bims-mibica 2022-12-04 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2022‒12‒04
thirty-one papers selected by
Kelsey Fisher-Wellman
East Carolina University

Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.
Hyperbaric oxygen enhanced the chemotherapy of mitochondrial targeting molecule IR-780 in bladder cancer.
Activation of the PP2A-B56α heterocomplex synergizes with venetoclax therapies in AML through BCL2 and MCL1 modulation.
Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.
Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.
SMAGP regulates doxorubicin sensitivity in triple-negative breast cancer cells via modulating mitochondrial respiration.
STING Suppresses Mitochondrial VDAC2 to Govern RCC Growth Independent of Innate Immunity.
Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.
Identification of natural products and FDA-approved drugs for targeting cancer stem cell (CSC) propagation.
Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.
METTL16 epigenetically enhances GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.
Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.
Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
Mitochondrial copper in human genetic disorders.
Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids.
Metabolic profiling of colorectal cancer organoids: a comparison between HR MAS MRS and solution NMR spectroscopy of polar extracts.
Identification of the mitochondrial protein ADCK2 as a therapeutic oncotarget of NSCLC.
Pharmacological targeting of type phosphodiesterase 4 inhibits the development of acute myeloid leukemia by impairing mitochondrial function through the Wnt/β-catenin pathway.
BRAFV600E in colorectal cancer reduces sensitivity to oxidative stress and promotes site-specific metastasis by stimulating glutathione synthesis.
The Association of Ketolytic Enzyme Gene Expression Levels with Mitochondrial Activity and Content in Oral Squamous Cell Carcinoma.
Ras drives malignancy through stem cell crosstalk with the microenvironment.
An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.
CRISPR Cas9-mediated ablation of pyruvate carboxylase gene in colon cancer cell line HT-29 inhibits growth and migration, induces apoptosis and increases sensitivity to 5-fluorouracil and glutaminase inhibitor.
Inclusion of Exercise in Cancer Treatment Planning: When Is the Right Time?
PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.
Pyruvate dehydrogenase phosphatase 1 (PDP1) stimulates HIF activity by supporting histone acetylation under hypoxia.
Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors.
Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.
Cellular distribution of IDH mutations in AML during morphologic remission.
Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.
High tumor mutation burden indicates better prognosis in colorectal cancer patients with KRAS mutations.

J Biol Chem. 2022 Oct 28. pii: S0021-9258(22)01091-2. [Epub ahead of print]298(12): 102648

Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.

Ebru S Selen, Susana Rodriguez, Kyle S Cavagnini, Han-Byeol Kim, Chan Hyun Na, Michael J Wolfgang.

  Pyruvate has two major fates upon entry into mitochondria, the oxidative decarboxylation to acetyl-CoA via the pyruvate decarboxylase complex or the biotin-dependent carboxylation to oxaloacetate via pyruvate carboxylase (Pcx). Here, we have generated mice with a liver-specific KO of pyruvate carboxylase (PcxL-/-) to understand the role of Pcx in hepatic mitochondrial metabolism under disparate physiological states. PcxL-/- mice exhibited a deficit in hepatic gluconeogenesis and enhanced ketogenesis as expected but were able to maintain systemic euglycemia following a 24 h fast. Feeding a high-fat diet to PcxL-/- mice resulted in animals that were resistant to glucose intolerance without affecting body weight. However, we found that PcxL-/- mice fed a ketogenic diet for 1 week became severely hypoglycemic, demonstrating a requirement for hepatic Pcx for long-term glycemia under carbohydrate-limited diets. Additionally, we determined that loss of Pcx was associated with an induction in the abundance of lysine-acetylated proteins in PcxL-/- mice regardless of physiologic state. Furthermore, liver acetyl-proteomics revealed a biased induction in mitochondrial lysine-acetylated proteins. These data show that Pcx is important for maintaining the proper balance of pyruvate metabolism between oxidative and anaplerotic pathways.

Keywords:  Pyruvate Carboxylase; acetylation; fasting; gluconeogenesis; mitochondria

DOI:  https://doi.org/10.1016/j.jbc.2022.102648
J Cancer Res Clin Oncol. 2022 Nov 27.

Hyperbaric oxygen enhanced the chemotherapy of mitochondrial targeting molecule IR-780 in bladder cancer.

Chongxing Shen, Xiaofeng Yue, Linyong Dai, Jianwu Wang, Jinjin Li, Qiang Fang, Yi Zhi, Chunmeng Shi, Weibing Li.

  BACKGROUND: Bladder cancer has a high rate of recurrence and drug resistance due to the lack of effective therapies. IR-780 iodide, a near-infrared (NIR) mitochondria-targeting fluorescent agent, has been demonstrated to achieve higher selectivity than other drugs in different tumor types and exhibited tumor-killing effects in some cancers. However, this therapeutic strategy is rarely studied in bladder cancer.MATERIAL AND METHODS: The accumulation of IR-780 in bladder cancer was measured by NIR imaging. Human bladder cell lines (T24, 5637, and TCCSUP) were treated with IR-780 or combined IR-780 and hyperbaric oxygen (HBO). Cell viability, cell apoptosis, cellular ATP production, mitochondrial reactive oxygen species (ROS), and plasma membrane potential were detected. Mitochondrial complex I protein NDUFS1 was measured by western blot. To confirm the anti-tumor efficacy of IR-780 + HBO, mouse bladder cell line (MB49) tumor-bearing mice were established and tumor size and weight were recorded. Besides, cell apoptosis and tumor size were assessed in drug-resistant bladder cancer cells (T24/DDP) and xenografts to evaluate the effect of IR-780 + HBO on drug-resistant bladder cancer.
RESULTS: IR-780 selectively accumulated in bladder cancer (bladder cancer cells, transplanted tumors, and bladder cancer tissue from patients) and could induce cancer cell apoptosis by targeting the mitochondrial complex I protein NDUFS1. The combination with HBO could significantly enhance the anti-tumor effect of IR-780 in vitro by promoting cancer cell uptake and inducing excessive mitochondrial ROS production, while suppressing tumor growth and recurrence in animal models without causing apparent toxicity. Moreover, this combination antitumor strategy was also demonstrated in drug-resistant bladder cancer cells (T24/DDP) and xenografts.
CONCLUSION: We identified for the first time a combination of IR-780 and HBO (IR-780 + HBO), which exhibits mitochondria-targeting and therapeutic capabilities, as a novel treatment paradigm for bladder cancer.

Keywords:  Bladder cancer; Drug-resistant; HBO; IR-780 dye; Mitochondria-targeting

DOI:  https://doi.org/10.1007/s00432-022-04385-4
Blood. 2022 Dec 01. pii: blood.2022016466. [Epub ahead of print]

Activation of the PP2A-B56α heterocomplex synergizes with venetoclax therapies in AML through BCL2 and MCL1 modulation.

Irene Peris, Silvia Romero-Murillo, Elena Martínez-Balsalobre, Caroline C Farrington, Elena Arriazu, Nerea Marcotegui, Marta Jiménez-Muñoz, Cristina Alburquerque-Prieto, Andrea Torres-López, Vicente Jose Fresquet, Jose-Angel Martinez-Climent, Maria C Mateos, Maria Luisa Cayuela, Goutham Narla, Maria D Odero, Carmen Vicente.

Venetoclax-combination therapies are becoming the standard-of-care in acute myeloid leukemia (AML). However, the therapeutic benefit of these drugs in older/unfit patients is limited to only a few months, highlighting the need for more effective therapies. PP2A is a tumor suppressor phosphatase with pleiotropic functions that becomes inactivated in ~70% of AML cases. PP2A promotes cancer cell death by modulating the phosphorylation state in a variety of proteins along the mitochondrial apoptotic pathway. We therefore hypothesized that pharmacological PP2A reactivation could increase BCL2 dependency in AML cells and thus potentiate venetoclax-induced cell death. Here, by using three structurally distinct PP2A-activating drugs, we show that PP2A reactivation synergistically enhances venetoclax activity in AML cell lines, primary cells, and xenograft models. Through the use of CRISPR-Cas9 models and pharmacologic approaches, we demonstrate that the observed therapeutic synergy relies on PP2A complexes containing the B56α regulatory subunit, which expression dictates response to the combination therapy. Mechanistically, PP2A reactivation enhances venetoclax-driven apoptosis through simultaneous inhibition of anti-apoptotic BCL2 and ERK signaling, the later decreasing MCL1 protein stability. Finally, PP2A targeting increases the efficacy of the clinically approved venetoclax and azacitidine combination in vitro, in primary cells, and in an AML patient-derived xenograft model. These preclinical results provide a scientific rationale for testing PP2A-activating drugs with venetoclax combinations in AML.

DOI: https://doi.org/10.1182/blood.2022016466
iScience. 2022 Dec 22. 25(12): 105610

Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.

Freek Manders, Jip van Dinter, Ruben van Boxtel.

  Mitochondria are small organelles that play an essential role in the energy production of eukaryotic cells. Defects in their genomes are associated with diseases, such as aging and cancer. Here, we analyzed the mitochondrial genomes of 532 whole-genome sequencing samples from cancers and normal clonally expanded single cells. We show that the mitochondria of normal cells accumulate mutations with age and that most of the mitochondrial mutations found in cancer are the result of healthy mutation accumulation. We also show that the normal HSPCs of patients with leukemia have an increased mitochondrial mutation load. Finally, we show that secondary pediatric cancers and chemotherapy treatments do not impact the mitochondrial mutation load and mtDNA copy numbers of most cells, suggesting that damage to the mitochondrial genome is not a major driver for carcinogenesis. Overall, these findings may contribute to our understanding of mitochondrial genomes and their role in cancer.

Keywords:  Cancer; Genomics; Stem cells research

DOI:  https://doi.org/10.1016/j.isci.2022.105610
Redox Biol. 2022 Nov 19. pii: S2213-2317(22)00305-6. [Epub ahead of print]58 102533

Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.

Johannes Cw Hermeling, Marija Herholz, Linda Baumann, Estela Cepeda Cores, Aleksandra Zečić, Thorsten Hoppe, Jan Riemer, Aleksandra Trifunovic.

Alternations of redox metabolism have been associated with the extension of lifespan in roundworm Caenorhabditis elegans, caused by moderate mitochondrial dysfunction, although the underlying signalling cascades are largely unknown. Previously, we identified transcriptional factor Krüppel-like factor-1 (KLF-1) as the main regulator of cytoprotective longevity-assurance pathways in the C. elegans long-lived mitochondrial mutants. Here, we show that KLF-1 translocation to the nucleus and the activation of the signalling cascade is dependent on the mitochondria-derived hydrogen peroxide (H2O2) produced during late developmental phases where aerobic respiration and somatic mitochondrial biogenesis peak. We further show that mitochondrial-inducible superoxide dismutase-3 (SOD-3), together with voltage-dependent anion channel-1 (VDAC-1), is required for the life-promoting H2O2 signalling that is further regulated by peroxiredoxin-3 (PRDX-3). Increased H2O2 release in the cytoplasm activates the p38 MAPK signalling cascade that induces KLF-1 translocation to the nucleus and the activation of transcription of C. elegans longevity-promoting genes, including cytoprotective cytochrome P450 oxidases. Taken together, our results underline the importance of redox-regulated signalling as the key regulator of longevity-inducing pathways in C. elegans, and position precisely timed mitochondria-derived H2O2 in the middle of it.

DOI: https://doi.org/10.1016/j.redox.2022.102533
Cancer Chemother Pharmacol. 2022 Nov 27.

SMAGP regulates doxorubicin sensitivity in triple-negative breast cancer cells via modulating mitochondrial respiration.

Huawei Xiao, Xifeng Yang, Shaoyan Huang.

  Doxorubicin-based chemotherapy remains as a major therapeutic approach for patients with triple-negative breast cancer (TNBC). However, insensitivity or resistance to doxorubicin treatment limits the therapeutic efficacy. Mitochondrial respiration plays a critical role in regulating the sensitivity of cancer cells to chemotherapy drugs. Here, we found that small trans-membrane and glycosylated protein (SMAGP) is upregulated in TNBC cells in comparison to normal breast and other subtypes of breast cancer cells. High SMAGP expression is associated with poorer overall survival of TNBC patients. Importantly, loss of SMAGP enhanced the sensitivity of TNBC cells to doxorubicin treatment. Mechanistically, we detected a functional pool of SMAGP in the mitochondria of TNBC cells controlling doxorubicin sensitivity via regulating mitochondrial respiration. Thus, our data suggest that SMAGP acts as a novel regulator of doxorubicin sensitivity in TNBC, identifying SMAGP as a promising therapeutic target for improving the efficacy of doxorubicin-based chemotherapy in TNBC patients.

Keywords:  Doxorubicin resistance; Mitochondrial respiration; Triple-negative breast cancer

DOI:  https://doi.org/10.1007/s00280-022-04496-2
Adv Sci (Weinh). 2022 Nov 29. e2203718

STING Suppresses Mitochondrial VDAC2 to Govern RCC Growth Independent of Innate Immunity.

Zhichuan Zhu, Xin Zhou, Hongwei Du, Erica W Cloer, Jiaming Zhang, Liu Mei, Ying Wang, Xianming Tan, Austin J Hepperla, Jeremy M Simon, Jeanette Gowen Cook, Michael B Major, Gianpietro Dotti, Pengda Liu.

  STING is an innate immune sensor for immune surveillance of viral/bacterial infection and maintenance of an immune-friendly microenvironment to prevent tumorigenesis. However, if and how STING exerts innate immunity-independent function remains elusive. Here, the authors report that STING expression is increased in renal cell carcinoma (RCC) patients and governs tumor growth through non-canonical innate immune signaling involving mitochondrial ROS maintenance and calcium homeostasis. Mitochondrial voltage-dependent anion channel VDAC2 is identified as a new STING binding partner. STING depletion potentiates VDAC2/GRP75-mediated MERC (mitochondria-ER contact) formation to increase mitochondrial ROS/calcium levels, impairs mitochondria function, and suppresses mTORC1/S6K signaling leading to RCC growth retardation. STING interaction with VDAC2 occurs through STING-C88/C91 palmitoylation and inhibiting STING palmitoyl-transferases ZDHHCs by 2-BP significantly impedes RCC cell growth alone or in combination with sorafenib. Together, these studies reveal an innate immunity-independent function of STING in regulating mitochondrial function and growth in RCC, providing a rationale to target the STING/VDAC2 interaction in treating RCC.

Keywords:  2-BP; STING; VDAC2; innate immunity-independent; mTORC1; mitochondrial homeostasis

DOI:  https://doi.org/10.1002/advs.202203718
Cell Rep. 2022 Nov 29. pii: S2211-1247(22)01622-9. [Epub ahead of print]41(9): 111744

Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.

Debanik Choudhury, Na Rong, Izuagie Ikhapoh, Nika Rajabian, Georgios Tseropoulos, Yulun Wu, Pihu Mehrotra, Ramkumar Thiyagarajan, Aref Shahini, Kenneth L Seldeen, Bruce R Troen, Pedro Lei, Stelios T Andreadis.

  Mitochondrial dysfunction, a hallmark of aging, has been associated with the onset of aging phenotypes and age-related diseases. Here, we report that impaired mitochondrial function is associated with increased glutamine catabolism in senescent human mesenchymal stem cells (MSCs) and myofibroblasts derived from patients suffering from Hutchinson-Gilford progeria syndrome. Increased glutaminase (GLS1) activity accompanied by loss of urea transporter SLC14A1 induces urea accumulation, mitochondrial dysfunction, and DNA damage. Conversely, blocking GLS1 activity restores mitochondrial function and leads to amelioration of aging hallmarks. Interestingly, GLS1 expression is regulated through the JNK pathway, as demonstrated by chemical and genetic inhibition. In agreement with our in vitro findings, tissues isolated from aged or progeria mice display increased urea accumulation and GLS1 activity, concomitant with declined mitochondrial function. Inhibition of glutaminolysis in progeria mice improves mitochondrial respiratory chain activity, suggesting that targeting glutaminolysis may be a promising strategy for restoring age-associated loss of mitochondrial function.

Keywords:  CP: Cell biology; GLS1; Hutchinson-Gilford progeria syndrome; JNK; SLC14A1; aging; glutamine; mitochondria; senescence; urea

DOI:  https://doi.org/10.1016/j.celrep.2022.111744
Aging (Albany NY). 2022 Dec 01. 14

Identification of natural products and FDA-approved drugs for targeting cancer stem cell (CSC) propagation.

Gloria Bonuccelli, Federica Sotgia, Michael P Lisanti.

  Here, we report the identification of key compounds that effectively inhibit the anchorage-independent growth and propagation of cancer stem cells (CSCs), as determined via screening using MCF7 cells, a human breast adenocarcinoma cell line. More specifically, we employed the mammosphere assay as an experimental format, which involves the generation of 3D spheroid cultures, using low-attachment plates. These positive hit compounds can be divided into 5 categories: 1) dietary supplements (quercetin and glucosamine); 2) FDA-approved drugs (carvedilol and ciprofloxacin); 3) natural products (aloe emodin, aloin, tannic acid, chlorophyllin copper salt, azelaic acid and adipic acid); 4) flavours (citral and limonene); and 5) vitamins (nicotinamide and nicotinic acid). In addition, for the compounds quercetin, glucosamine and carvedilol, we further assessed their metabolic action, using the Seahorse to conduct metabolic flux analysis. Our results indicate that these treatments can affect glycolytic flux and suppress oxidative mitochondrial metabolism (OXPHOS). Therefore, quercetin, glucosamine and carvedilol can reprogram the metabolic phenotype of breast cancer cells. Despite having diverse chemical structures, these compounds all interfere with mitochondrial metabolism. As these compounds halt CSCs propagation, ultimately, they may have therapeutic potential.

Keywords:  FDA approved drugs; cancer stem cells; drug screening; mammospheres; natural compounds

DOI:  https://doi.org/10.18632/aging.204412
Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2122073119

Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.

Ferdinando Insalata, Hanne Hoitzing, Juvid Aryaman, Nick S Jones.

  The expansion of mitochondrial DNA molecules with deletions has been associated with aging, particularly in skeletal muscle fibers; its mechanism has remained unclear for three decades. Previous accounts have assigned a replicative advantage (RA) to mitochondrial DNA containing deletion mutations, but there is also evidence that cells can selectively remove defective mitochondrial DNA. Here we present a spatial model that, without an RA, but instead through a combination of enhanced density for mutants and noise, produces a wave of expanding mutations with speeds consistent with experimental data. A standard model based on RA yields waves that are too fast. We provide a formula that predicts that wave speed drops with copy number, consonant with experimental data. Crucially, our model yields traveling waves of mutants even if mutants are preferentially eliminated. Additionally, we predict that mutant loads observed in single-cell experiments can be produced by de novo mutation rates that are drastically lower than previously thought for neutral models. Given this exemplar of how spatial structure (multiple linked mtDNA populations), noise, and density affect muscle cell aging, we introduce the mechanism of stochastic survival of the densest (SSD), an alternative to RA, that may underpin other evolutionary phenomena.

Keywords:  aging; biomathematics; evolution; mitochondria; stochastic

DOI:  https://doi.org/10.1073/pnas.2122073119
Biochem Biophys Res Commun. 2022 Oct 26. pii: S0006-291X(22)01468-1. [Epub ahead of print]638 1-6

METTL16 epigenetically enhances GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.

Feng Ye, Jin Wu, Fan Zhang.

  Breast cancer is malignant cancer that severely threatens the life quality of female patients. N6-methyladenosine (m6A) is a prevalent modification of RNA. METTL16 is an important methyltransferase. This work aims to study the role of METTL16 in breast cancer cell death. The expression of METTL16 in clinical breast cancer specimens was analyzed by qPCR assay. The in vitro and in vivo breast cancer cell proliferation was measured by CCK8, colony formation, and xenograft mouse model. Cell ferroptosis was assessed by measuring the accumulation of iron, Fe2+, and lipid ROS. The mechanistic study was performed by RNA degradation, qPCR, and Western blotting assay. METTL16 was overexpressed in tumor tissues from breast cancer patients compared with the para-tumor tissues. Knockdown of METTL16 suppressed in vitro cell proliferation and in vivo tumor growth of breast cancer cells. Meanwhile, METTL16 silencing led to elevated intracellular levels of iron, Fe2+, and lipid ROS, indicating the incidence of ferroptosis. Furthermore, siMETTL16 decreased m6A methylation and enhanced the degradation of GPX4 RNA. METTL16-regulated m6A methylation of GPX4 stimulates proliferation and suppresses ferroptosis of breast cancer cells. Therefore, we concluded that METTL16 epigenetically enhanced GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.

Keywords:  Breast cancer; Ferroptosis; METTL16; m6A methylation

DOI:  https://doi.org/10.1016/j.bbrc.2022.10.065
Nat Metab. 2022 Nov 28.

Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.

McKenzie Patrick, Zhimin Gu, Gen Zhang, R Max Wynn, Pranita Kaphle, Hui Cao, Hieu Vu, Feng Cai, Xiaofei Gao, Yuannyu Zhang, Mingyi Chen, Min Ni, David T Chuang, Ralph J DeBerardinis, Jian Xu.

The branched-chain aminotransferase isozymes BCAT1 and BCAT2, segregated into distinct subcellular compartments and tissues, initiate the catabolism of branched-chain amino acids (BCAAs). However, whether and how BCAT isozymes cooperate with downstream enzymes to control BCAA homeostasis in an intact organism remains largely unknown. Here, we analyse system-wide metabolomic changes in BCAT1- and BCAT2-deficient mouse models. Loss of BCAT2 but not BCAT1 leads to accumulation of BCAAs and branched-chain α-keto acids (BCKAs), causing morbidity and mortality that can be ameliorated by dietary BCAA restriction. Through proximity labelling, isotope tracing and enzymatic assays, we provide evidence for the formation of a mitochondrial BCAA metabolon involving BCAT2 and branched-chain α-keto acid dehydrogenase. Disabling the metabolon contributes to BCAT2 deficiency-induced phenotypes, which can be reversed by BCAT1-mediated BCKA reamination. These findings establish a role for metabolon formation in BCAA metabolism in vivo and suggest a new strategy to modulate this pathway in diseases involving dysfunctional BCAA metabolism.

DOI: https://doi.org/10.1038/s42255-022-00689-4
Nat Commun. 2022 Nov 28. 13(1): 7338

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.

Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M Bernard, Nourdine Bah, Mariana Silva Dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore, James I MacRae, Maria Greco, Thomas Reinheckel, Matthias Trost, Maximiliano G Gutierrez.

Transient lysosomal damage after infection with cytosolic pathogens or silica crystals uptake results in protease leakage. Whether limited leakage of lysosomal contents into the cytosol affects the function of cytoplasmic organelles is unknown. Here, we show that sterile and non-sterile lysosomal damage triggers a cell death independent proteolytic remodelling of the mitochondrial proteome in macrophages. Mitochondrial metabolic reprogramming required leakage of lysosomal cathepsins and was independent of mitophagy, mitoproteases and proteasome degradation. In an in vivo mouse model of endomembrane damage, live lung macrophages that internalised crystals displayed impaired mitochondrial function. Single-cell RNA-sequencing revealed that lysosomal damage skewed metabolic and immune responses in alveolar macrophages subsets with increased lysosomal content. Functionally, drug modulation of macrophage metabolism impacted host responses to Mycobacterium tuberculosis infection in an endomembrane damage dependent way. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprograming after endomembrane damage.

DOI: https://doi.org/10.1038/s41467-022-34632-8
Trends Endocrinol Metab. 2022 Nov 23. pii: S1043-2760(22)00199-0. [Epub ahead of print]

Mitochondrial copper in human genetic disorders.

Natalie M Garza, Abhinav B Swaminathan, Krishna P Maremanda, Mohammad Zulkifli, Vishal M Gohil.

  Copper is an essential micronutrient that serves as a cofactor for enzymes involved in diverse physiological processes, including mitochondrial energy generation. Copper enters cells through a dedicated copper transporter and is distributed to intracellular cuproenzymes by copper chaperones. Mitochondria are critical copper-utilizing organelles that harbor an essential cuproenzyme cytochrome c oxidase, which powers energy production. Mutations in copper transporters and chaperones that perturb mitochondrial copper homeostasis result in fatal genetic disorders. Recent studies have uncovered the therapeutic potential of elesclomol, a copper ionophore, for the treatment of copper deficiency disorders such as Menkes disease. Here we review the role of copper in mitochondrial energy metabolism in the context of human diseases and highlight the recent developments in copper therapeutics.

Keywords:  Menkes disease; Wilson disease; copper; elesclomol; mitochondria; mitochondrial disease

DOI:  https://doi.org/10.1016/j.tem.2022.11.001
Org Biomol Chem. 2022 Dec 01.

Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids.

Hugo MacDermott-Opeskin, Callum Clarke, Xin Wu, Ariane Roseblade, Edward York, Ethan Pacchini, Ritik Roy, Charles Cranfield, Philip A Gale, Megan L O'Mara, Michael Murray, Tristan Rawling.

Aryl-urea substituted fatty acids are protonophores and mitochondrial uncouplers that utilise a urea-based synthetic anion transport moiety to carry out the protonophoric cycle. Herein we show that replacement of the urea group with carbamate, a functional group not previously reported to possess anion transport activity, produces analogues that retain the activity of their urea counterparts. Thus, the aryl-carbamate substituted fatty acids uncouple oxidative phosphorylation and inhibit ATP production by collapsing the mitochondrial proton gradient. Proton transport proceeds via self-assembly of the deprotonated aryl-carbamates into membrane permeable dimeric species, formed by intermolecular binding of the carboxylate group to the carbamate moiety. These results highlight the anion transport capacity of the carbamate functional group.

DOI: https://doi.org/10.1039/d2ob02049a
NMR Biomed. 2022 Nov 30. e4882

Metabolic profiling of colorectal cancer organoids: a comparison between HR MAS MRS and solution NMR spectroscopy of polar extracts.

W J M van der Kemp, M T Grinde, J O Malvik, H W M van Laarhoven, J J Prompers, D W J Klomp, B M T Burgering, T F Bathen, S A Moestue.

  Patient-derived cancer cells cultured in vitro is a cornerstone for cancer metabolism research. More recently, the introduction of organoids has provided the research community with a more versatile model system. Physiological structure and organization of the cell source tissue is maintained in organoids, representing a closer link to in vivo tumor models. High resolution magic angle spinning MR spectroscopy (HR MAS MRS) is a commonly applied analytical approach for metabolic profiling of intact tissue, but its use has not been reported for organoids. The aim of the current work was to compare the performance of HR MAS MRS and extraction-based NMR in metabolic profiling of wild-type and tumor progression organoids (TPOs) from human colon cancer, and further to investigate how the sequentially increased genetic alterations of the TPOs affect the metabolic profile. Sixteen metabolites were reliably identified and quantified both in spectra based on NMR of extracts and HR MAS MRS of intact organoids. The metabolite concentrations from the two approaches were highly correlated (r=0.94), and both approaches were able to capture the systematic changes in metabolic features introduced by the genetic alterations characteristic for colorectal cancer progression, e.g. increased levels of lactate and decreased levels of myo-inositol and phophocholine with increasing number of mutations. The current work highlights that HR MAS MRS is a well-suited method for metabolic profiling of intact organoids, with the additional benefit that the non-destructive nature of HR-MAS enables subsequent recovery of the organoids for further analyses based on nucleic acids or proteins.

Keywords:  Colorectal cancer; HR MAS MRS; Lactate; Myo-Inositol; NMR; Organoids; Phosphocholine; Tumor progression organoids

DOI:  https://doi.org/10.1002/nbm.4882
Int J Biol Sci. 2022 ;18(16): 6163-6175

Identification of the mitochondrial protein ADCK2 as a therapeutic oncotarget of NSCLC.

Jin-Zhi Zhang, Jia Liu, Yi-Xin Xu, Wang-Yang Pu, Ming-Jing Shen, Kan-Qiu Jiang, Yi-Ling Yang, Jingjing Lu, Zhengbo Deng, Yi Yang, Wei-Hua Xu.

  The aarF domain containing kinase 2 (ADCK2) is a mitochondria-locating protein, important for fatty acid metabolism and coenzyme Q biosynthesis. The bioinformatics results show that elevated ADCK2 transcripts in NSCLC correlate with poor overall survival and poor anti-PD-1/PD-L1 therapy response. ADCK2 is overexpressed in local human NSCLC tissues and various primary and established NSCLC cells. In NSCLC cells, ADCK2 shRNA or CRISPR/Cas9 knockout remarkably suppressed cell viability, proliferation, cell cycle progression, cell mobility, and provoked cell apoptosis. Moreover, ADCK2 depletion disrupted mitochondrial functions in NSCLC cells, causing cytochrome C release, mitochondrial depolarization, DNA damage and ATP reduction. Contrarily, ectopic ADCK2 overexpression promoted NSCLC cell growth. Further studies revealed that ADCK2 depletion inactivated Akt-mTOR signaling in primary NSCLC cells. NSCLC xenograft growth in nude mice was significantly hindered after ADCK2 silencing or knockout. ADCK2 depletion, apoptosis induction and oxidative injury as well as ATP reduction and Akt-mTOR inactivation were detected in ADCK2-silenced or ADCK2-knockout NSCLC xenograft tissues. Together overexpressed ADCK2 is important for the growth of NSCLC cells, representing an important therapeutic molecular oncotarget.

Keywords:  ADCK2; NSCLC; cancer growth; mitochondrial function; therapeutic target

DOI:  https://doi.org/10.7150/ijbs.78354
Biomed Pharmacother. 2022 Nov 24. pii: S0753-3322(22)01416-0. [Epub ahead of print]157 114027

Pharmacological targeting of type phosphodiesterase 4 inhibits the development of acute myeloid leukemia by impairing mitochondrial function through the Wnt/β-catenin pathway.

Ping Mao, Changhao Huang, Yuyu Li, Yuanyi Zhao, Sujin Zhou, Zhenggang Zhao, Yunping Mu, Lina Wang, Fanghong Li, Allan Z Zhao.

  Acute myeloid leukemia (AML) is prone to drug-resistant relapse with a low 5-year survival rate. New therapeutic modalities are sorely needed to provide hope for AML relapse patients. Herein, we demonstrated a specific inhibitor of type 4 phosphodiesterase (PDE4), Zl-n-91, could significantly reduce the proliferation of AML cells, block DNA replication process, and increase AML cell death. Zl-n-91 also impeded the growth of subcutaneous xenograft and prolonged the survival of the MLL-AF9-driven AML model. Bioinformatic analysis revealed that elevated mitochondrial gene signatures inversely correlate with the survival of AML patients; and importantly, Zl-n-91 strongly suppressed the function of mitochondria. In addition, this PDE4 inhibitor induced alterations in multiple signaling pathways, including the reduction of β-catenin activity. Stimulation of the Wnt/β-catenin pathway could attenuate the inhibitory effect of Zl-n-91 on AML cell proliferation as well as mitochondrial function. Taken together, we revealed for the first time that targeting PDE4 activity could attenuate mitochondrial function through a Wnt/β-catenin pathway, which in turn would block the growth of AML cells. Specific PDE4 inhibitors can potentially serve as a new treatment modality for AML patients.

Keywords:  AML; Leukemia; Mitochondria; PDE4; WNT/β-catenin

DOI:  https://doi.org/10.1016/j.biopha.2022.114027
Cell Rep. 2022 Nov 29. pii: S2211-1247(22)01606-0. [Epub ahead of print]41(9): 111728

BRAFV600E in colorectal cancer reduces sensitivity to oxidative stress and promotes site-specific metastasis by stimulating glutathione synthesis.

Jamila Laoukili, Susanne van Schelven, Emre Küçükköse, André Verheem, Kaitlyn Goey, Miriam Koopman, Inne Borel Rinkes, Onno Kranenburg.

  The presence of BRAFV600E in colorectal cancer (CRC) is associated with a higher chance of distant metastasis. Oxidative stress in disseminated tumor cells limits metastatic capacity. To study the relationship between BRAFV600E, sensitivity to oxidative stress, and metastatic capacity in CRC, we use patient-derived organoids (PDOs) and tissue samples. BRAFV600E tumors and PDOs express high levels of glutamate-cysteine ligase (GCL), the rate-limiting enzyme in glutathione synthesis. Deletion of GCL in BRAFV600E PDOs strongly reduces their capacity to form distant liver and lung metastases but does not affect peritoneal metastasis outgrowth. Vice versa, the glutathione precursor N-acetyl-cysteine promotes organ-site-specific metastasis in the liver and the lungs but not in the peritoneum. BRAFV600E confers resistance to pharmacologically induced oxidative stress in vitro, which is partially overcome by treatment with the BRAF-inhibitor vemurafenib. We conclude that GCL-driven glutathione synthesis protects BRAFV600E-expressing tumors from oxidative stress during distant metastasis to the liver and the lungs.

Keywords:  BRAF(V600E); CP: Cancer; colorectal; glutathione; metastasis; metastatic organotropsim; oxidative stress

DOI:  https://doi.org/10.1016/j.celrep.2022.111728
Asian Pac J Cancer Prev. 2022 Nov 01. pii: 90389. [Epub ahead of print]23(11): 3953-3958

The Association of Ketolytic Enzyme Gene Expression Levels with Mitochondrial Activity and Content in Oral Squamous Cell Carcinoma.

Mahdisa Yousefi, Abbas Karimi, Afsaneh Goudarzi.

  BACKGROUND: Recent studies have pointed to the anti-tumour effects of a ketogenic diet (KD) in cancer. It is believed that patients with low ketolytic enzyme gene expression levels are more sensitive and may respond better to the KD therapy. However, the ketolytic enzyme gene expression levels and their association with mitochondrial activity and content in oral squamous cell carcinoma (OSCC) is not yet obvious. Therefore, the aim of this study was to explore the potential use of ketolytic enzymes as biomarkers for mitochondrial activity and content.MATERIALS AND METHODS: Here we aimed to compare the mRNA expression levels of ketolytic enzymes (ACAT1, BDH1, BDH2 and OXCT1) between tumour and adjacent pre-tumor tissues of 16 OSCC patients. Additionally, we examined the association of the mitochondrial ketolytic enzymes, including ACAT1, OXCT1, and BDH1 gene expression with mitochondrial activity and content.
RESULTS: Our findings did not show any significant difference in ketolytic gene expression levels between tumour and pre-tumor tissues of OSCC patients. ACAT1 and BDH1 mRNA expression levels were significantly correlated with the mRNA level of ND2 in tumour of OSCC patients. The mRNA levels of ACAT1, BDH1 and BDH2 were not correlated with the mRNA expression of 16srRNA.
CONCLUSION: Our data suggest that .mRNA gene expression levels of BDH1 and ACAT1 correlate with the mitochondrial activity in tumour of OSCC patients. BDH2 mRNA level significantly anti-correlate with tumour grade. We offer clues on the potential of ACAT1 as a biomarker of mitochondrial activity, but future studies are needed to establish this concept.

Keywords:  Ketolytic enzymes; MtDNA; mitochondria; oral squamous cell carcinoma

DOI:  https://doi.org/10.31557/APJCP.2022.23.11.3953
Nature. 2022 Nov 30.

Ras drives malignancy through stem cell crosstalk with the microenvironment.

Shaopeng Yuan, Katherine S Stewart, Yihao Yang, Merve Deniz Abdusselamoglu, S Martina Parigi, Tamar Y Feinberg, Karen Tumaneng, Hanseul Yang, John M Levorse, Lisa Polak, David Ng, Elaine Fuchs.

Squamous cell carcinomas are triggered by marked elevation of RAS-MAPK signalling and progression from benign papilloma to invasive malignancy1-4. At tumour-stromal interfaces, a subset of tumour-initiating progenitors, the cancer stem cells, obtain increased resistance to chemotherapy and immunotherapy along this pathway5,6. The distribution and changes in cancer stem cells during progression from a benign state to invasive squamous cell carcinoma remain unclear. Here we show in mice that, after oncogenic RAS activation, cancer stem cells rewire their gene expression program and trigger self-propelling, aberrant signalling crosstalk with their tissue microenvironment that drives their malignant progression. The non-genetic, dynamic cascade of intercellular exchanges involves downstream pathways that are often mutated in advanced metastatic squamous cell carcinomas with high mutational burden7. Coupling our clonal skin HRASG12V mouse model with single-cell transcriptomics, chromatin landscaping, lentiviral reporters and lineage tracing, we show that aberrant crosstalk between cancer stem cells and their microenvironment triggers angiogenesis and TGFβ signalling, creating conditions that are conducive for hijacking leptin and leptin receptor signalling, which in turn launches downstream phosphoinositide 3-kinase (PI3K)-AKT-mTOR signalling during the benign-to-malignant transition. By functionally examining each step in this pathway, we reveal how dynamic temporal crosstalk with the microenvironment orchestrated by the stem cells profoundly fuels this path to malignancy. These insights suggest broad implications for cancer therapeutics.

DOI: https://doi.org/10.1038/s41586-022-05475-6
Elife. 2022 Nov 30. pii: e84279. [Epub ahead of print]11

An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.

Tricia T Nguyen, Gia K Voeltz.

  Mitochondria are dynamic organelles that undergo cycles of fission and fusion at a unified platform defined by endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCSs). These MCSs or nodes co-localize fission and fusion machinery. We set out to identify how ER-associated mitochondrial nodes can regulate both fission and fusion machinery assembly. We have used a promiscuous biotin ligase linked to the fusion machinery, Mfn1, and proteomics to identify an ER membrane protein, ABHD16A, as a major regulator of node formation. In the absence of ABHD16A, fission and fusion machineries fail to recruit to ER-associated mitochondrial nodes and fission and fusion rates are significantly reduced. ABHD16A contains an acyltransferase motif and an α/β hydrolase domain and point mutations in critical residues of these regions fail to rescue the formation of ER-associated mitochondrial hot spots. These data suggest a mechanism whereby ABHD16A functions by altering phospholipid composition at ER-mitochondria MCSs. Our data present the first example of an ER membrane protein that regulates the recruitment of both fission and fusion machineries to mitochondria.

Keywords:  cell biology; human

DOI:  https://doi.org/10.7554/eLife.84279
Front Oncol. 2022 ;12 966089

CRISPR Cas9-mediated ablation of pyruvate carboxylase gene in colon cancer cell line HT-29 inhibits growth and migration, induces apoptosis and increases sensitivity to 5-fluorouracil and glutaminase inhibitor.

Jarunya Ngamkham, Siraprapa Siritutsoontorn, Saowaluk Saisomboon, Kulthida Vaeteewoottacharn, Sarawut Jitrapakdee.

  Pyruvate carboxylase (PC) is an important anaplerotic enzyme that replenishes the tricarboxylic acid cycle (TCA) intermediates. It prevents the collapse of the TCA cycle upon its intermediates are removed during high anabolic demand. We have recently shown that overexpression of PC protein was associated with staging, metastasis and poor survival of colorectal cancer patients. Herein, we generated the PC knockout (PC KO) colon cancer cell lines, HT-29, by CRISPR-Cas9 technique, as a model to understand the role of this enzyme in colorectal cancer. The PC KO HT-29 cell lines had no detectable PC protein and did not show abnormal cellular or nuclear structures. However, PC KO HT-29 cells showed a 50-60% reduction in their growth rate and a 60-70% reduction in migration. The deficient growth phenotype of PC KO HT-29 cells was associated with apoptotic induction with no apparent cell cycle disruption following five days of growth. Down-regulation of key lipogenic enzymes, including acetyl-CoA carboxylase-1 and fatty acid synthase, was also associated with growth inhibition, suggesting that the de novo lipogenesis is impaired. Furthermore, PC KO HT-29 cells were 50% and 60% more sensitive to 5-fluorouracil and glutaminase inhibitor, CB-839, at their IC50 concentrations, respectively, following 48 h exposure. The increased cytotoxicity of CB-839 to PC KO HT-29 cells was associated with increased poly (ADP-ribose) polymerase cleavage. However, this was not observed with PC KO cells exposed to 5-fluorouracil, suggesting that PC KO HT-29 cells were prone to CB-839-induced apoptosis. Collectively, these findings indicate that ablation of PC expression in HT-29 cells disrupts the metabolic homeostasis of cells and inhibits proliferation and migration, accompanied by apoptotic induction. This study highlights the crucial role of PC in supporting the survival of HT-29 cells during exposure to chemotherapeutic drugs.

Keywords:  5-FU; cancer metabolism; colorectal cancer; glutaminase; pyruvate carboxylase

DOI:  https://doi.org/10.3389/fonc.2022.966089
JACC CardioOncol. 2022 Nov;4(4): 504-506

Inclusion of Exercise in Cancer Treatment Planning: When Is the Right Time?

Neil M Iyengar.



Keywords:  breast cancer; cancer survivorship; colorectal cancer; exercise oncology; lymphoma; testicular cancer

DOI:  https://doi.org/10.1016/j.jaccao.2022.10.002
Nat Commun. 2022 Dec 01. 13(1): 7400

PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.

Zdenek Andrysik, Kelly D Sullivan, Jeffrey S Kieft, Joaquin M Espinosa.

The p53 transcription factor is a master regulator of cellular stress responses inhibited by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces apoptosis in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2α-ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2α, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2α phosphorylation. Pharmacological induction of eIF2α phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2α-ATF4, with clear therapeutic implications.

DOI: https://doi.org/10.1038/s41467-022-35089-5
FEBS J. 2022 Dec 01.

Pyruvate dehydrogenase phosphatase 1 (PDP1) stimulates HIF activity by supporting histone acetylation under hypoxia.

Angeliki Karagiota, Amalia Kanoura, Efrosyni Paraskeva, George Simos, Georgia Chachami.

  Cancer cells, when exposed to the hypoxic tumor microenvironment, respond by activating hypoxia-inducible factors (HIFs). HIF-1 mediates extensive metabolic re-programming, and expression of HIF-1α, its oxygen-regulated subunit, is associated with poor prognosis in cancer. Here we analyze the role of pyruvate dehydrogenase phosphatase 1 (PDP1) in the regulation of HIF-1 activity. PDP1 is a key hormone-regulated metabolic enzyme that dephosphorylates and activates pyruvate dehydrogenase (PDH), thereby stimulating conversion of pyruvate into acetyl-CoA. Silencing of PDP1 down-regulated HIF transcriptional activity and the expression of HIF-dependent genes, including that of PDK1, the kinase that phosphorylates and inactivates PDH, opposing the effects of PDP1. Inversely, PDP1 stimulation enhanced HIF activity under hypoxia. Alteration of PDP1 levels or activity did not have an effect on HIF-1α protein levels, nuclear accumulation or interaction with its partners ARNT and NPM1. However, depletion of PDP-1 decreased histone H3 acetylation of HIF-1 target gene promoters and inhibited binding of HIF-1 to the respective hypoxia-response elements (HREs) under hypoxia. Furthermore, the decrease of HIF transcriptional activity upon PDP1 depletion could be reversed by treating the cells with acetate, as an exogenous source of acetyl-CoA, or the histone deacetylase (HDAC) inhibitor trichostatin A. These data suggest that the PDP1/PDH/HIF-1/PDK1 axis is part of a homeostatic loop which, under hypoxia, preserves cellular acetyl-CoA production to a level sufficient to sustain chromatin acetylation and transcription of hypoxia-inducible genes.

Keywords:  HIF-1α; PDP1; acetyl-CoA; histone acetylation; hypoxia; pyruvate dehydrogenase phosphatase 1

DOI:  https://doi.org/10.1111/febs.16694
Antimicrob Agents Chemother. 2022 Nov 29. e0105622

Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors.

Chui Fann Wong, Wuan-Geok Saw, Sandip Basak, Mio Sano, Hiroshi Ueno, Hwee Wen Kerk, Dennis Litty, Priya Ragunathan, Thomas Dick, Volker Müller, Hiroyuki Noji, Gerhard Grüber.

  The F1FO-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F1-ATPase and the F1FO-ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors.

Keywords:  ATP synthesis; F-ATP synthase; OXPHOS; bioenergetics; nontuberculous mycobacteria; tuberculosis

DOI:  https://doi.org/10.1128/aac.01056-22
Nat Commun. 2022 Dec 02. 13(1): 7414

Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.

Wei Li, Qi Long, Hao Wu, Yanshuang Zhou, Lifan Duan, Hao Yuan, Yingzhe Ding, Yile Huang, Yi Wu, Jinyu Huang, Delong Liu, Baodan Chen, Jian Zhang, Juntao Qi, Shiwei Du, Linpeng Li, Yang Liu, Zifeng Ruan, Zihuang Liu, Zichao Liu, Yifan Zhao, Jianghuan Lu, Junwei Wang, Wai-Yee Chan, Xingguo Liu.

Pluripotent stem cells hold great promise in regenerative medicine and developmental biology studies. Mitochondrial metabolites, including tricarboxylic acid (TCA) cycle intermediates, have been reported to play critical roles in pluripotency. Here we show that TCA cycle enzymes including Pdha1, Pcb, Aco2, Cs, Idh3a, Ogdh, Sdha and Mdh2 are translocated to the nucleus during somatic cell reprogramming, primed-to-naive transition and totipotency acquisition. The nuclear-localized TCA cycle enzymes Pdha1, Pcb, Aco2, Cs, Idh3a promote somatic cell reprogramming and primed-to-naive transition. In addition, nuclear-localized TCA cycle enzymes, particularly nuclear-targeted Pdha1, facilitate the 2-cell program in pluripotent stem cells. Mechanistically, nuclear Pdha1 increases the acetyl-CoA and metabolite pool in the nucleus, leading to chromatin remodeling at pluripotency genes by enhancing histone H3 acetylation. Our results reveal an important role of mitochondrial TCA cycle enzymes in the epigenetic regulation of pluripotency that constitutes a mitochondria-to-nucleus retrograde signaling mode in different states of pluripotent acquisition.

DOI: https://doi.org/10.1038/s41467-022-35199-0
Leuk Res. 2022 Nov 25. pii: S0145-2126(22)00369-1. [Epub ahead of print]124 106993

Cellular distribution of IDH mutations in AML during morphologic remission.

Radha Ramanan, Ing Soo Tiong, Adam Ivey, Doen Ming Ong, Fiona C Brown, Chyn Chua, Tongted Das, David Curtis.

  Limited information exists about the cellular distribution of mutations which persist in remission in acute myeloid leukemia (AML) (variable considered pre-leukemic mutations). We hypothesized that mutations detectable in all cell compartments may be less pathogenic than those that are myeloid-restricted. Here, we describe the cellular compartments that have IDH mutations in five patients with IDH-mutated AML in morphologic remission. Unlike pre-leukemic clones harboring the more common DNMT3A, TET2 and ASXL1 (DTA) mutations, we show that IDH mutations are myeloid-restricted. This finding provides an explanation for the reports that IDH mutations carry a higher risk for relapse than DTA mutations. Detailed analysis of one case also shows acquisition of additional mutations in distinct cellular compartments, illustrating subclonal complexity associated with therapeutics.

Keywords:  AML; Cellular distribution; IDH; Preleukemic; Remission

DOI:  https://doi.org/10.1016/j.leukres.2022.106993
iScience. 2022 Dec 22. 25(12): 105502

Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.

Shao-Ting Chiu, Wen-Wei Tseng, An-Chi Wei.

  Mitochondria, semi-autonomous eukaryotic organelles, participate in energy production and metabolism, making mitochondrial quality control crucial. As most mitochondrial proteins are encoded by nuclear genes, maintaining mitochondrial function and quality depends on proper mitochondria-nucleus communication and designated mitochondrial retrograde signaling. Early studies focused on retrograde signaling participants and specific gene knockouts. However, mitochondrial signal modulation remains elusive. A mathematical model based on ordinary differential equations was proposed to simulate signal propagation to nucleus following mitochondrial damage in yeast. Mitochondrial retrograde signaling decisions were described using a Boolean model. Dynamics of retrograde signaling were analyzed and extended to evaluate the model response to noisy damage signals. Simulation revealed localized protein concentration dynamics, including waveforms, frequency response, and robustness under noise. Retrograde signaling is bistable with localized steady states, and increased damage compromises robustness. We elucidated mitochondrial retrograde signaling, thus providing a basis for drug design against yeast and fungi.

Keywords:  Biological sciences; Cell biology; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2022.105502
Front Oncol. 2022 ;12 1015308

High tumor mutation burden indicates better prognosis in colorectal cancer patients with KRAS mutations.

Jianlei Wang, Jianping Song, Zeyang Liu, Tingxiao Zhang, Yanfeng Liu.

  Objective: Colorectal cancer (CRC) is a common type of malignant tumor of the digestive tract. Tumor mutation burden (TMB) is a potential prognostic indicator of numerous malignant tumors. This study investigated the prognostic value of TMB in CRC.Methods: This study analyzed the clinical and somatic mutation data of patients with CRC from the Memorial Sloan Kettering Cancer Center (MSKCC) and The Cancer Genome Atlas (TCGA) cohorts. The genetic landscape was visualized using the maftools package in R software. Survival curves were constructed using the Kaplan-Meier method, and Cox regression analysis was performed to confirm that TMB is an independent prognostic indicator. A nomogram was developed to construct the prognostic model, which was evaluated using the C-index, calibration curve, and decision curve analysis.
Results: In patients with CRC, APC mutations indicated longer overall survival (OS), whereas KRAS mutations indicated shorter OS. For all included patients, there was no significant difference in the OS between the TMB-high and TMB-low groups. For patients with KRAS mutations, the OS in the TMB-high group was longer than that in the TMB-low group. Cox regression analysis showed that TMB was an independent prognostic factor in CRC patients with KRAS mutations. This explains the good accuracy of the nomogram prognostic model using TMB and indicates its good prospect in clinical applications.
Conclusions: A high TMB indicates better prognosis in CRC patients with KRAS mutations, thus confirming the value of TMB in clinical applications.

Keywords:  KRAS mutation; colorectal cancer; nomogram; prognosis; tumor mutation burden

DOI:  https://doi.org/10.3389/fonc.2022.1015308