bims-tubesc 2022-11-13 papers

bims-tubesc

Biomed News

on Molecular mechanisms in tuberous sclerosis

Issue of 2022‒11‒13
eight papers selected by
Marti Cadena Sandoval
Columbia University

An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss.
Identification of the electrogenic 2Cl-/H+ exchanger, ClC5, as a chloride secreting transporter candidate in kidney cyst epithelium in tuberous sclerosis.
Role of mTOR1 signaling in the antidepressant effects of ketamine and the potential of mTORC1 activators as novel antidepressants.
The Impact of TSC-1 and -2 Mutations on Response to Therapy in Malignant PEComa: A Multicenter Retrospective Analysis.
The MASTL/PP2A cell cycle kinase-phosphatase module restrains PI3K-Akt activity in an mTORC1-dependent manner.
The Genetic Variability of Members of the SLC38 Family of Amino Acid Transporters (SLC38A3, SLC38A7 and SLC38A9) Affects Susceptibility to Type 2 Diabetes and Vascular Complications.
Longin domain GAP complexes in nutrient signaling, membrane traffic, and neurodegeneration.
How cells recognize and remove the perforated lysosome.

Nat Commun. 2022 Nov 10. 13(1): 6808

An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss.

Kaushal Asrani, Juhyung Woo, Adrianna A Mendes, Ethan Schaffer, Thiago Vidotto, Clarence Rachel Villanueva, Kewen Feng, Lia Oliveira, Sanjana Murali, Hans B Liu, Daniela C Salles, Brandon Lam, Pedram Argani, Tamara L Lotan.

The mechanistic target of rapamycin complex 1 (mTORC1) integrates inputs from growth factors and nutrients, but how mTORC1 autoregulates its activity remains unclear. The MiT/TFE transcription factors are phosphorylated and inactivated by mTORC1 following lysosomal recruitment by RagC/D GTPases in response to amino acid stimulation. We find that starvation-induced lysosomal localization of the RagC/D GAP complex, FLCN:FNIP2, is markedly impaired in a mTORC1-sensitive manner in renal cells with TSC2 loss, resulting in unexpected TFEB hypophosphorylation and activation upon feeding. TFEB phosphorylation in TSC2-null renal cells is partially restored by destabilization of the lysosomal folliculin complex (LFC) induced by FLCN mutants and is fully rescued by forced lysosomal localization of the FLCN:FNIP2 dimer. Our data indicate that a negative feedback loop constrains amino acid-induced, FLCN:FNIP2-mediated RagC activity in renal cells with constitutive mTORC1 signaling, and the resulting MiT/TFE hyperactivation may drive oncogenesis with loss of the TSC2 tumor suppressor.

DOI: https://doi.org/10.1038/s41467-022-34617-7
Am J Pathol. 2022 Nov 03. pii: S0002-9440(22)00356-X. [Epub ahead of print]

Identification of the electrogenic 2Cl-/H+ exchanger, ClC5, as a chloride secreting transporter candidate in kidney cyst epithelium in tuberous sclerosis.

Sharon Barone, Marybeth Brooks, Kamyar Zahedi, L Shannon Holliday, John Bissler, Jane J Yu, Manoocher Soleimani.

Kidney cyst expansion in Tuberous Sclerosis Complex (TSC) or Polycystic Kidney Disease (PKD) requires active secretion of chloride into the cyst lumen. In PKD, Cl- secretion is primarily mediated via CFTR in principal cells. Kidney cystogenesis in TSC is predominantly comprised of A-intercalated cells, which do not exhibit noticeable expression of CFTR. The identity of the Cl- secreting molecule(s) in TSC cyst epithelia remains speculative. Based on RNA seq analysis studies, we examined the expression of FOXi1, the chief regulator of acid base transporters in intercalated cells, along with localization of ClC-5, in kidneys of various models of TSC. Our results in Tsc2+/- mice demonstrate that the expansion of kidney cysts corresponds to the induction of Foxi1 and correlates with the strong appearance of ClC-5 and H+-ATPase on the apical membrane of cyst epithelia. In various mouse models of TSC, Foxi1 is robustly induced in the kidney, and ClC-5 appears along with H+-ATPase on the apical membrane of cyst epithelia. Expression of ClC-5 was also detected on the apical membrane of cyst epithelia in humans with TSC but was absent in humans with ADPKD or in a mouse model of PKD. These results indicate that ClC-5 is expressed on the apical membrane of cyst epithelia and is a likely candidate mediating Cl- secretion into the kidney cyst lumen in TSC.

DOI: https://doi.org/10.1016/j.ajpath.2022.10.007
Neuropharmacology. 2022 Nov 02. pii: S0028-3908(22)00384-7. [Epub ahead of print] 109325

Role of mTOR1 signaling in the antidepressant effects of ketamine and the potential of mTORC1 activators as novel antidepressants.

Taro Kato.

  Conventional antidepressant medications act on monoaminergic systems and have important limitations, including a therapeutic delay of weeks to months and low rates of efficacy. Recently, clinical findings have indicated that ketamine, a dissociative anesthetic that blocks N-methyl-d-aspartate receptor channel activity, causes rapid and long-lasting antidepressant effects. Although the exact mechanisms underlying the antidepressant effects of ketamine are not fully known, preclinical studies have demonstrated a key role for mechanistic target of rapamycin complex 1 (mTORC1) signaling and a subsequent increase in synapse formation in the medial prefrontal cortex. In this review, we discuss the role of mTORC1 and its subsequent signaling cascade in the antidepressant effects of ketamine and other compounds with glutamatergic mechanisms of action. We also present the possibility that mTORC1 signaling itself is a drug discovery target.

Keywords:  Antidepressants; Glutamatergic signaling; Ketamine; Major depressive disorder; mTOR; mTORC1

DOI:  https://doi.org/10.1016/j.neuropharm.2022.109325
Genes (Basel). 2022 Oct 24. pii: 1932. [Epub ahead of print]13(11):

The Impact of TSC-1 and -2 Mutations on Response to Therapy in Malignant PEComa: A Multicenter Retrospective Analysis.

Lawrence Liu, Carina Dehner, Nikhil Grandhi, Yang Lyu, Dana C Borcherding, John S A Chrisinger, Xiao Zhang, Jingqin Luo, Yu Tao, Amanda Parkes, Nam Q Bui, Elizabeth J Davis, Mohammed M Milhem, Varun Monga, Mia Weiss, Brian Van Tine, Angela C Hirbe.

  BACKGROUND: Perivascular epithelioid cell neoplasms (PEComas) are a diverse family of mesenchymal tumors with myomelanocytic differentiation that disproportionately affect women and can be associated with tuberous sclerosis (TS). Although mTOR inhibition is widely used as first-line treatment, it is unclear what genomic alterations exist in these tumors and how they influence the response to therapy.METHODS: This was a multicenter study conducted at five sites within the US. The data were collected from 1 January 2004 to 31 January 2021. We conducted a retrospective analysis to identify PEComa patients with next-generation sequencing (NGS) data and compared outcomes based on mutations.
RESULTS: No significant differences in survival were identified between TSC-1 and TSC-2 mutated PEComa or TSC-1/-2 versus other mutations. No significant difference was seen in progression-free survival (PFS) after first-line therapy between mTOR inhibition versus other systemic therapies.
CONCLUSIONS: We were unable to detect differences in survival based on genomic alterations or PFS between mTOR inhibition versus other systemic therapies. Future studies should seek to identify other drivers of TSC-1/-2 silencing that could predict response to mTOR inhibition.

Keywords:  PEComa; angiomyolipoma; everolimus; lymphangiomyomatosis; mTOR inhibitor; sirolimus; temsirolimus

DOI:  https://doi.org/10.3390/genes13111932
EMBO J. 2022 Nov 10. e110833

The MASTL/PP2A cell cycle kinase-phosphatase module restrains PI3K-Akt activity in an mTORC1-dependent manner.

Belén Sanz-Castillo, Begoña Hurtado, Diana Vara-Ciruelos, Aicha El Bakkali, Dario Hermida, Beatriz Salvador-Barbero, Diego Martínez-Alonso, José González-Martínez, Clara Santiveri, Ramón Campos-Olivas, Pilar Ximénez-Embún, Javier Muñoz, Mónica Álvarez-Fernández, Marcos Malumbres.

  The AKT-mTOR pathway is a central regulator of cell growth and metabolism. Upon sustained mTOR activity, AKT activity is attenuated by a feedback loop that restrains upstream signaling. However, how cells control the signals that limit AKT activity is not fully understood. Here, we show that MASTL/Greatwall, a cell cycle kinase that supports mitosis by phosphorylating the PP2A/B55 inhibitors ENSA/ARPP19, inhibits PI3K-AKT activity by sustaining mTORC1- and S6K1-dependent phosphorylation of IRS1 and GRB10. Genetic depletion of MASTL results in an inefficient feedback loop and AKT hyperactivity. These defects are rescued by the expression of phosphomimetic ENSA/ARPP19 or inhibition of PP2A/B55 phosphatases. MASTL is directly phosphorylated by mTORC1, thereby limiting the PP2A/B55-dependent dephosphorylation of IRS1 and GRB10 downstream of mTORC1. Downregulation of MASTL results in increased glucose uptake in vitro and increased glucose tolerance in adult mice, suggesting the relevance of the MASTL-PP2A/B55 kinase-phosphatase module in controlling AKT and maintaining metabolic homeostasis.

Keywords:  AKT; MASTL; cell cycle; glucose homeostasis; mTOR

DOI:  https://doi.org/10.15252/embj.2022110833
Nutrients. 2022 Oct 22. pii: 4440. [Epub ahead of print]14(21):

The Genetic Variability of Members of the SLC38 Family of Amino Acid Transporters (SLC38A3, SLC38A7 and SLC38A9) Affects Susceptibility to Type 2 Diabetes and Vascular Complications.

Paolina Crocco, Serena Dato, Alberto Montesanto, Anna Rita Bonfigli, Roberto Testa, Fabiola Olivieri, Giuseppe Passarino, Giuseppina Rose.

  Type 2 Diabetes (T2D) is a metabolic disease associated with long-term complications, with a multifactorial pathogenesis related to the interplay between genetic and modifiable risk factors, of which nutrition is the most relevant. In particular, the importance of proteins and constitutive amino acids (AAs) in disease susceptibility is emerging. The ability to sense and respond to changes in AA supplies is mediated by complex networks, of which AA transporters (AATs) are crucial components acting also as sensors of AA availability. This study explored the associations between polymorphisms in selected AATs genes and T2D and vascular complications in 433 patients and 506 healthy controls. Analyses revealed significant association of SLC38A3-rs1858828 with disease risk. Stratification of patients based on presence/absence of vascular complications highlighted significant associations of SLC7A8-rs3783436 and SLC38A7-rs9806843 with diabetic retinopathy. Additionally, the SLC38A9-rs4865615 resulted associated with chronic kidney disease. Notably, these genes function as AAs sensors, specifically glutamine, leucine, and arginine, linked to the main nutrient signaling pathway mammalian target of rapamycin complex 1 (mTORC1). Thus, their genetic variability may contribute to T2D by influencing the ability to properly transduce a signal activating mTORC1 in response to AA availability. In this scenario, the contribution of dietary AAs supply to disease risk may be relevant.

Keywords:  SLC38 family; Type 2 Diabetes; amino acid availability; amino acid sensing; amino acid transporters; diabetes complications; genetic variability; mTORC1 pathway

DOI:  https://doi.org/10.3390/nu14214440
FEBS Lett. 2022 Nov 11.

Longin domain GAP complexes in nutrient signaling, membrane traffic, and neurodegeneration.

Rachel M Jansen, James H Hurley.

  Small GTPases act as molecular switches and control numerous cellular processes by virtue of their binding and hydrolysis of guanosine triphosphate (GTP). The activity of small GTPases is coordinated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). Recent structural and functional studies have characterized a subset of GAPs whose catalytic units consist of longin domains. Longin domain containing GAPs regulate small GTPases that facilitate nutrient signaling, autophagy, vesicular trafficking, and lysosome homeostasis. All known examples in this GAP family function as part of larger multiprotein complexes. The three characterized mammalian protein complexes in this class are FLCN:FNIP, GATOR1, and C9orf72:SMCR8. Each complex carries out a unique cellular function by regulating distinct small GTPases. In this article, we explore the roles of longin domain GAPs in nutrient sensing, membrane dynamic, vesicular trafficking, and disease. Through a structural lens, we examine the mechanism of each longin domain GAP and highlight potential therapeutic applications.

Keywords:  C9orf72; FLCN; GAPs; GATOR1; GTPase activating proteins; autophagy; membrane trafficking; nutrient signaling; small GTPases

DOI:  https://doi.org/10.1002/1873-3468.14538
Autophagy. 2022 Nov 11. 1-3

How cells recognize and remove the perforated lysosome.

Keisuke Tabata, Marika Saeki, Tamotsu Yoshimori, Maho Hamasaki.

  Macroautophagy (hereafter autophagy) is a highly conserved intracellular degradation system to maintain cellular homeostasis by degrading cellular components such as misfolded proteins, nonfunctional organelles, pathogens, and cytosol. Conversely, selective autophagy targets and degrades specific cargo, such as organelles, bacteria, etc. We previously reported that damaged lysosomes are autophagy targets, via a process called lysophagy. However, how cells target damaged lysosomes through autophagy is not known. We performed proteomics analysis followed by siRNA screening to identify genes involved in targeting damaged lysosomes and identified a new E3 ligase complex, involving CUL4A (cullin 4A), as a regulatory complex in lysophagy. We also found that this complex mediates K48-linked poly-ubiquitination on lysosome protein LAMP2 during lysosomal damage; particularly, the lumenal side of LAMP2 is important to recruit the complex to damaged lysosomes. This protein modification is thus critical to initiate the clearance of damaged lysosomes.

Keywords:  CUL4A; LAMP2; lysophagy; lysosomal membrane damage; selective autophagy; ubiquitination

DOI:  https://doi.org/10.1080/15548627.2022.2138686