bims-nenemi Biomed News
on Neuroinflammation, neurodegeneration and mitochondria
Issue of 2022‒06‒05
twelve papers selected by
Marco Tigano
Thomas Jefferson University
  1. Mitochondrial matrix-localized Src kinase regulates mitochondrial morphology.
  2. ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
  3. TRPML1-induced autophagy inhibition triggers mitochondrial mediated apoptosis.
  4. A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression.
  5. Genome Replication Is Associated With Release of Immunogenic DNA Waste.
  6. Leukocyte cytokine responses in adult patients with mitochondrial DNA defects.
  7. Stimuli-responsive nano vehicle enhances cancer immunotherapy by coordinating mitochondria-targeted immunogenic cell death and PD-L1 blockade.
  8. Putative role of STING-mitochondria associated membrane crosstalk in immunity.
  9. Artificial neural networks enable genome-scale simulations of intracellular signaling.
  10. Targeting mitochondrial DNA polymerase gamma for selective inhibition of MLH1 deficient colon cancer growth.
  11. A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs.
  12. Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells.
  1. Cell Mol Life Sci. 2022 May 30. 79(6): 327
    Mitochondrial matrix-localized Src kinase regulates mitochondrial morphology.
    Olivier Lurette, Hala Guedouari, Jordan L Morris, Rebeca Martín-Jiménez, Julie-Pier Robichaud, Geneviève Hamel-Côté, Mehtab Khan, Nicholas Dauphinee, Nicolas Pichaud, Julien Prudent, Etienne Hebert-Chatelain.
      The architecture of mitochondria adapts to physiological contexts: while mitochondrial fragmentation is usually associated to quality control and cell death, mitochondrial elongation often enhances cell survival during stress. Understanding how these events are regulated is important to elucidate how mitochondrial dynamics control cell fate. Here, we show that the tyrosine kinase Src regulates mitochondrial morphology. Deletion of Src increased mitochondrial size and reduced cellular respiration independently of mitochondrial mass, mitochondrial membrane potential or ATP levels. Re-expression of Src targeted to the mitochondrial matrix, but not of Src targeted to the plasma membrane, rescued mitochondrial morphology in a kinase activity-dependent manner. These findings highlight a novel function for Src in the control of mitochondrial dynamics.
    Keywords:  Cellular respiration; Mitochondria-shaping protein; Mitochondrial dynamics; Oxidative phosphorylation
    DOI:  https://doi.org/10.1007/s00018-022-04325-y
  2. J Cell Biol. 2022 Jul 04. pii: e202106046. [Epub ahead of print]221(7):
    ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
    William Hancock-Cerutti, Zheng Wu, Peng Xu, Narayana Yadavalli, Marianna Leonzino, Arun Kumar Tharkeshwar, Shawn M Ferguson, Gerald S Shadel, Pietro De Camilli.
      Mutations in VPS13C cause early-onset, autosomal recessive Parkinson's disease (PD). We have established that VPS13C encodes a lipid transfer protein localized to contact sites between the ER and late endosomes/lysosomes. In the current study, we demonstrate that depleting VPS13C in HeLa cells causes an accumulation of lysosomes with an altered lipid profile, including an accumulation of di-22:6-BMP, a biomarker of the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation. In addition, the DNA-sensing cGAS-STING pathway, which was recently implicated in PD pathogenesis, is activated in these cells. This activation results from a combination of elevated mitochondrial DNA in the cytosol and a defect in the degradation of activated STING, a lysosome-dependent process. These results suggest a link between ER-lysosome lipid transfer and innate immune activation in a model human cell line and place VPS13C in pathways relevant to PD pathogenesis.
    DOI:  https://doi.org/10.1083/jcb.202106046
  3. Cancer Lett. 2022 May 26. pii: S0304-3835(22)00236-1. [Epub ahead of print]541 215752
    TRPML1-induced autophagy inhibition triggers mitochondrial mediated apoptosis.
    Yucheng Liu, Xinyan Wang, Wucheng Zhu, Zhongheng Sui, Xiangqing Wei, Yang Zhang, Jiansong Qi, Yanhong Xing, Wuyang Wang.
      Previous studies have demonstrated that autophagy tightly regulates apoptosis. However, the underlying mechanism whereby autophagy regulates apoptosis remains unclear. Here, we discover a "autophagy inhibition-mitochondrial turnover disruption-ROS elevation-DNA damage-p53 transactivation-apoptosis" axis that explicates the process of autophagy modulating apoptosis. We found that autophagy inhibition induced by TRPML1, a cationic channel localized in the lysosome, results in accumulation of damaged mitochondria via blocking the mitophagic flux to lysosomes in human melanoma and glioblastoma cells. The disrupted mitochondria turnover leads to ROS elevation, which in turn causes severe damage to DNA in these cancer cells. Damage to DNA resulted from TRPML1-mediated autophagy inhibition subsequently activates p53, which ultimately triggers mitochondrial mediated apoptosis by modulating pro- and anti-apoptosis proteins in these cancer cells. As a result, by triggering apoptosis, TRPML1-induced autophagy inhibition greatly suppresses growth of human melanoma and glioma both in vitro and in vivo. In summary, our findings define the mechanism underling the regulation of autophagy inhibition in apoptosis and represent TRPML1 as a novel target for potentially treating melanoma and glioblastoma in the clinical setting.
    Keywords:  DNA damage; Glioblastoma; Lysosomes; Melanoma; p53
    DOI:  https://doi.org/10.1016/j.canlet.2022.215752
  4. Nat Cell Biol. 2022 Jun 02.
    A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression.
    Ioannis I Verginadis, Harris Avgousti, James Monslow, Giorgos Skoufos, Frank Chinga, Kyle Kim, Nektaria Maria Leli, Ilias V Karagounis, Brett I Bell, Anastasia Velalopoulou, Carlo Salas Salinas, Victoria S Wu, Yang Li, Jiangbin Ye, David A Scott, Andrei L Osterman, Arjun Sengupta, Aalim Weljie, Menggui Huang, Duo Zhang, Yi Fan, Enrico Radaelli, John W Tobias, Florian Rambow, Panagiotis Karras, Jean-Christophe Marine, Xiaowei Xu, Artemis G Hatzigeorgiou, Sandra Ryeom, J Alan Diehl, Serge Y Fuchs, Ellen Puré, Constantinos Koumenis.
      Bidirectional signalling between the tumour and stroma shapes tumour aggressiveness and metastasis. ATF4 is a major effector of the Integrated Stress Response, a homeostatic mechanism that couples cell growth and survival to bioenergetic demands. Using conditional knockout ATF4 mice, we show that global, or fibroblast-specific loss of host ATF4, results in deficient vascularization and a pronounced growth delay of syngeneic melanoma and pancreatic tumours. Single-cell transcriptomics of tumours grown in Atf4Δ/Δ mice uncovered a reduction in activation markers in perivascular cancer-associated fibroblasts (CAFs). Atf4Δ/Δ fibroblasts displayed significant defects in collagen biosynthesis and deposition and a reduced ability to support angiogenesis. Mechanistically, ATF4 regulates the expression of the Col1a1 gene and levels of glycine and proline, the major amino acids of collagen. Analyses of human melanoma and pancreatic tumours revealed a strong correlation between ATF4 and collagen levels. Our findings establish stromal ATF4 as a key driver of CAF functionality, malignant progression and metastasis.
    DOI:  https://doi.org/10.1038/s41556-022-00918-8
  5. Front Immunol. 2022 ;13 880413
    Genome Replication Is Associated With Release of Immunogenic DNA Waste.
    Nadja Schubert, Tina Schumann, Elena Daum, Karolin Flade, Yan Ge, Lara Hagedorn, Winfried Edelmann, Luise Müller, Marc Schmitz, Gunnar Kuut, Veit Hornung, Rayk Behrendt, Axel Roers.
      Innate DNA sensors detect foreign and endogenous DNA to induce responses to infection and cellular stress or damage. Inappropriate activation by self-DNA triggers severe autoinflammatory conditions, including Aicardi-Goutières syndrome (AGS) that can be caused by defects of the cytosolic DNase 3'repair exonuclease 1 (TREX1). TREX1 loss-of-function alleles are also associated with systemic lupus erythematosus (SLE). Chronic activation of innate antiviral immunity in TREX1-deficient cells depends on the DNA sensor cGAS, implying that accumulating TREX1 DNA substrates cause the inflammatory pathology. Retrotransposon-derived cDNAs were shown to activate cGAS in TREX1-deficient neuronal cells. We addressed other endogenous sources of cGAS ligands in cells lacking TREX1. We find that induced loss of TREX1 in primary cells induces a rapid IFN response that requires ongoing proliferation. The inflammatory phenotype of Trex1-/- mice was partially rescued by additional knock out of exonuclease 1, a multifunctional enzyme providing 5' flap endonuclease activity for Okazaki fragment processing and postreplicative ribonucleotide excision repair. Our data imply genome replication as a source of DNA waste with pathogenic potential that is efficiently degraded by TREX1.
    Keywords:  Exo1; Trex1; cytosolic DNA; interferonopathy; replication; type I interferon
    DOI:  https://doi.org/10.3389/fimmu.2022.880413
  6. J Mol Med (Berl). 2022 Jun;100(6): 963-971
    Leukocyte cytokine responses in adult patients with mitochondrial DNA defects.
    Kalpita R Karan, Caroline Trumpff, Marissa Cross, Kristin M Engelstad, Anna L Marsland, Peter J McGuire, Michio Hirano, Martin Picard.
      Patients with oxidative phosphorylation (OxPhos) defects causing mitochondrial diseases appear particularly vulnerable to infections. Although OxPhos defects modulate cytokine production in vitro and in animal models, little is known about how circulating leukocytes of patients with inherited mitochondrial DNA (mtDNA) defects respond to acute immune challenges. In a small cohort of healthy controls (n = 21) and patients (n = 12) with either the m.3243A > G mutation or single, large-scale mtDNA deletions, we examined (i) cytokine responses (IL-6, TNF-α, IL-1β) in response to acute lipopolysaccharide (LPS) exposure and (ii) sensitivity to the immunosuppressive effects of glucocorticoid signaling (dexamethasone) on cytokine production. In dose-response experiments to determine the half-maximal effective LPS concentration (EC50), relative to controls, leukocytes from patients with mtDNA deletions showed 74-79% lower responses for IL-6 and IL-1β (pIL-6 = 0.031, pIL-1β = 0.009). Moreover, whole blood from patients with mtDNA deletions (pIL-6 = 0.006), but not patients with the m.3243A > G mutation, showed greater sensitivity to the immunosuppressive effects of dexamethasone. Together, these ex vivo data provide preliminary evidence that some systemic OxPhos defects may compromise immune cytokine responses and increase the sensitivity to immune cytokine suppression by glucocorticoids. Further work in larger cohorts is needed to define the nature of immune dysregulation in patients with mitochondrial disease, and their potential implications for disease phenotypes. KEY MESSAGES: Little is known about leukocyte cytokine responses in patients with mitochondrial diseases. Leukocytes of patients with mtDNA deletions show blunted LPS sensitivity and cytokine responses. Leukocytes of patients with mtDNA deletions are more sensitive to glucocorticoid-mediated IL-6 suppression. Work in larger cohorts is needed to delineate potential immune alterations in mitochondrial diseases.
    Keywords:  3243A > G; Cytokine; Glucocorticoid; Inflammation; Inflammation Suppression; Interleukin; Mitochondrial disease; mtDNA deletion
    DOI:  https://doi.org/10.1007/s00109-022-02206-2
  7. Acta Pharm Sin B. 2022 May;12(5): 2533-2549
    Stimuli-responsive nano vehicle enhances cancer immunotherapy by coordinating mitochondria-targeted immunogenic cell death and PD-L1 blockade.
    Qiuyi Li, Cheng Chen, Jinxia Kong, Lian Li, Junlin Li, Yuan Huang.
      Induction of immunogenic cell death promotes antitumor immunity against cancer. However, majority of clinically-approved drugs are unable to elicit sufficient ICD. Here, our study revealed that mitochondria-targeted delivery of doxorubicin (DOX) massively amplified ICD via substantial generation of reactive oxygen species (ROS) after mitochondrial damage. The underlying mechanism behind increased ICD was further demonstrated to be ascribed to two pathways: (1) ROS elevated endoplasmic reticulum (ER) stress, leading to surface exposure of calreticulin; (2) ROS promoted release of various mitochondria-associated damage molecules including mitochondrial transcription factor A. Nevertheless, adaptive upregulation of PD-L1 was found after such ICD-inducing treatment. To overcome such immunosuppressive feedback, we developed a tumor stimuli-responsive nano vehicle to simultaneously exert mitochondrial targeted ICD induction and PD-L1 blockade. The nano vehicle was self-assembled from ICD-inducing copolymer and PD-L1 blocking copolymer, and possessed long-circulating property which contributed to better tumor accumulation and mitochondrial targeting. As a result, the nano vehicle remarkably activated antitumor immune responses and exhibited robust antitumor efficacy in both immunogenic and non-immunogenic tumor mouse models.
    Keywords:  Antitumor efficacy; Antitumor immune responses; Endoplasmic reticulum stress; Immunogenic cell death; Mitochondria-associated damage molecules; Mitochondrial targeting; PD-L1 blockade; Stimuli-responsive
    DOI:  https://doi.org/10.1016/j.apsb.2021.11.005
  8. Trends Immunol. 2022 May 27. pii: S1471-4906(22)00097-7. [Epub ahead of print]
    Putative role of STING-mitochondria associated membrane crosstalk in immunity.
    Chenyu Xue, Na Dong, Anshan Shan.
      Stimulator of interferon genes (STING) has emerged as a key regulator of innate immunity, recognizing intracellular exogenous and endogenous DNA. Recent findings reveal that STING has multiple cell-specific immune functions in various pathological settings, including pathogenic infections, cancer, and autoimmune diseases. Here, we hypothesize that this unique location of STING in the mitochondria-associated membrane (MAM) might lead to the specificity of the cellular functions of STING mediated by mitochondria-ER communication. This new insight suggests that STING on the MAM might act as a hub that translates multiple cues on MAM into distinct cellular responses. This innovative view of STING biology might impart insights for future putative treatments in cancer and immune diseases that have been attributed to STING dysfunction.
    DOI:  https://doi.org/10.1016/j.it.2022.04.011
  9. Nat Commun. 2022 Jun 02. 13(1): 3069
    Artificial neural networks enable genome-scale simulations of intracellular signaling.
    Avlant Nilsson, Joshua M Peters, Nikolaos Meimetis, Bryan Bryson, Douglas A Lauffenburger.
      Mammalian cells adapt their functional state in response to external signals in form of ligands that bind receptors on the cell-surface. Mechanistically, this involves signal-processing through a complex network of molecular interactions that govern transcription factor activity patterns. Computer simulations of the information flow through this network could help predict cellular responses in health and disease. Here we develop a recurrent neural network framework constrained by prior knowledge of the signaling network with ligand-concentrations as input and transcription factor-activity as output. Applied to synthetic data, it predicts unseen test-data (Pearson correlation r = 0.98) and the effects of gene knockouts (r = 0.8). We stimulate macrophages with 59 different ligands, with and without the addition of lipopolysaccharide, and collect transcriptomics data. The framework predicts this data under cross-validation (r = 0.8) and knockout simulations suggest a role for RIPK1 in modulating the lipopolysaccharide response. This work demonstrates the feasibility of genome-scale simulations of intracellular signaling.
    DOI:  https://doi.org/10.1038/s41467-022-30684-y
  10. PLoS One. 2022 ;17(6): e0268391
    Targeting mitochondrial DNA polymerase gamma for selective inhibition of MLH1 deficient colon cancer growth.
    Berna Somuncu, Aysegul Ekmekcioglu, Fatma Merve Antmen, Tugce Ertuzun, Emre Deniz, Nazli Keskin, Joon Park, Ilgu Ece Yazici, Busra Simsek, Batu Erman, Whitney Yin, Burak Erman, Meltem Muftuoglu.
      Synthetic lethality in DNA repair pathways is an important strategy for the selective treatment of cancer cells without harming healthy cells and developing cancer-specific drugs. The synthetic lethal interaction between the mismatch repair (MMR) protein, MutL homolog 1 (MLH1), and the mitochondrial base excision repair protein, DNA polymerase γ (Pol γ) was used in this study for the selective treatment of MLH1 deficient cancers. Germline mutations in the MLH1 gene and aberrant MLH1 promoter methylation result in an increased risk of developing many cancers, including nonpolyposis colorectal and endometrial cancers. Because the inhibition of Pol γ in MLH1 deficient cancer cells provides the synthetic lethal selectivity, we conducted a comprehensive small molecule screening from various databases and chemical drug library molecules for novel Pol γ inhibitors that selectively kill MLH1 deficient cancer cells. We characterized these Pol γ inhibitor molecules in vitro and in vivo, and identified 3,3'-[(1,1'-Biphenyl)-4',4'-diyl)bis(azo)]bis[4-amino-1-naphthalenesulfonic acid] (congo red; CR; Zinc 03830554) as a high-affinity binder to the Pol γ protein and potent inhibitor of the Pol γ strand displacement and one-nucleotide incorporation DNA synthesis activities in vitro and in vivo. CR reduced the cell proliferation of MLH1 deficient HCT116 human colon cancer cells and suppressed HCT116 xenograft tumor growth whereas it did not affect the MLH1 proficient cell proliferation and xenograft tumor growth. CR caused mitochondrial dysfunction and cell death by inhibiting Pol γ activity and oxidative mtDNA damage repair, increasing the production of reactive oxygen species and oxidative mtDNA damage in MLH1 deficient cells. This study suggests that the Pol γ inhibitor, CR may be further evaluated for the MLH1 deficient cancers' therapy.
    DOI:  https://doi.org/10.1371/journal.pone.0268391
  11. Mol Cell. 2022 May 26. pii: S1097-2765(22)00442-7. [Epub ahead of print]
    A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs.
    Xuhang Liu, Wenbin Mei, Veena Padmanaban, Hanan Alwaseem, Henrik Molina, Maria C Passarelli, Bernardo Tavora, Sohail F Tavazoie.
      Stress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to humans; yet, its mechanistic underpinnings and pathological consequences remain poorly defined. Small RNA profiling revealed increased abundance of a cysteine tRNA fragment (5'-tRFCys) during breast cancer metastatic progression. 5'-tRFCys was required for efficient breast cancer metastatic lung colonization and cancer cell survival. We identified Nucleolin as the direct binding partner of 5'-tRFCys. 5'-tRFCys promoted the oligomerization of Nucleolin and its bound metabolic transcripts Mthfd1l and Pafah1b1 into a higher-order transcript stabilizing ribonucleoprotein complex, which protected these transcripts from exonucleolytic degradation. Consistent with this, Mthfd1l and Pafah1b1 mediated pro-metastatic and metabolic effects downstream of 5'-tRFCys-impacting folate, one-carbon, and phosphatidylcholine metabolism. Our findings reveal that a tRF can promote oligomerization of an RNA-binding protein into a transcript stabilizing ribonucleoprotein complex, thereby driving specific metabolic pathways underlying cancer progression.
    Keywords:  Mthfd1l; Pafah1b1; breast cancer; metastasis; nucleolin; oligomerization; post-transcriptional; tRF; tRNA fragment; transcript stability
    DOI:  https://doi.org/10.1016/j.molcel.2022.05.008
  12. Mol Biol Rep. 2022 May 30.
    Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells.
    Nupur Bhargava, Priya Thakur, Thulasi Priyadharshini Muruganandam, Shashank Jaitly, Pragya Gupta, Neelam Lohani, Sangam Giri Goswami, Vinodh Saravanakumar, Saurabh Kumar Bhattacharya, Suman Jain, Sivaprakash Ramalingam.
      BACKGROUND: Disease-specific human induced pluripotent stem cells (hiPSCs) can be generated directly from individuals with known disease characteristics or alternatively be modified using genome editing approaches to introduce disease causing genetic mutations to study the biological response of those mutations. The genome editing procedure in hiPSCs is still inefficient, particularly when it comes to homology directed repair (HDR) of genetic mutations or targeted transgene insertion in the genome and single cell cloning of edited cells. In addition, genome editing processes also involve additional cellular stresses such as poor cell viability and genetic stability of hiPSCs. Therefore, efficient workflows are desired to increase genome editing application to hiPSC disease models and therapeutic applications.METHODS AND RESULTS: To this end, we demonstrate an efficient workflow for feeder-free single cell clone generation and expansion in both CRISPR-mediated knock-out (KO) and knock-in (KI) hiPSC lines. Using StemFlex medium and CloneR supplement in conjunction with Matrigel cell culture matrix, we show that cell viability and expansion during single-cell cloning in edited and unedited cells is significantly enhanced. Keeping all factors into account, we have successfully achieved hiPSC single-cell survival and cloning in both edited and unedited cells with rates as maximum as 70% in less than 2 weeks.
    CONCLUSION: This simplified and efficient workflow will allow for a new level of sophistication in generating hiPSC-based disease models to promote rapid advancement in basic research and also the development of novel cellular therapeutics.
    Keywords:  Disease modeling; Drug discovery; Genome-editing; Induced pluripotent stem cells; Regenerative medicine; Single-cell cloning
    DOI:  https://doi.org/10.1007/s11033-022-07621-9
This page is being maintained by Thomas Krichel. It was last updated on 2022‒06‒06 at 13:38:48.