-transcriptional axis.
Methionine adenosyltransferase 1a antisense oligonucleotides activate the liver-brown adipose tissue axis preventing obesity and associated hepatosteatosis.
MTHFD2, metabolic mastermind of CD4+ T cell destiny.
ATAD3A oligomerization promotes neuropathology and cognitive deficits in Alzheimer's disease models.
Dedifferentiation-associated inflammatory factors of long-term expanded human hepatocytes exacerbate their elimination by macrophages during liver engraftment.
Interferon-γ promotes monocyte-mediated lung injury during influenza infection.
Snapshots of nascent RNA reveal cell- and stimulus- specific responses to acute kidney injury.
Reverse cholesterol transport and hepatic osteodystrophy.
Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells.
Mitochondria in cone photoreceptors act as microlenses to enhance photon delivery and confer directional sensitivity to light.
CD47 Blockade Leads to Chemokine-Dependent Monocyte Infiltration and Loss of B Cells from the Splenic Marginal Zone.
Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy.
Activity-dependent PI4P synthesis by PI4KIIIα regulates long-term synaptic potentiation.
A miRNA cassette reprograms smooth muscle cells into endothelial cells.
Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA.
Resident memory CD4+ T lymphocytes mobilize from bone marrow to contribute to a systemic secondary immune reaction.

iScience. 2022 Mar 18. 25(3): 103932

Nicotinamide breaks effector CD8 T cell responses by targeting mTOR signaling.

Federica Agliano, Timofey A Karginov, Antoine Ménoret, Anthony Provatas, Anthony T Vella.

  Nicotinamide (NAM) shapes T cell responses but its precise molecular mechanism of action remains elusive. Here, we show that NAM impairs naive T cell effector transition but also effector T cells themselves. Although aerobic glycolysis is a hallmark of activated T cells, CD8+ T cells exposed to NAM displayed enhanced glycolysis, yet producing significantly less IFNγ. Mechanistically, NAM reduced mTORC1 activity independently of NAD+ metabolism, decreasing IFNγ translation and regulating T cell transcriptional factors critical to effector/memory fate. Finally, the role of NAM in a biomedically relevant model of lung injury was tested. Specifically, a NAM-supplemented diet reduced systemic IL-2, antigen-specific T cell clonal expansion, and effector function after inhalation of Staphylococcus aureus enterotoxin A. These findings identify NAM as a potential therapeutic supplement that uncouples glycolysis from effector cytokine production and may be a powerful treatment for diseases associated with T cell hyperactivation.

Keywords:  Biological sciences; Immunology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2022.103932
Nature. 2022 Mar 02.

Establishment of fetomaternal tolerance through glycan-mediated B cell suppression.

G Rizzuto, J F Brooks, S T Tuomivaara, T I McIntyre, S Ma, D Rideaux, J Zikherman, S J Fisher, A Erlebacher.

Discrimination of self from non-self is fundamental to a wide range of immunological processes1. During pregnancy, the mother does not recognize the placenta as immunologically foreign because antigens expressed by trophoblasts, the placental cells that interface with the maternal immune system, do not activate maternal T cells2. Currently, these activation defects are thought to reflect suppression by regulatory T cells3. By contrast, mechanisms of B cell tolerance to trophoblast antigens have not been identified. Here we provide evidence that glycan-mediated B cell suppression has a key role in establishing fetomaternal tolerance in mice. B cells specific for a model trophoblast antigen are strongly suppressed through CD22-LYN inhibitory signalling, which in turn implicates the sialylated glycans of the antigen as key suppressive determinants. Moreover, B cells mediate the MHC-class-II-restricted presentation of antigens to CD4+ T cells, which leads to T cell suppression, and trophoblast-derived sialoglycoproteins are released into the maternal circulation during pregnancy in mice and humans. How protein glycosylation promotes non-immunogenic placental self-recognition may have relevance to immune-mediated pregnancy complications and to tumour immune evasion. We also anticipate that our findings will bolster efforts to harness glycan biology to control antigen-specific immune responses in autoimmune disease.

DOI: https://doi.org/10.1038/s41586-022-04471-0
Science. 2022 Mar 04. 375(6584): eabk2432

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

FCA Consortium§

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

DOI: https://doi.org/10.1126/science.abk2432
JCI Insight. 2022 Mar 01. pii: e150696. [Epub ahead of print]

Intact mitochondrial substrate efflux is essential to prevent tubular injury in a sex-dependent manner.

Allison McCrimmon, Kerin M Cahill, Claudia Kruger, Margaret E Mangelli, Emily Bouffard, Timothy Dobroski, Kelly N Michanczyk, Susan J Burke, Robert C Noland, Daria V Ilatovskaya, Krisztian Stadler.

  The importance of healthy mitochondrial function is implicated in the prevention of chronic/diabetic kidney diseases (CKD/DKD). Sex differences also play an important role in DKD. Our previous studies revealed that mitochondrial substrate overload (modeled by homozygous deletion of carnitine acetyl-transferase - CrAT) in proximal tubules causes renal injury. Here we demonstrate the importance of intact mitochondrial substrate efflux by titrating the amount of overload through the generation of a heterozygous CrAT knockout model ("PT-CrATHET" mouse). Intriguingly, these animals developed renal injury similarly to their homozygous counterparts. Mitochondria were structurally and functionally impaired in both sexes. Transcriptomic analyses, however, revealed striking sex differences. Male mice shut down fatty acid oxidation and several other metabolism-related pathways. Females had a significantly weaker transcriptional response in metabolism but activation of inflammatory pathways was prominent. Proximal tubular cells from PT-CrATHET mice of both sexes exhibited a shift towards a more glycolytic phenotype, but females were still able to oxidize fatty acid-based substrates. Our results demonstrate that maintaining mitochondrial substrate metabolism balance is crucial to satisfy proximal tubular energy demand. Our findings have potentially broad implications as both the glycolytic shift and the sexual dimorphisms discovered herein offer new modalities for future interventions for treating kidney disease.

Keywords:  Chronic kidney disease; Fatty acid oxidation; Metabolism; Mitochondria; Nephrology

DOI:  https://doi.org/10.1172/jci.insight.150696
Cell Rep. 2022 Mar 01. pii: S2211-1247(22)00173-5. [Epub ahead of print]38(9): 110446

Creatine transport and creatine kinase activity is required for CD8+ T cell immunity.

Bozena Samborska, Dominic G Roy, Janane F Rahbani, Mohammed F Hussain, Eric H Ma, Russell G Jones, Lawrence Kazak.

  The factors that promote T cell expansion are not fully known. Creatine is an abundant circulating metabolite that has recently been implicated in T cell function; however, its cell-autonomous role in immune-cell function is unknown. Here, we show that creatine supports cell-intrinsic CD8+ T cell homeostasis. We further identify creatine kinase B (CKB) as the creatine kinase isoenzyme that supports these T cell properties. Loss of the creatine transporter (Slc6a8) or Ckb results in compromised CD8+ T cell expansion in response to infection without influencing adenylate energy charge. Rather, loss of Slc6a8 or Ckb disrupts naive T cell homeostasis and weakens TCR-mediated activation of mechanistic target of rapamycin complex 1 (mTORC1) signaling required for CD8+ T cell expansion. These data demonstrate a cell-intrinsic role for creatine transport and creatine transphosphorylation, independent of their effects on global cellular energy charge, in supporting CD8+ T cell homeostasis and effector function.

Keywords:  CD8+ T cells; adoptive transfer; creatine kinase; creatine metabolism; infection

DOI:  https://doi.org/10.1016/j.celrep.2022.110446
Cell. 2022 Feb 24. pii: S0092-8674(22)00146-5. [Epub ahead of print]

A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement.

Hidehiko K Inagaki, Susu Chen, Margreet C Ridder, Pankaj Sah, Nuo Li, Zidan Yang, Hana Hasanbegovic, Zhenyu Gao, Charles R Gerfen, Karel Svoboda.

  Motor behaviors are often planned long before execution but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here, we investigate the multi-regional neural circuits that link an auditory "Go cue" and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short latency and phasic changes in spike rate that are selective for the Go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how midbrain can control cortical dynamics via the thalamus for rapid and precise motor behavior.

Keywords:  Neuropixels; dimensionality reduction; licking; midbrain locomotor region; motor control; optogenetics; short-term memory; silicon probe; spikes; state space

DOI:  https://doi.org/10.1016/j.cell.2022.02.006
Hepatology. 2022 Mar 04.

Single-cell profiling of human CD127+ innate lymphoid cells reveals diverse immune phenotypes in hepatocellular carcinoma.

Yuanlin He, Jiajing Luo, Guannan Zhang, Yu Jin, Nanxi Wang, Jinying Lu, Changxian Li, Xiaohuan Guo, Na Qin, Juncheng Dai, Yun Chen.

   BACKGROUND & AIMS: Innate lymphoid cells (ILCs) are tissue-resident lymphocytes that play critical roles in cytokine-mediated regulation of homeostasis and inflammation.However, relationships between their immune phenotypic characteristics and hepatocellular carcinoma (HCC) remain largely unexplored.
APPROACH & RESULTS: We performed single-cell RNA sequencing (scRNA-seq) analysis on sorted hepatic ILC cells from human HCC patientsand validated using flow cytometry, multiplex immunofluorescence staining, and functional experiments. Moreover, we applied selection strategies to enrich ILC populations in HCC samples to investigate the effects of B cells on the immune reaction of ICOS+ ILC2 cells. Dysregulation of ILCs was manifested by the changes in cell numbers or subset proportions in HCC. Seven subsets of 3,433 ILCs were identified with unique properties, of which ICOS+ ILC2a were preferentially enriched in HCC and correlated with poor prognosis. Mechanistically, we report that B cells, particularly resting naïve B cells, have a previously unrecognized function that is involved in inflammatory differentiation of ILC2 cells. B cell-derived ICOSL signaling was responsible for exacerbating inflammation through the increased production of IL-13 in ICOS+ ILC2a cells. HSP70 genes HSPA1A and HSPA1B were highly expressed in ILC2s in late-stage HCC, and targeting to ICOS and its downstream effector HSP70 in ILC2s suppressed tumor growth and remodeled the immunosuppressive tumor microenvironment.
CONCLUSIONS: This in-depth understanding sheds new light on B cell-driven innate type 2 inflammation and provides a potential strategy for HCC immunotherapy.

Keywords:  HSP70; hepatocellular carcinoma; immunotherapy; innate lymphoid cells; single-cell RNA sequencing

DOI:  https://doi.org/10.1002/hep.32444
Cell Rep. 2022 Mar 01. pii: S2211-1247(22)00171-1. [Epub ahead of print]38(9): 110444

Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis.

Hitomi Yamamoto-Imoto, Satoshi Minami, Tatsuya Shioda, Yurina Yamashita, Shinsuke Sakai, Shihomi Maeda, Takeshi Yamamoto, Shinya Oki, Mizuki Takashima, Tadashi Yamamuro, Kyosuke Yanagawa, Ryuya Edahiro, Miki Iwatani, Mizue So, Ayaka Tokumura, Toyofumi Abe, Ryoichi Imamura, Norio Nonomura, Yukinori Okada, Donald E Ayer, Hidesato Ogawa, Eiji Hara, Yoshitsugu Takabatake, Yoshitaka Isaka, Shuhei Nakamura, Tamotsu Yoshimori.

  Accumulation of senescent cells affects organismal aging and the prevalence of age-associated disease. Emerging evidence suggests that activation of autophagy protects against age-associated diseases and promotes longevity, but the roles and regulatory mechanisms of autophagy in cellular senescence are not well understood. Here, we identify the transcription factor, MondoA, as a regulator of cellular senescence, autophagy, and mitochondrial homeostasis. MondoA protects against cellular senescence by activating autophagy partly through the suppression of an autophagy-negative regulator, Rubicon. In addition, we identify peroxiredoxin 3 (Prdx3) as another downstream regulator of MondoA essential for mitochondrial homeostasis and autophagy. Rubicon and Prdx3 work independently to regulate senescence. Furthermore, we find that MondoA knockout mice have exacerbated senescence during ischemic acute kidney injury (AKI), and a decrease of MondoA in the nucleus is correlated with human aging and ischemic AKI. Our results suggest that decline of MondoA worsens senescence and age-associated disease.

Keywords:  C. elegans; MondoA; Rubicon; aging; autophagy; cellular senescence; kidney; mitochondrial homeostasis; mml-1; peroxiredoxin 3

DOI:  https://doi.org/10.1016/j.celrep.2022.110444
Nat Metab. 2022 Feb;4(2): 284-299

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.

HPAP Consortium

Type 1 diabetes (T1D) is an autoimmune disease in which immune cells destroy insulin-producing beta cells. The aetiology of this complex disease is dependent on the interplay of multiple heterogeneous cell types in the pancreatic environment. Here, we provide a single-cell atlas of pancreatic islets of 24 T1D, autoantibody-positive and nondiabetic organ donors across multiple quantitative modalities including ~80,000 cells using single-cell transcriptomics, ~7,000,000 cells using cytometry by time of flight and ~1,000,000 cells using in situ imaging mass cytometry. We develop an advanced integrative analytical strategy to assess pancreatic islets and identify canonical cell types. We show that a subset of exocrine ductal cells acquires a signature of tolerogenic dendritic cells in an apparent attempt at immune suppression in T1D donors. Our multimodal analyses delineate cell types and processes that may contribute to T1D immunopathogenesis and provide an integrative procedure for exploration and discovery of human pancreatic function.

DOI: https://doi.org/10.1038/s42255-022-00531-x
Nat Biotechnol. 2022 Mar 03.

Designing sensitive viral diagnostics with machine learning.

Hayden C Metsky, Nicole L Welch, Priya P Pillai, Nicholas J Haradhvala, Laurie Rumker, Sreekar Mantena, Yibin B Zhang, David K Yang, Cheri M Ackerman, Juliane Weller, Paul C Blainey, Cameron Myhrvold, Michael Mitzenmacher, Pardis C Sabeti.

Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.

DOI: https://doi.org/10.1038/s41587-022-01213-5
Nat Commun. 2022 Mar 01. 13(1): 1109

ADAP1 promotes latent HIV-1 reactivation by selectively tuning KRAS-ERK-AP-1 T cell signaling-transcriptional axis.

Nora-Guadalupe P Ramirez, Jeon Lee, Yue Zheng, Lianbo Li, Bryce Dennis, Didi Chen, Ashwini Challa, Vicente Planelles, Kenneth D Westover, Neal M Alto, Iván D'Orso.

Immune stimulation fuels cell signaling-transcriptional programs inducing biological responses to eliminate virus-infected cells. Yet, retroviruses that integrate into host cell chromatin, such as HIV-1, co-opt these programs to switch between latent and reactivated states; however, the regulatory mechanisms are still unfolding. Here, we implemented a functional screen leveraging HIV-1's dependence on CD4+ T cell signaling-transcriptional programs and discovered ADAP1 is an undescribed modulator of HIV-1 proviral fate. Specifically, we report ADAP1 (ArfGAP with dual PH domain-containing protein 1), a previously thought neuronal-restricted factor, is an amplifier of select T cell signaling programs. Using complementary biochemical and cellular assays, we demonstrate ADAP1 inducibly interacts with the immune signalosome to directly stimulate KRAS GTPase activity thereby augmenting T cell signaling through targeted activation of the ERK-AP-1 axis. Single cell transcriptomics analysis revealed loss of ADAP1 function blunts gene programs upon T cell stimulation consequently dampening latent HIV-1 reactivation. Our combined experimental approach defines ADAP1 as an unexpected tuner of T cell programs facilitating HIV-1 latency escape.

DOI: https://doi.org/10.1038/s41467-022-28772-0
Nat Commun. 2022 Mar 01. 13(1): 1096

Methionine adenosyltransferase 1a antisense oligonucleotides activate the liver-brown adipose tissue axis preventing obesity and associated hepatosteatosis.

Diego Sáenz de Urturi, Xabier Buqué, Begoña Porteiro, Cintia Folgueira, Alfonso Mora, Teresa C Delgado, Endika Prieto-Fernández, Paula Olaizola, Beatriz Gómez-Santos, Maider Apodaka-Biguri, Francisco González-Romero, Ane Nieva-Zuluaga, Mikel Ruiz de Gauna, Naroa Goikoetxea-Usandizaga, Juan Luis García-Rodríguez, Virginia Gutierrez de Juan, Igor Aurrekoetxea, Valle Montalvo-Romeral, Eva M Novoa, Idoia Martín-Guerrero, Marta Varela-Rey, Sanjay Bhanot, Richard Lee, Jesus M Banales, Wing-Kin Syn, Guadalupe Sabio, María L Martínez-Chantar, Rubén Nogueiras, Patricia Aspichueta.

Altered methionine metabolism is associated with weight gain in obesity. The methionine adenosyltransferase (MAT), catalyzing the first reaction of the methionine cycle, plays an important role regulating lipid metabolism. However, its role in obesity, when a plethora of metabolic diseases occurs, is still unknown. By using antisense oligonucleotides (ASO) and genetic depletion of Mat1a, here, we demonstrate that Mat1a deficiency in diet-induce obese or genetically obese mice prevented and reversed obesity and obesity-associated insulin resistance and hepatosteatosis by increasing energy expenditure in a hepatocyte FGF21 dependent fashion. The increased NRF2-mediated FGF21 secretion induced by targeting Mat1a, mobilized plasma lipids towards the BAT to be catabolized, induced thermogenesis and reduced body weight, inhibiting hepatic de novo lipogenesis. The beneficial effects of Mat1a ASO were abolished following FGF21 depletion in hepatocytes. Thus, targeting Mat1a activates the liver-BAT axis by increasing NRF2-mediated FGF21 secretion, which prevents obesity, insulin resistance and hepatosteatosis.

DOI: https://doi.org/10.1038/s41467-022-28749-z
Sci Immunol. 2022 Mar 04. 7(69): eabo6765

MTHFD2, metabolic mastermind of CD4+ T cell destiny.

Victoire Gouirand, Michael D Rosenblum.

MTHFD2 is a metabolic checkpoint of T cell fate and function.

DOI: https://doi.org/10.1126/sciimmunol.abo6765
Nat Commun. 2022 Mar 02. 13(1): 1121

ATAD3A oligomerization promotes neuropathology and cognitive deficits in Alzheimer's disease models.

Yuanyuan Zhao, Di Hu, Rihua Wang, Xiaoyan Sun, Philip Ropelewski, Zita Hubler, Kathleen Lundberg, Quanqiu Wang, Drew J Adams, Rong Xu, Xin Qi.

Predisposition to Alzheimer's disease (AD) may arise from lipid metabolism perturbation, however, the underlying mechanism remains elusive. Here, we identify ATPase family AAA-domain containing protein 3A (ATAD3A), a mitochondrial AAA-ATPase, as a molecular switch that links cholesterol metabolism impairment to AD phenotypes. In neuronal models of AD, the 5XFAD mouse model and post-mortem AD brains, ATAD3A is oligomerized and accumulated at the mitochondria-associated ER membranes (MAMs), where it induces cholesterol accumulation by inhibiting gene expression of CYP46A1, an enzyme governing brain cholesterol clearance. ATAD3A and CYP46A1 cooperate to promote APP processing and synaptic loss. Suppressing ATAD3A oligomerization by heterozygous ATAD3A knockout or pharmacological inhibition with DA1 restores neuronal CYP46A1 levels, normalizes brain cholesterol turnover and MAM integrity, suppresses APP processing and synaptic loss, and consequently reduces AD neuropathology and cognitive deficits in AD transgenic mice. These findings reveal a role for ATAD3A oligomerization in AD pathogenesis and suggest ATAD3A as a potential therapeutic target for AD.

DOI: https://doi.org/10.1038/s41467-022-28769-9
Hepatology. 2022 Mar 01.

Dedifferentiation-associated inflammatory factors of long-term expanded human hepatocytes exacerbate their elimination by macrophages during liver engraftment.

Chenhua Wang, Ludi Zhang, Zhen Sun, Xiang Yuan, Baihua Wu, Jin Cen, Lei Cui, Kun Zhang, Chun Li, Jingqi Wu, Yajing Shu, Wenbin Sun, Jing Wang, Lijian Hui.

   BACKGROUND & AIMS: Hepatocyte transplantation has been demonstrated to be effective to treat liver metabolic disease and acute liver failure. Nevertheless, the shortage of donor hepatocytes restrained its application in clinics. To expand human hepatocytes in large scale, several dedifferentiation-based protocols have been established, including Proliferating Human Hepatocytes (ProliHH). However, the decreased transplantation efficiency of these cells after long-term expansion largely impedes their application.
APPROACH & RESULTS: We found that accompanying with dedifferentiation, long-term cultured ProliHH (lc-ProliHH) upregulated a panel of chemokines and cytokines related to innate immunity, which were referred as dedifferentiation-associated inflammatory factors (DAIF). DAIF elicited excessive macrophage responses, accounting for the elimination of lc-ProliHH specifically during engraftment. Two possible strategies to increase ProliHH transplantation were then characterized. Blockage of innate immune response by dexamethasone reverted the engraftment and repopulation of lc-ProliHH to a level comparable to primary hepatocytes, resulting in improved liver function and a better survival of Fah-deficient mice. Alternatively, re-maturation of lc-ProliHH as organoids reduced the expression of DAIF and led to markedly improved engraftment.
CONCLUSIONS: These results revealed that lc-ProliHH triggers exacerbated macrophage activation by DAIF and provided potential solutions for clinical transplantation of lc-ProliHH.

Keywords:  Hepatocyte transplantation; hepatocyte culture; innate immune response; macrophage; organoid

DOI:  https://doi.org/10.1002/hep.32436
Cell Rep. 2022 Mar 01. pii: S2211-1247(22)00183-8. [Epub ahead of print]38(9): 110456

Interferon-γ promotes monocyte-mediated lung injury during influenza infection.

Taylor Schmit, Kai Guo, Jitendra Kumar Tripathi, Zhihan Wang, Brett McGregor, Mitch Klomp, Ganesh Ambigapathy, Ramkumar Mathur, Junguk Hur, Michael Pichichero, Jay Kolls, M Nadeem Khan.

  Influenza A virus (IAV) infection triggers an exuberant host response that promotes acute lung injury. However, the host response factors that promote the development of a pathologic inflammatory response to IAV remain incompletely understood. In this study, we identify an interferon-γ (IFN-γ)-regulated subset of monocytes, CCR2+ monocytes, as a driver of lung damage during IAV infection. IFN-γ regulates the recruitment and inflammatory phenotype of CCR2+ monocytes, and mice deficient in CCR2 (CCR2-/-) or IFN-γ (IFN-γ-/-) exhibit reduced lung inflammation, pathology, and disease severity. Adoptive transfer of wild-type (WT) (IFN-γR1+/+) but not IFN-γR1-/- CCR2+ monocytes restore the WT-like pathological phenotype of lung damage in IAV-infected CCR2-/- mice. CD8+ T cells are the main source of IFN-γ in IAV-infected lungs. Collectively, our data highlight the requirement of IFN-γ signaling in the regulation of CCR2+ monocyte-mediated lung pathology during IAV infection.

Keywords:  CCR2(+) monocyte; Streptococcus pneumoniae; acute lung injury; influenza; interferon-γ; single-cell RNA sequencing

DOI:  https://doi.org/10.1016/j.celrep.2022.110456
JCI Insight. 2022 Mar 01. pii: e146374. [Epub ahead of print]

Snapshots of nascent RNA reveal cell- and stimulus- specific responses to acute kidney injury.

Tian Huai Shen, Jacob Stauber, Katherine Xu, Alexandra Jacunski, Neal Paragas, Miriam Callahan, Run Banlengchit, Abraham D Levitman, Beatriz Desanti de Oliveira, Andrew Beenken, Madeleine S Grau, Edwin Mathieu, Qingyin Zhang, Yuanji Li, Tejashree Gopal, Nathaniel Askanase, Siddarth Arumugam, Sumit Mohan, Pamela I Good, Jacob S Stevens, Fangming Lin, Samuel K Sia, Chyuan-Sheng Lin, Vivette D'Agati, Krzysztof Kiryluk, Nicholas P Tatonetti, Jonathan Barasch.

  The current strategy to detect acute injury of kidney tubular cells relies on changes in serum levels of creatinine. Yet serum creatinine (sCr) is a marker of both functional and pathological processes and does not specifically assay tubular injury. In addition, sCr may require days to reach diagnostic thresholds, yet tubular cells respond with programs of damage and repair within minutes or hours. To detect acute responses to clinically relevant stimuli, we created Rosa26-floxed-stop uracil phosphoribosyl-transferase (Uprt) expressing mice and inoculated 4-thiouracil (TU) to tag nascent RNA at selected time points. Cre-driven TU-tagged RNA was isolated from whole kidneys and demonstrated that volume depletion and ischemia induced different genetic programs. Even lineage related cell types expressed different genes in response to the two stressors. TU-tagging also demonstrated the transient nature of the responses. Because we placed Uprt in the ubiquitously active Rosa-26 locus, RNAs from many cell types can be tagged in vivo and their roles interrogated under various conditions. In short, TU labeling identifies stimulus-specific, cell-specific, and time-dependent acute responses that are otherwise difficult to detect with other technologies and are entirely obscured when sCr is the sole metric of kidney damage.

Keywords:  Chronic kidney disease; Nephrology

DOI:  https://doi.org/10.1172/jci.insight.146374
Cell Metab. 2022 Mar 01. pii: S1550-4131(22)00051-1. [Epub ahead of print]34(3): 347-349

Reverse cholesterol transport and hepatic osteodystrophy.

Mone Zaidi, Tony Yuen, Jameel Iqbal.

In this issue of Cell Metabolism, Lu et al. show that chronic liver disease increases the expression and activity of PP2Ac, a phosphatase that downregulates the excretion of lecithin-cholesterol aceyltransferase (LCAT). LCAT, a liver-derived enzyme, protects bone and prevents bone loss, and its lowered levels in progressive liver injury cause hepatic osteodystrophy (HOD) and worsen liver fibrosis. These discoveries open the possibility that recombinant LCAT may be a treatment for both HOD and liver fibrosis.

DOI: https://doi.org/10.1016/j.cmet.2022.02.007
Nat Biotechnol. 2022 Mar 03.

Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells.

Khrystyna North, Salima Benbarche, Bo Liu, Joseph Pangallo, Sisi Chen, Maximilian Stahl, Jan Philipp Bewersdorf, Robert F Stanley, Caroline Erickson, Hana Cho, Jose Mario Bello Pineda, James D Thomas, Jacob T Polaski, Andrea E Belleville, Austin M Gabel, Dylan B Udy, Olivier Humbert, Hans-Peter Kiem, Omar Abdel-Wahab, Robert K Bradley.

Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors. Here, we describe a method to harness this abnormal splicing activity to drive splicing factor mutation-dependent gene expression to selectively eliminate tumor cells. We engineered synthetic introns that were efficiently spliced in cancer cells bearing SF3B1 mutations, but unspliced in otherwise isogenic wild-type cells, to yield mutation-dependent protein production. A massively parallel screen of 8,878 introns delineated ideal intronic size and mapped elements underlying mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus-thymidine kinase (HSV-TK) and subsequent ganciclovir (GCV)-mediated killing of SF3B1-mutant leukemia, breast cancer, uveal melanoma and pancreatic cancer cells in vitro, while leaving wild-type cells unaffected. Delivery of synthetic intron-containing HSV-TK constructs to leukemia, breast cancer and uveal melanoma cells and GCV treatment in vivo significantly suppressed the growth of these otherwise lethal xenografts and improved mouse host survival. Synthetic introns provide a means to exploit tumor-specific changes in RNA splicing for cancer gene therapy.

DOI: https://doi.org/10.1038/s41587-022-01224-2
Sci Adv. 2022 Mar 04. 8(9): eabn2070

Mitochondria in cone photoreceptors act as microlenses to enhance photon delivery and confer directional sensitivity to light.

John M Ball, Shan Chen, Wei Li.

Mammalian photoreceptors aggregate numerous mitochondria, organelles chiefly for energy production, in the ellipsoid region immediately adjacent to the light-sensitive outer segment to support the high metabolic demands of phototransduction. However, these complex, lipid-rich organelles are also poised to affect light passage into the outer segment. Here, we show, via live imaging and simulations, that despite this risk of light scattering or absorption, these tightly packed mitochondria "focus" light for entry into the outer segment and that mitochondrial remodeling affects such light concentration. This "microlens"-like feature of cone mitochondria delivers light with an angular dependence akin to the Stiles-Crawford effect (SCE), providing a simple explanation for this essential visual phenomenon that improves resolution. This new insight into the optical role of mitochondria is relevant for the interpretation of clinical ophthalmological imaging, lending support for the use of SCE as an early diagnostic tool in retinal disease.

DOI: https://doi.org/10.1126/sciadv.abn2070
J Immunol. 2022 Mar 02. pii: ji2100352. [Epub ahead of print]

CD47 Blockade Leads to Chemokine-Dependent Monocyte Infiltration and Loss of B Cells from the Splenic Marginal Zone.

Ying Ying Yiu, Paige S Hansen, Laughing Bear Torrez Dulgeroff, Grace Blacker, Lara Myers, Sarah Galloway, Eric Gars, Olivia Colace, Paul Mansfield, Kim J Hasenkrug, Irving L Weissman, Michal Caspi Tal.

CD47 is an important innate immune checkpoint through its interaction with its inhibitory receptor on macrophages, signal-regulatory protein α (SIRPα). Therapeutic blockade of CD47-SIRPα interactions is a promising immuno-oncology treatment that promotes clearance of cancer cells. However, CD47-SIRPα interactions also maintain homeostatic lymphocyte levels. In this study, we report that the mouse splenic marginal zone B cell population is dependent on intact CD47-SIRPα interactions and blockade of CD47 leads to the loss of these cells. This depletion is accompanied by elevated levels of monocyte-recruiting chemokines CCL2 and CCL7 and infiltration of CCR2+Ly6Chi monocytes into the mouse spleen. In the absence of CCR2 signaling, there is no infiltration and reduced marginal zone B cell depletion. These data suggest that CD47 blockade leads to clearance of splenic marginal zone B cells.

DOI: https://doi.org/10.4049/jimmunol.2100352
J Clin Invest. 2022 Mar 01. pii: e155251. [Epub ahead of print]

Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy.

Justin Harper, Susan P Ribeiro, Chi Ngai Chan, Malika Aid, Claire Deleage, Luca Micci, Maria Pino, Barbara Cervasi, Gopalan Raghunathan, Eric Rimmer, Gulesi Ayanoglu, Guoxin Wu, Neeta Shenvi, Richard Jo Barnard, Gregory Q Del Prete, Kathleen Busman-Sahay, Guido Silvestri, Deanna A Kulpa, Steven E Bosinger, Kirk Easley, Bonnie J Howell, Dan Gorman, Daria J Hazuda, Jacob D Estes, Rafick-Pierre Sekaly, Mirko Paiardini.

  Interleukin (IL)-10 is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper cell (TFH) differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph node (LN) were induced by infection and not normalized with ART. During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including TFH, and predicted the frequency of CD4+ TFH and their cell-associated SIV-DNA content during ART, respectively. In ART-treated RMs, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B-cell follicle in proximity to IL-10. Finally, we demonstrated that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques reduced B cell follicle maintenance and by extension LN memory CD4+ T-cells, including TFH and those expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T-cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.

Keywords:  AIDS/HIV; Immunology; Immunotherapy; T cells

DOI:  https://doi.org/10.1172/JCI155251
Cell Rep. 2022 Mar 01. pii: S2211-1247(22)00179-6. [Epub ahead of print]38(9): 110452

Activity-dependent PI4P synthesis by PI4KIIIα regulates long-term synaptic potentiation.

Zhenzhen Guo, Chao-Hua Jiang, Chunfang Tong, Yanrui Yang, Zehua Wang, Sin Man Lam, Dou Wang, Rui Li, Guanghou Shui, Yun Stone Shi, Jia-Jia Liu.

  Phosphatidylinositol 4-phosphate (PI4P) is a low abundant phospholipid with important roles in lipid transport and membrane trafficking. However, little is known of its metabolism and function in neurons. Here, we investigate its subcellular distribution and functional roles in dendrites of rodent hippocampal neurons during resting state and long-term synaptic potentiation (LTP). We show that neural activity causes dynamic reversible changes in PI4P metabolism in dendrites. Upon LTP induction, PI4KIIIα, a type III phosphatidylinositol 4-kinase, localizes to the dendritic plasma membrane (PM) in a calcium-dependent manner and causes substantial increase in the levels of PI4P. Acute inhibition of PI4KIIIα activity abolishes trafficking of the AMPA-type glutamate receptor to the PM during LTP induction, and silencing of PI4KIIIα expression in the hippocampal CA1 region causes severe impairment of LTP and long-term memory. Collectively, our results identify an essential role for PI4KIIIα-dependent PI4P synthesis in synaptic plasticity of central nervous system neurons.

Keywords:  AMPAR; GluA1; PI4KIIIa; PI4P; calcium; exocytosis; lipid metabolism; long-term potentiation; plasma membrane; trafficking

DOI:  https://doi.org/10.1016/j.celrep.2022.110452
FASEB J. 2022 Apr;36(4): e22239

A miRNA cassette reprograms smooth muscle cells into endothelial cells.

Michael G McCoy, Daniel Pérez-Cremades, Nathan Belkin, Wenhui Peng, Bofang Zhang, Jingshu Chen, Madhur Sachan, A K M Khyrul Wara, Rulin Zhuang, Henry S Cheng, Mark W Feinberg.

  Cellular reprogramming through targeting microRNAs (miRNAs) holds promise for regenerative therapy due to their profound regulatory effects in proliferation, differentiation, and function. We hypothesized that transdifferentiation of vascular smooth muscle cells (SMCs) into endothelial cells (ECs) using a miRNA cassette may provide a novel approach for use in vascular disease states associated with endothelial injury or dysfunction. miRNA profiling of SMCs and ECs and iterative combinatorial miRNA transfections of human coronary SMCs revealed a 4-miRNA cassette consisting of miR-143-3p and miR-145-5p inhibitors and miR-146a-5p and miR-181b-5p mimics that efficiently produced induced endothelial cells (iECs). Transcriptome profiling, protein expression, and functional studies demonstrated that iECs exhibit high similarity to ECs. Injected iECs restored blood flow recovery even faster than conventional ECs in a murine hindlimb ischemia model. This study demonstrates that a 4-miRNA cassette is sufficient to reprogram SMCs into ECs and shows promise as a novel regenerative strategy for endothelial repair.

Keywords:  angiogenesis; endothelial miRNA; miRNA; miRNA reprogramming; transdifferentiation

DOI:  https://doi.org/10.1096/fj.202101872R
Nat Commun. 2022 Mar 03. 13(1): 1133

Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA.

Sunjoo Joo, Thamali Kariyawasam, Minjae Kim, EonSeon Jin, Ursula Goodenough, Jae-Hyeok Lee.

Most sexual organisms inherit organelles from one parent, commonly by excluding organelles from the smaller gametes. However, post-mating elimination of organelles derived from one gamete ensures uniparental inheritance, where the underlying mechanisms to distinguish organelles by their origin remain obscure. Mating in Chlamydomonas reinhardtii combines isomorphic plus and minus gametes, but chloroplast DNA from minus gametes is selectively degraded in zygotes. Here, we identify OTU2p (otubain protein 2), encoded in the plus mating-type locus MT+, as the protector of plus chloroplast. Otu2p is an otubain-like deubiquitinase, which prevents proteasome-mediated degradation of the preprotein translocase of the outer chloroplast membrane (TOC) during gametogenesis. Using OTU2p-knockouts and proteasome inhibitor treatment, we successfully redirect selective DNA degradation in chloroplasts with reduced TOC levels regardless of mating type, demonstrating that plus-specific Otu2p establishes uniparental chloroplast DNA inheritance. Our work documents that a sex-linked organelle quality control mechanism drives the uniparental organelle inheritance without dimorphic gametes.

DOI: https://doi.org/10.1038/s41467-022-28807-6
Eur J Immunol. 2022 Mar 04.

Resident memory CD4+ T lymphocytes mobilize from bone marrow to contribute to a systemic secondary immune reaction.

Carla Cendón, Weijie Du, Pawel Durek, Yuk-Chien Liu, Tobias Alexander, Lindsay Serene, Xinyi Yang, Gilles Gasparoni, Abdulrahman Salhab, Karl Nordström, Tina Lai, Axel R Schulz, Anna Rao, Gitta A Heinz, Ana L Stefanski, Anne Claußnitzer, Katherina Siewert, Thomas Dörner, Hyun-Dong Chang, Hans-Dieter Volk, Chiara Romagnani, Zhihai Qin, Sebastian Hardt, Carsten Perka, Simon Reinke, Jörn Walter, Mir-F Mashreghi, Kevin Thurley, Andreas Radbruch, Jun Dong.

  Resident memory T lymphocytes (TRM ) of epithelial tissues and the bone marrow protect their host tissue. To what extent these cells are mobilized and contribute to systemic immune reactions is less clear. Here we show that in secondary immune reactions to the measles-mumps-rubella (MMR) vaccine, CD4+ TRM are mobilized into the blood within 16 to 48 hours after immunization in humans. This mobilization of TRM is cognate: TRM recognizing other antigens are not mobilized, unless they cross-react with the vaccine. We also demonstrate through methylome analyses that TRM are mobilized from the bone marrow. These mobilized cells make significant contribution to the systemic immune reaction, as evidenced by their T-cell receptor Vβ clonotypes represented among the newly generated circulating memory T-cells, 14 days after vaccination. Thus, TRM of the bone marrow confer not only local, but also systemic immune memory. This article is protected by copyright. All rights reserved.

Keywords:  Bone marrow Trm cells; Epigenetic signature; Mobilization; Systemic memory; T cell receptor repertoire

DOI:  https://doi.org/10.1002/eji.202149726