bims-momema Biomed News
on Molecular mechanisms of macropinocytosis
Issue of 2022–02–13
eightteen papers selected by
Harilaos Filippakis, Harvard University
  1. The hallmarks of cancer metabolism: Still emerging.
  2. Targeting fuel pocket of cancer cell metabolism: A focus on glutaminolysis.
  3. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy.
  4. A mechanistic modeling framework reveals the key principles underlying tumor metabolism.
  5. Personalized Medicine for Prostate Cancer: Is Targeting Metabolism a Reality?
  6. Developmental and molecular response of bovine embryos to reduced nutrients in vitro.
  7. Increased mitochondrial proline metabolism sustains proliferation and survival of colorectal cancer cells.
  8. Deferoxamine Counteracts Cisplatin Resistance in A549 Lung Adenocarcinoma Cells by Increasing Vulnerability to Glutamine Deprivation-Induced Cell Death.
  9. Branched-Chain Amino Acid Metabolism in the Failing Heart.
  10. RAS-mediated tumor stress adaptation and the targeting opportunities it presents.
  11. Dynamic alteration of poroelastic attributes as determinant membrane nanorheology for endocytosis of organ specific targeted gold nanoparticles.
  12. Aptamer-armed nanostructures improve the chemotherapy outcome of triple-negative breast cancer.
  13. Structure-Function of TMEM16 Ion Channels and Lipid Scramblases.
  14. Signaling events that occur when cells of Escherichia coli encounter a glass surface.
  15. Tricyclic cell-penetrating peptides for efficient delivery of functional antibodies into cancer cells.
  16. Mammalian Cells Exocytose Alkylated Gold Nanoparticles via Extracellular Vesicles.
  17. Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins.
  18. DEG/ENaC Ion Channels in the Function of the Nervous System: From Worm to Man.
  1. Cell Metab. 2022 Feb 01. pii: S1550-4131(22)00022-5. [Epub ahead of print]
    The hallmarks of cancer metabolism: Still emerging.
    Natalya N Pavlova, Jiajun Zhu, Craig B Thompson.
      Metabolism of cancer cells is geared toward biomass production and proliferation. Since the metabolic resources within the local tissue are finite, this can lead to nutrient depletion and accumulation of metabolic waste. To maintain growth in these conditions, cancer cells employ a variety of metabolic adaptations, the nature of which is collectively determined by the physiology of their cell of origin, the identity of transforming lesions, and the tissue in which cancer cells reside. Furthermore, select metabolites not only serve as substrates for energy and biomass generation, but can also regulate gene and protein expression and influence the behavior of non-transformed cells in the tumor vicinity. As they grow and metastasize, tumors can also affect and be affected by the nutrient distribution within the body. In this hallmark update, recent advances are incorporated into a conceptual framework that may help guide further research efforts in exploring cancer cell metabolism.
    DOI:  https://doi.org/10.1016/j.cmet.2022.01.007
  2. Biochem Pharmacol. 2022 Feb 04. pii: S0006-2952(22)00037-5. [Epub ahead of print] 114943
    Targeting fuel pocket of cancer cell metabolism: A focus on glutaminolysis.
    Shagun Sharma, Navneet Agnihotri, Sandeep Kumar.
      Advances in cell metabolism over the past few decades have demonstrated glutamine as an essential nutrient for cancer cell survival and proliferation. Glutamine offers a remarkable capacity to fuel diverse metabolic pathways in cancer cells including the Krebs cycle, maintenance of redox homeostasis, and synthesis of cellular building blocks such as nucleic acids, fatty acids, glutathione, and other amino acids. The increase in glutaminolysis has further been linked to the accumulation of oncometabolites such as 2HG (2-Hydroxyglutarate), succinate, fumarate, etc., thereby contributing to tumorigenesis via regulating epigenetic modification of imprinted genes. Therefore, therapeutic targeting of glutaminolysis in cancer cells is worth exploring for possible treatment strategies for cancer management. In this review, we have discussed the detailed mechanism of glutamine uptake, transport, and its instrumental role in rewiring the metabolic adaptation of cancer cells in the tumor microenvironment under nutrient deprivation and hypoxia. Furthermore, we have attempted to provide an updated therapeutic intervention of glutamine metabolism as a treatment strategy for cancer management.
    Keywords:  Cancer Cell Metabolism; Glutamine; Glutaminolysis; Tumor Microenvironment, Chemotherapy
    DOI:  https://doi.org/10.1016/j.bcp.2022.114943
  3. Cancer Res. 2022 Feb 11. pii: canres.1168.2021. [Epub ahead of print]
    Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy.
    Mario R Fernandez, Franz X Schaub, Chunying Yang, Weimin Li, Seongseok Yun, Stephanie K Schaub, Frank C Dorsey, Min Liu, Meredith A Steeves, Andrea Ballabio, Alexandar Tzankov, Zhihua Chen, John M Koomen, Anders E Berglund, John L Cleveland.
      MYC family oncoproteins are regulators of metabolic reprogramming that sustains cancer cell anabolism. Normal cells adapt to nutrient-limiting conditions by activating autophagy, which is required for amino acid (AA) homeostasis. Here we report that the autophagy pathway is suppressed by Myc in normal B cells, in premalignant and neoplastic B cells of Eμ-Myc transgenic mice, and in human MYC-driven Burkitt lymphoma. Myc suppresses autophagy by antagonizing the expression and function of transcription factor EB (TFEB), a master regulator of autophagy. Mechanisms that sustained AA pools in MYC-expressing B cells include coordinated induction of the proteasome and increases in AA transport. Reactivation of the autophagy-lysosomal pathway by TFEB disabled the malignant state by disrupting mitochondrial functions, proteasome activity, amino acid transport, and amino acid and nucleotide metabolism, leading to metabolic anergy, growth arrest and apoptosis. This phenotype provides therapeutic opportunities to disable MYC-driven malignancies, including AA restriction and treatment with proteasome inhibitors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1168
  4. PLoS Comput Biol. 2022 Feb 11. 18(2): e1009841
    A mechanistic modeling framework reveals the key principles underlying tumor metabolism.
    Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine.
      While aerobic glycolysis, or the Warburg effect, has for a long time been considered a hallmark of tumor metabolism, recent studies have revealed a far more complex picture. Tumor cells exhibit widespread metabolic heterogeneity, not only in their presentation of the Warburg effect but also in the nutrients and the metabolic pathways they are dependent on. Moreover, tumor cells can switch between different metabolic phenotypes in response to environmental cues and therapeutic interventions. A framework to analyze the observed metabolic heterogeneity and plasticity is, however, lacking. Using a mechanistic model that includes the key metabolic pathways active in tumor cells, we show that the inhibition of phosphofructokinase by excess ATP in the cytoplasm can drive a preference for aerobic glycolysis in fast-proliferating tumor cells. The differing rates of ATP utilization by tumor cells can therefore drive heterogeneity with respect to the presentation of the Warburg effect. Building upon this idea, we couple the metabolic phenotype of tumor cells to their migratory phenotype, and show that our model predictions are in agreement with previous experiments. Next, we report that the reliance of proliferating cells on different anaplerotic pathways depends on the relative availability of glucose and glutamine, and can further drive metabolic heterogeneity. Finally, using treatment of melanoma cells with a BRAF inhibitor as an example, we show that our model can be used to predict the metabolic and gene expression changes in cancer cells in response to drug treatment. By making predictions that are far more generalizable and interpretable as compared to previous tumor metabolism modeling approaches, our framework identifies key principles that govern tumor cell metabolism, and the reported heterogeneity and plasticity. These principles could be key to targeting the metabolic vulnerabilities of cancer.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009841
  5. Front Oncol. 2021 ;11 778761
    Personalized Medicine for Prostate Cancer: Is Targeting Metabolism a Reality?
    Gio Fidelito, Matthew J Watt, Renea A Taylor.
      Prostate cancer invokes major shifts in gene transcription and metabolic signaling to mediate alterations in nutrient acquisition and metabolic substrate selection when compared to normal tissues. Exploiting such metabolic reprogramming is proposed to enable the development of targeted therapies for prostate cancer, yet there are several challenges to overcome before this becomes a reality. Herein, we outline the role of several nutrients known to contribute to prostate tumorigenesis, including fatty acids, glucose, lactate and glutamine, and discuss the major factors contributing to variability in prostate cancer metabolism, including cellular heterogeneity, genetic drivers and mutations, as well as complexity in the tumor microenvironment. The review draws from original studies employing immortalized prostate cancer cells, as well as more complex experimental models, including animals and humans, that more accurately reflect the complexity of the in vivo tumor microenvironment. In synthesizing this information, we consider the feasibility and potential limitations of implementing metabolic therapies for prostate cancer management.
    Keywords:  lipid metabolism; metabolic heterogeneity; metabolic targeting; metabolism; obesity; patient-derived xenograft; prostate neoplasia
    DOI:  https://doi.org/10.3389/fonc.2021.778761
  6. Reprod Fertil. 2020 Jul;1(1): 51-65
    Developmental and molecular response of bovine embryos to reduced nutrients in vitro.
    Jason R Herrick, Sandeep Rajput, Rolando Pasquariello, Alison Ermisch, Nicolas Santiquet, William B Schoolcraft, Rebecca L Krisher.
      Recent studies in our laboratory have indicated that bovine embryos only use a small amount of the nutrients available to them in culture. Our objective was to evaluate the developmental and molecular response of bovine embryos when nutrient concentrations in the culture medium were significantly reduced. Following IVM and IVF, embryos were cultured in media containing 75, 50, and 25% (experiment 1) or 25, 12.5, and 6.25% (experiment 2) of the concentrations of nutrients (carbohydrates, amino acids, and vitamins) present in our control medium (100%). Blastocyst formation, hatching, and allocation of cells to the inner cell mass (ICM) and trophectoderm (TE) were evaluated on day 7. Although the number of TE cells was decreased (P < 0.05) when nutrient concentrations were ≤25% (73.8-124.1 cells), it was not until nutrient concentrations were reduced to 6.25% that blastocyst formation (18.3 ± 3.0%) and hatching (3.0 ± 1.3%) were inhibited (P < 0.05) compared to embryos cultured in the control medium (156.1 ± 14.1 cells, 40.0 ± 3.8%, 20.0 ± 3.1%, respectively). Inhibition of fatty acid oxidation (etomoxir) reduced (P < 0.05) blastocyst development, with more pronounced effects at lower nutrient concentrations (≤12.5%). Reducing nutrient concentrations was associated with increased activity of AMPK, decreased activity of mTOR, and altered abundance of transcripts for hexokinase 1 (HK1), carnitine palmitoyl transferase 2 (CPT2), lactate dehydrogenase A (LDHA), and pyruvate dehydrogenase kinase 1 (PDK1), consistent with an increase in glucose and fatty acid metabolism. Reduced nutrient conditions provide a unique perspective on embryo metabolism that may facilitate the optimization of culture media.
    Lay summary: To support early embryo development in the first week after fertilisation, an appropriate mixture of nutrients (carbohydrates, amino acids, and vitamins) is needed in the culturing solution. However, refining these solutions to support optimal embryo health remains challenging. In this study, bovine (cow) embryos derived from abattoir material were used as a model for the development of other mammalian embryos, including humans. These embryos were cultured in the presence of 75, 50, 25, 12.5, or 6.25% of the nutrients present in control conditions (100%), which are similar to those reported for the fluids of the fallopian tubes and uterus. Embryo development was largely unaffected in the 75, 50, and 25% treatments, with some embryos developing in the presence of only 6.25% nutrients. Cow embryos are remarkably resilient to reduced concentrations of nutrients in their environment because they can utilize internal stores of fat as a source of energy.
    Keywords:  AMPK; blastocyst; fatty acid oxidation; mTOR; metabolism
    DOI:  https://doi.org/10.1530/RAF-20-0033
  7. PLoS One. 2022 ;17(2): e0262364
    Increased mitochondrial proline metabolism sustains proliferation and survival of colorectal cancer cells.
    Saif Sattar Alaqbi, Lynsey Burke, Inna Guterman, Caleb Green, Kevin West, Raquel Palacios-Gallego, Hong Cai, Constantinos Alexandrou, Ni Ni Moe Myint, Emma Parrott, Lynne M Howells, Jennifer A Higgins, Donald J L Jones, Rajinder Singh, Robert G Britton, Cristina Tufarelli, Anne Thomas, Alessandro Rufini.
      Research into the metabolism of the non-essential amino acid (NEAA) proline in cancer has gained traction in recent years. The last step in the proline biosynthesis pathway is catalyzed by pyrroline-5-carboxylate reductase (PYCR) enzymes. There are three PYCR enzymes: mitochondrial PYCR1 and 2 and cytosolic PYCR3 encoded by separate genes. The expression of the PYCR1 gene is increased in numerous malignancies and correlates with poor prognosis. PYCR1 expression sustains cancer cells' proliferation and survival and several mechanisms have been implicated to explain its oncogenic role. It has been suggested that the biosynthesis of proline is key to sustain protein synthesis, support mitochondrial function and nucleotide biosynthesis. However, the links between proline metabolism and cancer remain ill-defined and are likely to be tissue specific. Here we use a combination of human dataset, human tissue and mouse models to show that the expression levels of the proline biosynthesis enzymes are significantly increased during colorectal tumorigenesis. Functionally, the expression of mitochondrial PYCRs is necessary for cancer cells' survival and proliferation. However, the phenotypic consequences of PYCRs depletion could not be rescued by external supplementation with either proline or nucleotides. Overall, our data suggest that, despite the mechanisms underlying the role of proline metabolism in colorectal tumorigenesis remain elusive, targeting the proline biosynthesis pathway is a suitable approach for the development of novel anti-cancer therapies.
    DOI:  https://doi.org/10.1371/journal.pone.0262364
  8. Front Oncol. 2021 ;11 794735
    Deferoxamine Counteracts Cisplatin Resistance in A549 Lung Adenocarcinoma Cells by Increasing Vulnerability to Glutamine Deprivation-Induced Cell Death.
    Wen-Jun Liu, Peng-Yu Pan, Ye Sun, Jian-Bo Wang, Huan Zhou, Xin Xie, Zhi-Yuan Duan, Han-Yu Dong, Wen-Na Chen, Li-de Zhang, Chun Wang.
      Glutamine, like glucose, is a major nutrient consumed by cancer cells, yet these cells undergo glutamine starvation in the cores of tumors, forcing them to evolve adaptive metabolic responses. Pharmacologically targeting glutamine metabolism or withdrawal has been exploited for therapeutic purposes, but does not always induce cancer cell death. The mechanism by which cancer cells adapt to resist glutamine starvation in cisplatin-resistant non-small-cell lung cancer (NSCLC) also remains uncertain. Here, we report the potential metabolic vulnerabilities of A549/DDP (drug-resistant human lung adenocarcinoma cell lines) cells, which were more easily killed by the iron chelator deferoxamine (DFO) during glutamine deprivation than their parental cisplatin-sensitive A549 cells. We demonstrate that phenotype resistance to cisplatin is accompanied by adaptive responses during glutamine deprivation partly via higher levels of autophagic activity and apoptosis resistance characteristics. Moreover, this adaptation could be explained by sustained glucose instead of glutamine-dominant complex II-dependent oxidative phosphorylation (OXPHOS). Further investigation revealed that cisplatin-resistant cells sustain OXPHOS partly via iron metabolism reprogramming during glutamine deprivation. This reprogramming might be responsible for mitochondrial iron-sulfur [Fe-S] cluster biogenesis, which has become an "Achilles' heel," rendering cancer cells vulnerable to DFO-induced autophagic cell death and apoptosis through c-Jun N-terminal kinase (JNK) signaling. Finally, in vivo studies using xenograft mouse models also confirmed the growth-slowing effect of DFO. In summary, we have elucidated the adaptive responses of cisplatin-resistant NSCLC cells, which balanced stability and plasticity to overcome metabolic reprogramming and permitted them to survive under stress induced by chemotherapy or glutamine starvation. In addition, for the first time, we show that suppressing the growth of cisplatin-resistant NSCLC cells via iron chelator-induced autophagic cell death and apoptosis was possible with DFO treatment. These findings provide a solid basis for targeting mitochondria iron metabolism in cisplatin-resistant NSCLC for therapeutic purposes, and it is plausible to consider that DFO facilitates in the improvement of treatment responses in cisplatin-resistant NSCLC patients.
    Keywords:  NSCLC; cell death; cisplatin resistance; deferoxamine; glutamine deprivation; metabolic reprogramming
    DOI:  https://doi.org/10.3389/fonc.2021.794735
  9. Cardiovasc Drugs Ther. 2022 Feb 12.
    Branched-Chain Amino Acid Metabolism in the Failing Heart.
    Qutuba G Karwi, Gary D Lopaschuk.
      Branched-chain amino acids (BCAAs) are essential amino acids which have critical roles in protein synthesis and energy metabolism in the body. In the heart, there is a strong correlation between impaired BCAA oxidation and contractile dysfunction in heart failure. Plasma and myocardial levels of BCAA and their metabolites, namely branched-chain keto acids (BCKAs), are also linked to cardiac insulin resistance and worsening adverse remodelling in the failing heart. This review discusses the regulation of BCAA metabolism in the heart and the impact of depressed cardiac BCAA oxidation on cardiac energy metabolism, function, and structure in heart failure. While impaired BCAA oxidation in the failing heart causes the accumulation of BCAA and BCKA in the myocardium, recent evidence suggested that the BCAAs and BCKAs have divergent effects on the insulin signalling pathway and the mammalian target of the rapamycin (mTOR) signalling pathway. Dietary and pharmacological interventions that enhance cardiac BCAA oxidation and limit the accumulation of cardiac BCAAs and BCKAs have been shown to have cardioprotective effects in the setting of ischemic heart disease and heart failure. Thus, targeting cardiac BCAA oxidation may be a promising therapeutic approach for heart failure.
    Keywords:  Branched-chain amino acids; Branched-chain keto acids; Cardiac insulin resistance; Glucose oxidation; Heart failure
    DOI:  https://doi.org/10.1007/s10557-022-07320-4
  10. Dis Model Mech. 2022 Feb 01. pii: dmm049280. [Epub ahead of print]15(2):
    RAS-mediated tumor stress adaptation and the targeting opportunities it presents.
    Alexandra Redding, Andrew E Aplin, Elda Grabocka.
      Cellular stress is known to function in synergistic cooperation with oncogenic mutations during tumorigenesis to drive cancer progression. Oncogenic RAS is a strong inducer of a variety of pro-tumorigenic cellular stresses, and also enhances the ability of cells to tolerate these stresses through multiple mechanisms. Many of these oncogenic, RAS-driven, stress-adaptive mechanisms have also been implicated in tolerance and resistance to chemotherapy and to therapies that target the RAS pathway. Understanding how oncogenic RAS shapes cellular stress adaptation and how this functions in drug resistance is of vital importance for identifying new therapeutic targets and therapeutic combinations to treat RAS-driven cancers.
    Keywords:  Drug resistance; RAS; RAS-pathway targeting; Stress adaptation; Tumor-associated stress
    DOI:  https://doi.org/10.1242/dmm.049280
  11. J Nanobiotechnology. 2022 Feb 08. 20(1): 74
    Dynamic alteration of poroelastic attributes as determinant membrane nanorheology for endocytosis of organ specific targeted gold nanoparticles.
    Tanmay Kulkarni, Debabrata Mukhopadhyay, Santanu Bhattacharya.
       BACKGROUND: Efficacy of targeted drug delivery using nanoparticles relies on several factors including the uptake mechanisms such as phagocytosis, macropinocytosis, micropinocytosis and receptor mediated endocytosis. These mechanisms have been studied with respect to the alteration in signaling mechanisms, cellular morphology, and linear nanomechanical properties (NMPs). Commonly employed classical contact mechanics models to address cellular NMPs fail to address mesh like structure consisting of bilayer lipids and proteins of cell membrane. To overcome this technical challenge, we employed poroelastic model which accounts for the biphasic nature of cells including their porous behavior exhibiting both solid like (fluid storage) and liquid like (fluid dissipate) behavior.
    RESULTS: In this study, we employed atomic force microscopy to monitor the influence of surface engineering of gold nanoparticles (GNPs) to the alteration of nonlinear NMPs such as drained Poisson's ratio, effective shear stress, diffusion constant and pore dimensions of cell membranes during their uptake. Herein, we used pancreatic cancer (PDAC) cell lines including Panc1, AsPC-1 and endothelial cell (HUVECs) to understand the receptor-dependent and -independent endocytosis of two different GNPs derived using plectin-1 targeting peptide (PTP-GNP) and corresponding scrambled peptide (sPEP-GNP). Compared to untreated cells, in case of receptor dependent endocytosis of PTP-GNPs diffusion coefficient altered ~ 1264-fold and ~ 1530-fold and pore size altered ~ 320-fold and ~ 260-fold in Panc1 and AsPC-1 cells, respectively. Whereas for receptor independent mechanisms, we observed modest alteration in diffusion coefficient and pore size, in these cells compared to untreated cells. Effective shear stress corresponding to 7.38 ± 0.15 kPa and 20.49 ± 0.39 kPa in PTP-GNP treatment in Panc1 and AsPC-1, respectively was significantly more than that for sPEP-GNP. These results demonstrate that with temporal recruitment of plectin-1 during receptor mediated endocytosis affects the poroelastic attributes of the membrane.
    CONCLUSION: This study confirms that nonlinear NMPs of cell membrane are directly associated with the uptake mechanism of nanoparticles and can provide promising insights of the nature of endocytosis mechanism involved for organ specific drug delivery using nanoparticles. Hence, nanomechanical analysis of cell membrane using this noninvasive, label-free and live-cell analytical tool can therefore be instrumental to evaluate therapeutic benefit of nanoformulations.
    Keywords:  Diffusion coefficient; Drained Poisson’s ratio; Effective shear stress; Pancreatic cancer; Plectin-1 targeting; Pore size and Real-time membrane dynamics; Poroelasticity; Receptor mediated endocytosis; Targeted gold nanoparticle
    DOI:  https://doi.org/10.1186/s12951-022-01276-1
  12. Mol Ther. 2022 Feb 07. pii: S1525-0016(22)00087-9. [Epub ahead of print]
    Aptamer-armed nanostructures improve the chemotherapy outcome of triple-negative breast cancer.
    Quanyuan Wan, Zihua Zeng, Jianjun Qi, Zhenghu Chen, Xiaohui Liu, Youli Zu.
      Triple-negative breast cancer is an aggressive subtype of breast cancer that is primarily treated using systemic chemotherapy due to the lack of a specific cell surface marker for drug delivery. Cancer cell-specific aptamer-mediated drug delivery is a promising targeted chemotherapy for marker-unknown cancers. Using a poorly differentiated carcinoma cell-specific DNA aptamer (PDGC21T), we formed a self-assembling circinate DNA nanoparticle (Apt21TNP) that binds triple-negative breast cancer cells. Using our previously designed pH-sensitive dendrimer-conjugated doxorubicin (DDOX) as the payload, we found that each nanoparticle loaded 30 doxorubicin molecules to form an Apt21TNP-DDOX nanomedicine that is stable in human plasma. Upon cell binding, Apt21TNP-DDOX is internalized by triple-negative breast cancer cells through the macropinocytosis pathway. Once inside cells, the low pH microenvironment in lysosomes induces doxorubicin drug payload release from Apt21TNP-DDOX. Our in vitro studies demonstrate that Apt21TNP-DDOX can preferentially bind triple-negative breast cancer cells to induce cell death. Further, we show that Apt21TNP-DDOX can accumulate in subcutaneous MDA-MB-231 tumors in mice following systemic administration to reduce tumor burden, minimize side effects, and improve animal survival. Together, our results demonstrate that Apt21TNP-mediated doxorubicin delivery is a potent, targeted chemotherapy for triple-negative breast cancer that may alleviate side effects in patients.
    DOI:  https://doi.org/10.1016/j.ymthe.2022.02.004
  13. Adv Exp Med Biol. 2021 ;1349 87-109
    Structure-Function of TMEM16 Ion Channels and Lipid Scramblases.
    Son C Le, Huanghe Yang.
      The TMEM16 protein family comprises two novel classes of structurally conserved but functionally distinct membrane transporters that function as Ca2+-dependent Cl- channels (CaCCs) or dual functional Ca2+-dependent ion channels and phospholipid scramblases. Extensive functional and structural studies have advanced our understanding of TMEM16 molecular mechanisms and physiological functions. TMEM16A and TMEM16B CaCCs control transepithelial fluid transport, smooth muscle contraction, and neuronal excitability, whereas TMEM16 phospholipid scramblases mediate the flip-flop of phospholipids across the membrane to allow phosphatidylserine externalization, which is essential in a plethora of important processes such as blood coagulation, bone development, and viral and cell fusion. In this chapter, we summarize the major methods in studying TMEM16 ion channels and scramblases and then focus on the current mechanistic understanding of TMEM16 Ca2+- and voltage-dependent channel gating as well as their ion and phospholipid permeation.
    Keywords:  Anoctamin; CaCC; CaPLSase; Gating; Permeation; Scramblase; TMEM16
    DOI:  https://doi.org/10.1007/978-981-16-4254-8_6
  14. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2116830119. [Epub ahead of print]119(6):
    Signaling events that occur when cells of Escherichia coli encounter a glass surface.
    Alina M Vrabioiu, Howard C Berg.
      Bacterial cells interact with solid surfaces and change their lifestyle from single free-swimming cells to sessile communal structures (biofilms). Cyclic di-guanosine monophosphate (c-di-GMP) is central to this process, yet we lack tools for direct dynamic visualization of c-di-GMP in single cells. Here, we developed a fluorescent protein-based c-di-GMP-sensing system for Escherichia coli that allowed us to visualize initial signaling events and assess the role played by the flagellar motor. The sensor was pH sensitive, and the events that appeared on a seconds' timescale were alkaline spikes in the intracellular pH. These spikes were not apparent when signals from different cells were averaged. Instead, a signal appeared on a minutes' timescale that proved to be due to an increase in intracellular c-di-GMP. This increase, but not the alkaline spikes, depended upon a functional flagellar motor. The kinetics and the amplitude of both the pH and c-di-GMP responses displayed cell-to-cell variability indicative of the distinct ways the cells approached and interacted with the surface. The energetic status of a cell can modulate these events. In particular, the alkaline spikes displayed an oscillatory behavior and the c-di-GMP increase was modest in the presence of glucose.
    Keywords:  biofilm; cAMP; cyclic-di-GMP; pH; surface sensing
    DOI:  https://doi.org/10.1073/pnas.2116830119
  15. Nat Chem. 2022 Feb 10.
    Tricyclic cell-penetrating peptides for efficient delivery of functional antibodies into cancer cells.
    Ole Tietz, Fernando Cortezon-Tamarit, Rod Chalk, Sarah Able, Katherine A Vallis.
      The intracellular environment hosts a large number of cancer- and other disease-relevant human proteins. Targeting these with internalized antibodies would allow therapeutic modulation of hitherto undruggable pathways, such as those mediated by protein-protein interactions. However, one of the major obstacles in intracellular targeting is the entrapment of biomacromolecules in the endosome. Here we report an approach to delivering antibodies and antibody fragments into the cytosol and nucleus of cells using trimeric cell-penetrating peptides (CPPs). Four trimers, based on linear and cyclic sequences of the archetypal CPP Tat, are significantly more potent than monomers and can be tuned to function by direct interaction with the plasma membrane or escape from vesicle-like bodies. These studies identify a tricyclic Tat construct that enables intracellular delivery of functional immunoglobulin-G antibodies and Fab fragments that bind intracellular targets in the cytosol and nuclei of live cells at effective concentrations as low as 1 μM.
    DOI:  https://doi.org/10.1038/s41557-021-00866-0
  16. ACS Nano. 2022 Feb 09.
    Mammalian Cells Exocytose Alkylated Gold Nanoparticles via Extracellular Vesicles.
    Lok Wai Cola Ho, Cecilia Ka Wing Chan, Ruifang Han, Yolanda Fong Yung Lau, Huize Li, Yi-Ping Ho, Xiaohong Zhuang, Chung Hang Jonathan Choi.
      Understanding the exocytosis of nanoparticles (NPs) from cells is valuable because it informs design rules of NPs that support desirable cellular retention for nanomedicine applications, but investigations into the mechanism for the exocytosis of NPs remain scarce. We elucidate the mechanism for the exocytosis of dodecyl-terminated, polyethylene glycol-coated gold NPs (termed "dodecyl-PEG-AuNP"). The Au core enables ultrastructural differentiation of the exocytosed NPs from the nearby extracellular vesicles (EVs). The PEG shell prevents interparticle agglomeration or aggregation that disfavors exocytosis. The minute amounts of alkyl chains on the PEG shell not only promote cellular uptake but also improve exocytosis by up to 4-fold higher probability and upregulate exocytosis- and vesicle-related genes. After entering Kera-308 keratinocytes and trafficking to multivesicular bodies and lysosomes, these NPs exit the cell predominantly via unconventional exocytosis, accompanied by enhanced secretion of sub-100 nm, CD81-enriched exosomes. The pathway for NP exocytosis and subpopulation of EVs that are secreted alongside the exocytosed NPs depends on dodecyl loading. This work provides insights into dissecting the mechanism of NP exocytosis and its relationship with EV secretion.
    Keywords:  alkylation; exocytosis; exosomes; extracellular vesicles; gold nanoparticles; lysosomes; multivesicular bodies
    DOI:  https://doi.org/10.1021/acsnano.1c07418
  17. Annu Rev Biophys. 2022 Feb 08.
    Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins.
    Cecilia Tommos.
      Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, are active substrates, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-biophys-100521-103031
  18. Adv Exp Med Biol. 2021 ;1349 165-192
    DEG/ENaC Ion Channels in the Function of the Nervous System: From Worm to Man.
    Laura Bianchi.
      DEG/ENaC channels are voltage-independent Na+/Ca2+ channels that are conserved across species and are expressed in many different cell types and tissues, where they contribute to a wide array of physiological functions from transepithelial Na+ transport, to sensory perception, and learning and memory. In this chapter, we focus on the members of this family that are expressed in the nervous system, grouping them based on their function. Structurally, DEG/ENaC channels are trimers formed by either identical or homologous subunits, each one protruding from the plasma membrane like a clenched hand. Crystallographic studies on chicken ASIC1a in the closed, inactivated, and open states revealed important details about the gating and permeation properties of these channels, and overall they show that the extracellular domain of the channel undergoes large conformational changes during gating. The vast majority of the channel's extracellular domain is conserved across different members and species; however, key changes including the insertion of extra loops near the finger and palm domains most likely confers gating specificity. Indeed, DEG/ENaC channels are gated by a wide range of stimuli, including mechanical forces, protons, and peptides, owing to the wide array of physiological functions they serve. Interestingly, DEG/ENaC channels are not only expressed in neurons but also in glia. Work in C. elegans is now beginning to shed new light on the role of glial DEG/ENaC in the function of the nervous system and suggests that they may be implicated in controlling ionic concentrations in the extracellular microenvironment. Finally, DEG/ENaC channels can become toxic and cause neuronal death when they are hyperactivated by genetic mutations or prolonged acidosis causing them to contribute to neuronal demise in stroke and ischemia. Taken together, molecular, structural, and behavioral work on DEG/ENaC channels expressed in the nervous system of different species highlights the crucial role of these channels in neuronal function. These data place DEG/ENaC channels in an excellent position for being considered as drug targets for the treatment of several neurological conditions and disorders from pain to epilepsy and ischemia.
    Keywords:  ASIC; C. elegans; DEG/ENaC; Drosophila; Ischemia; MEC-4; Paraoxonase; Stomatin; Touch
    DOI:  https://doi.org/10.1007/978-981-16-4254-8_9
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