bims-nenemi 2023-12-10 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2023‒12‒10
ten papers selected by
Marco Tigano, Thomas Jefferson University

CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality.
The integrated stress response signaling during the persistent HIV infection.
Caspase-9 inhibition triggers Hsp90-based chemotherapy-mediated tumor intrinsic innate sensing and enhances antitumor immunity.
Non-canonical STING-PERK pathway dependent epigenetic regulation of vascular endothelial dysfunction via integrating IRF3 and NF-κB in inflammatory response.
Dictionary of immune responses to cytokines at single-cell resolution.
A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation.
MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.
JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer's disease.
Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity.
Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

ACS Chem Biol. 2023 Dec 06.

CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality.

Tanja Sack, Piriththiv Dhavarasa, Daniel Szames, Siobhan O'Brien, Stephane Angers, Shana O Kelley.

A major impediment to the characterization of mtDNA repair mechanisms in comparison to nuclear DNA repair mechanisms is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of an mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox), we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted doxorubicin (Dox) screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentiality of our top hit, WRNIP1─observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.

DOI: https://doi.org/10.1021/acschembio.3c00620
iScience. 2023 Dec 15. 26(12): 108418

The integrated stress response signaling during the persistent HIV infection.

Erica A Mendes, Yuyang Tang, Guochun Jiang.

  Human immunodeficiency virus-1 (HIV) infection is a chronic disease under antiretroviral therapy (ART), during which active HIV replication is effectively suppressed. Stable viral reservoirs are established early in infection and cannot be eradicated in people with HIV (PWH) by ART alone, which features residual immune inflammation with disease-associated secondary comorbidities. Mammalian cells are equipped with integrated stress response (ISR) machinery to detect intrinsic and extrinsic stresses such as heme deficiency, nutrient fluctuation, the accumulation of unfolded proteins, and viral infection. ISR is the part of the innate immunity that defends against pathogen infection or environmental alteration, thereby maintaining homeostasis to avoid diseases. Here, we describe how this machinery responds to the off-target effects of ART and persistent HIV infection in both the peripheral compartments and the brain. The latter may be important for us to better understand the mechanisms of stable HIV reservoirs and HIV-associated neurocognitive disorders.

Keywords:  Cell biology; Virology

DOI:  https://doi.org/10.1016/j.isci.2023.108418
J Immunother Cancer. 2023 Dec 06. pii: e007625. [Epub ahead of print]11(12):

Caspase-9 inhibition triggers Hsp90-based chemotherapy-mediated tumor intrinsic innate sensing and enhances antitumor immunity.

Jingyang Li, Xiaoyu Han, Mayu Sun, Weida Li, Guanghuan Yang, Huiyi Chen, Bao Guo, Jingquan Li, Xiaoguang Li, Hui Wang.

BACKGROUND: Antineoplastic chemotherapies are dramatically efficient when they provoke immunogenic cell death (ICD), thus inducing an antitumor immune response and even tumor elimination. However, activated caspases, the hallmark of most cancer chemotherapeutic agents, render apoptosis immunologically silent. Whether they are dispensable for chemotherapy-induced cell death and the apoptotic clearance of cells in vivo is still elusive.METHODS: A rational cell-based anticancer drug library screening was performed to explore the immunogenic apoptosis pathway and therapeutic targets under apoptotic caspase inhibition. Based on this screening, the potential of caspase inhibition in enhancing chemotherapy-induced antitumor immunity and the mechanism of actions was investigated by various cells and mouse models.
RESULTS: Heat shock protein 90 (Hsp90) inhibition activates caspases in tumor cells to produce abundant genomic and mitochondrial DNA fragments and results in cell apoptosis. Meanwhile, it hijacks Caspase-9 signaling to suppress intrinsic DNA sensing. Pharmacological blockade or genetic deletion of Caspase-9 causes tumor cells to secrete interferon (IFN)-β via tumor intrinsic mitochondrial DNA/the second messenger cyclic GMP-AMP (cGAS) /stimulator of interferon genes (STING) pathway without impairing Hsp90 inhibition-induced cell death. Importantly, both Caspase-9 and Hsp90 inhibition triggers an ICD, leading to the release of numerous damage-associated molecular patterns such as high-mobility group box protein 1, ATP and type I IFNs in vitro and remarkable antitumor effects in vivo. Moreover, the combination treatment also induces adaptive resistance by upregulating programmed death-ligand 1 (PD-L1). Additional PD-L1 blockade can further overcome this acquired immune resistance and achieve complete tumor regression.
CONCLUSIONS: Blockade of Caspase-9 signaling selectively provokes Hsp90-based chemotherapy-mediated tumor innate sensing, leading to CD8+ T cell-dependent tumor control. Our findings implicate that pharmacological modulation of caspase pathway increases the tumor-intrinsic innate sensing and immunogenicity of chemotherapy-induced apoptosis, and synergizes with immunotherapy to overcome adaptive resistance.

DOI: https://doi.org/10.1136/jitc-2023-007625
Acta Pharm Sin B. 2023 Dec;13(12): 4765-4784

Non-canonical STING-PERK pathway dependent epigenetic regulation of vascular endothelial dysfunction via integrating IRF3 and NF-κB in inflammatory response.

Xuesong Li, Xiang Chen, Longbin Zheng, Minghong Chen, Yunjia Zhang, Ruigong Zhu, Jiajing Chen, Jiaming Gu, Quanwen Yin, Hong Jiang, Xuan Wu, Xian Ji, Xin Tang, Mengdie Dong, Qingguo Li, Yuanqing Gao, Hongshan Chen.

  Inflammation-driven endothelial dysfunction is the major initiating factor in atherosclerosis, while the underlying mechanism remains elusive. Here, we report that the non-canonical stimulator of interferon genes (STING)-PKR-like ER kinase (PERK) pathway was significantly activated in both human and mice atherosclerotic arteries. Typically, STING activation leads to the activation of interferon regulatory factor 3 (IRF3) and nuclear factor-kappa B (NF-κB)/p65, thereby facilitating IFN signals and inflammation. In contrast, our study reveals the activated non-canonical STING-PERK pathway increases scaffold protein bromodomain protein 4 (BRD4) expression, which encourages the formation of super-enhancers on the proximal promoter regions of the proinflammatory cytokines, thereby enabling the transactivation of these cytokines by integrating activated IRF3 and NF-κB via a condensation process. Endothelium-specific STING and BRD4 deficiency significantly decreased the plaque area and inflammation. Mechanistically, this pathway is triggered by leaked mitochondrial DNA (mtDNA) via mitochondrial permeability transition pore (mPTP), formed by voltage-dependent anion channel 1 (VDAC1) oligomer interaction with oxidized mtDNA upon cholesterol oxidation stimulation. Especially, compared to macrophages, endothelial STING activation plays a more pronounced role in atherosclerosis. We propose a non-canonical STING-PERK pathway-dependent epigenetic paradigm in atherosclerosis that integrates IRF3, NF-κB and BRD4 in inflammatory responses, which provides emerging therapeutic modalities for vascular endothelial dysfunction.

Keywords:  Atherosclerosis; BRD4; Endothelial dysfunction; Inflammation; Mitochondrial DNA; PERK; ROS; STING

DOI:  https://doi.org/10.1016/j.apsb.2023.08.015
Nature. 2023 Dec 06.

Dictionary of immune responses to cytokines at single-cell resolution.

Ang Cui, Teddy Huang, Shuqiang Li, Aileen Ma, Jorge L Pérez, Chris Sander, Derin B Keskin, Catherine J Wu, Ernest Fraenkel, Nir Hacohen.

Cytokines mediate cell-cell communication in the immune system and represent important therapeutic targets1-3. A myriad of studies have highlighted their central role in immune function4-13, yet we lack a global view of the cellular responses of each immune cell type to each cytokine. To address this gap, we created the Immune Dictionary, a compendium of single-cell transcriptomic profiles of more than 17 immune cell types in response to each of 86 cytokines (>1,400 cytokine-cell type combinations) in mouse lymph nodes in vivo. A cytokine-centric view of the dictionary revealed that most cytokines induce highly cell-type-specific responses. For example, the inflammatory cytokine interleukin-1β induces distinct gene programmes in almost every cell type. A cell-type-centric view of the dictionary identified more than 66 cytokine-driven cellular polarization states across immune cell types, including previously uncharacterized states such as an interleukin-18-induced polyfunctional natural killer cell state. Based on this dictionary, we developed companion software, Immune Response Enrichment Analysis, for assessing cytokine activities and immune cell polarization from gene expression data, and applied it to reveal cytokine networks in tumours following immune checkpoint blockade therapy. Our dictionary generates new hypotheses for cytokine functions, illuminates pleiotropic effects of cytokines, expands our knowledge of activation states of each immune cell type, and provides a framework to deduce the roles of specific cytokines and cell-cell communication networks in any immune response.

DOI: https://doi.org/10.1038/s41586-023-06816-9
bioRxiv. 2023 Nov 21. pii: 2023.11.20.567963. [Epub ahead of print]

A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation.

Karl N Miller, Brightany Li, Hannah R Pierce-Hoffman, Xue Lei, Aaron P Havas, Shreeya Patel, Carolina Cano Macip, Stella G Victorelli, Seung-Hwa Woo, Anthony B Lagnado, Tianhui Liu, Nirmalya Dasgupta, Jun Lyu, Yoav Altman, Rebecca A Porritt, Guillermina Garcia, Carolin Mogler, Zhixun Dou, Chongyi Chen, João F Passos, Peter D Adams.

Genomic instability and inflammation are distinct hallmarks of aging, but the connection between them is poorly understood. Understanding their interrelationship will help unravel new mechanisms and therapeutic targets of aging and age-associated diseases. Here we report a novel mechanism directly linking genomic instability and inflammation in senescent cells, through a mitochondria-regulated molecular circuit that connects the p53 tumor suppressor and cytoplasmic chromatin fragments (CCF), a driver of inflammation through the cGAS-STING pathway. Activation or inactivation of p53 by genetic and pharmacologic approaches showed that p53 suppresses CCF accumulation and the downstream inflammatory senescence-associated secretory phenotype (SASP), independent of its effects on cell cycle arrest. p53 activation suppressed CCF formation by promoting DNA repair, reflected in maintenance of genomic integrity, particularly in subtelomeric regions, as shown by single cell genome resequencing. Activation of p53 by pharmacological inhibition of MDM2 in old mice decreased features of SASP in liver, indicating a senomorphic role in vivo . Remarkably, mitochondria in senescent cells suppressed p53 activity by promoting CCF formation and thereby restricting ATM-dependent nuclear DNA damage signaling. These data provide evidence for a mitochondria-regulated p53-CCF circuit in senescent cells that controls DNA repair, genome integrity and inflammatory SASP, and is a potential target for senomorphic healthy aging interventions.

DOI: https://doi.org/10.1101/2023.11.20.567963
bioRxiv. 2023 Nov 22. pii: 2023.11.22.568285. [Epub ahead of print]

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.

Xuexin Yu, Jing Hu, Yuhao Tan, Mingyao Pan, Hongyi Zhang, Bo Li.

Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells.Teaser: MitoTracer enables automatically and accurately discover informative mitochondrial mutations for lineage tracing.

DOI: https://doi.org/10.1101/2023.11.22.568285
Nat Commun. 2023 Dec 04. 14(1): 8021

JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer's disease.

Chiara Scopa, Samantha M Barnada, Maria E Cicardi, Mo Singer, Davide Trotti, Marco Trizzino.

Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death in AD progenitors and neurons. Notably, inhibiting c-Jun effectively blocks all these downstream molecular processes and rescues neuronal death and the impaired neurogenesis phenotype in AD progenitors. Our findings open new avenues for identifying therapeutic strategies and biomarkers to counteract disease progression and diagnose AD in the early, pre-symptomatic stages.

DOI: https://doi.org/10.1038/s41467-023-43728-8
Comput Struct Biotechnol J. 2023 ;21 5609-5619

Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity.

Sophie Charrasse, Titouan Poquillon, Charlotte Saint-Omer, Manuela Pastore, Benoit Bordignon, Richard E Frye, Christelle Reynes, Victor Racine, Abdel Aouacheria.

  Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.

Keywords:  Cellular stress; Confocal microscopy; Environmental health; High content analysis; Live-cell imaging; Mitochondria; Pesticides; Quantitative imaging

DOI:  https://doi.org/10.1016/j.csbj.2023.11.015
bioRxiv. 2023 Nov 20. pii: 2023.11.20.567799. [Epub ahead of print]

Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

Zulong Chen, Xin Wang, Xinlei Gao, Nina Arslanovic, Kaifu Chen, Jessica Tyler.

In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G 1 or G 2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.

DOI: https://doi.org/10.1101/2023.11.20.567799