Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level

DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.

Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth

Background

Ketogenic diet is a potential means of augmenting cancer therapy. Here, we explore ketone body metabolism and its interplay with chemotherapy in pancreatic cancer.

Methods

Metabolism and therapeutic responses of murine pancreatic cancer were studied using KPC primary tumors and tumor chunk allografts. Mice on standard high-carbohydrate diet or ketogenic diet were treated with cytotoxic chemotherapy (nab-paclitaxel, gemcitabine, cisplatin). Metabolic activity was monitored with metabolomics and isotope tracing, including 2H- and 13C-tracers, liquid chromatography-mass spectrometry, and imaging mass spectrometry.

Findings

Ketone bodies are unidirectionally oxidized to make NADH. This stands in contrast to the carbohydrate-derived carboxylic acids lactate and pyruvate, which rapidly interconvert, buffering NADH/NAD. In murine pancreatic tumors, ketogenic diet decreases glucose's concentration and tricarboxylic acid cycle contribution, enhances 3-hydroxybutyrate's concentration and tricarboxylic acid contribution, and modestly elevates NADH, but does not impact tumor growth. In contrast, the combination of ketogenic diet and cytotoxic chemotherapy substantially raises tumor NADH and synergistically suppresses tumor growth, tripling the survival benefits of chemotherapy alone. Chemotherapy and ketogenic diet also synergize in immune-deficient mice, although long-term growth suppression was only observed in mice with an intact immune system.

Conclusions

Ketogenic diet sensitizes murine pancreatic cancer tumors to cytotoxic chemotherapy. Based on these data, we have initiated a randomized clinical trial of chemotherapy with standard versus ketogenic diet for patients with metastatic pancreatic cancer (NCT04631445).

GCN2 adapts protein synthesis to scavenging-dependent growth

Pancreatic cancer cells with limited access to free amino acids can grow by scavenging extracellular protein. In a murine model of pancreatic cancer, we performed a genome-wide CRISPR screen for genes required for scavenging-dependent growth. The screen identified key mediators of macropinocytosis, peripheral lysosome positioning, endosome-lysosome fusion, lysosomal protein catabolism, and translational control. The top hit was GCN2, a kinase that suppresses translation initiation upon amino acid depletion. Using isotope tracers, we show that GCN2 is not required for protein scavenging. Instead, GCN2 prevents ribosome stalling but without slowing protein synthesis; cells still use all of the limiting amino acids as they emerge from lysosomes. GCN2 also adapts gene expression to the nutrient-poor environment, reorienting protein synthesis away from ribosomes and toward lysosomal hydrolases, such as cathepsin L. GCN2, cathepsin L, and the other genes identified in the screen are potential therapeutic targets in pancreatic cancer.

Monitoring mammalian mitochondrial translation with MitoRiboSeq

Several essential components of the electron transport chain, the major producer of ATP in mammalian cells, are encoded in the mitochondrial genome. These 13 proteins are translated within mitochondria by 'mitoribosomes'. Defective mitochondrial translation underlies multiple inborn errors of metabolism and has been implicated in pathologies such as aging, metabolic syndrome and cancer. Here, we provide a detailed ribosome profiling protocol optimized to interrogate mitochondrial translation in mammalian cells (MitoRiboSeq), wherein mitoribosome footprints are generated with micrococcal nuclease and mitoribosomes are separated from cytosolic ribosomes and other RNAs by ultracentrifugation in a single straightforward step. We highlight critical steps during library preparation and provide a step-by-step guide to data analysis accompanied by open-source bioinformatic code. Our method outputs mitoribosome footprints at single-codon resolution. Codons with high footprint densities are sites of mitoribosome stalling. We recently applied this approach to demonstrate that defects in mitochondrial serine catabolism or in mitochondrial tRNA methylation cause stalling of mitoribosomes at specific codons. Our method can be applied to study basic mitochondrial biology or to characterize abnormalities in mitochondrial translation in patients with mitochondrial disorders.

A Unified Approach to Targeting the Lysosome's Degradative and Growth Signaling Roles

Lysosomes serve dual roles in cancer metabolism, executing catabolic programs (i.e., autophagy and macropinocytosis) while promoting mTORC1-dependent anabolism. Antimalarial compounds such as chloroquine or quinacrine have been used as lysosomal inhibitors, but fail to inhibit mTOR signaling. Further, the molecular target of these agents has not been identified. We report a screen of novel dimeric antimalarials that identifies dimeric quinacrines (DQ) as potent anticancer compounds, which concurrently inhibit mTOR and autophagy. Central nitrogen methylation of the DQ linker enhances lysosomal localization and potency. An in situ photoaffinity pulldown identified palmitoyl-protein thioesterase 1 (PPT1) as the molecular target of DQ661. PPT1 inhibition concurrently impairs mTOR and lysosomal catabolism through the rapid accumulation of palmitoylated proteins. DQ661 inhibits the in vivo tumor growth of melanoma, pancreatic cancer, and colorectal cancer mouse models and can be safely combined with chemotherapy. Thus, lysosome-directed PPT1 inhibitors represent a new approach to concurrently targeting mTORC1 and lysosomal catabolism in cancer.Significance: This study identifies chemical features of dimeric compounds that increase their lysosomal specificity, and a new molecular target for these compounds, reclassifying these compounds as targeted therapies. Targeting PPT1 blocks mTOR signaling in a manner distinct from catalytic inhibitors, while concurrently inhibiting autophagy, thereby providing a new strategy for cancer therapy. Cancer Discov; 7(11); 1266-83. ©2017 AACR.See related commentary by Towers and Thorburn, p. 1218This article is highlighted in the In This Issue feature, p. 1201.

Abstract LB-279: Quantitative flux measurements of serum protein catabolism in PDAC and other KRAS-mutant cancers

Activating KRAS mutations are prevalent in human cancer and are associated with poor prognosis. Among these malignancies is pancreatic ductal adenocarcinoma (PDAC), which is universally KRAS-driven and almost universally lethal. PDAC tumors are extremely fibrotic and hypovascularized, limiting perfusion of nutrients into the tumor, and tumor cells exhibit an altered metabolic program to support survival and proliferation in this environment. One metabolic activity upregulated in these tumor cells is the uptake and catabolism of serum protein. This process yields a substantial alternative source of amino acids and can support the proliferation of cultured cells lacking free essential amino acids. However, existing methods for assaying the uptake and degradation of intact protein provide qualitative outputs, and as such, do not yield accurate estimates of flux from serum protein to amino acid monomers. Here, we present a method for quantitative measurement of the catabolic production of amino acids from serum protein in cultured cells. By culturing cells in medium containing fully 13C-labeled glucose and amino acids supplemented with unlabeled albumin, we distinguish amino acids taken up as monomers from the medium from serum protein-derived amino acids. Using a variant of classical metabolic flux analysis, we derive flux estimates for serum protein catabolism from measurements of amino acid abundance and isotopic labeling over time. Our method is highly sensitive (i.e. can estimate “baseline” serum protein catabolism in KRAS wild-type cell lines) and yields precise estimates of amino acid influx from serum protein for all proteinogenic amino acids. We have measured serum protein catabolism in a variety of cultured cell lines and find that protein catabolism yields amino acids in comparable amounts to conventional uptake in various pancreatic and non-pancreatic lines. This approach enables estimation of protein catabolic flux in any cell line and can be used to assay the effects of various genetic and pharmacological perturbations on serum protein catabolism with high sensitivity and while accounting for growth rate differences.

Citation Format: Michel Nofal, Kevin Zhang, Josh Rabinowitz. Quantitative flux measurements of serum protein catabolism in PDAC and other KRAS-mutant cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-279. doi:10.1158/1538-7445.AM2015-LB-279

Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein

Glucose and amino acids are key nutrients supporting cell growth. Amino acids are imported as monomers, but an alternative route induced by oncogenic KRAS involves uptake of extracellular proteins via macropinocytosis and subsequent lysosomal degradation of these proteins as a source of amino acids. In this study, we examined the metabolism of pancreatic ductal adenocarcinoma (PDAC), a poorly vascularized lethal KRAS-driven malignancy. Metabolomic comparisons of human PDAC and benign adjacent tissue revealed that tumor tissue was low in glucose, upper glycolytic intermediates, creatine phosphate, and the amino acids glutamine and serine, two major metabolic substrates. Surprisingly, PDAC accumulated essential amino acids. Such accumulation could arise from extracellular proteins being degraded through macropinocytosis in quantities necessary to meet glutamine requirements, which in turn produces excess of most other amino acids. Consistent with this hypothesis, active macropinocytosis is observed in primary human PDAC specimens. Moreover, in the presence of physiologic albumin, we found that cultured murine PDAC cells grow indefinitely in media lacking single essential amino acids and replicate once in the absence of free amino acids. Growth under these conditions was characterized by simultaneous glutamine depletion and essential amino acid accumulation. Overall, our findings argue that the scavenging of extracellular proteins is an important mode of nutrient uptake in PDAC.

Microscopic study of hydroxyapatite dissolution as affected by fluoride ions

Fluoride ions play a critical role in preventing tooth decay. We investigated the microscopic effects of fluoride ions on hydroxyapatite (100) surface dissolution using in situ atomic force microscopy. In the presence of 10 mM NaF, individual surface step retraction velocities decreased by about a factor of 5 as compared to NaF-free conditions. Importantly, elongated hexagonal etch pits, which are characteristic of (100) surface dissolution, were no longer observed when NaF was present. The alteration of pit shape is more distinct at a higher NaF concentration (50 mM) where triangular etch pits evolved during dissolution. Furthermore, in a fluoride concentration typical for tap water (10 μM), we observed roughening of individual step lines, resulting in the formation of scalloped morphologies. Morphological changes to individual steps across a wide range of fluoride concentrations suggest that the cariostatic capabilities of fluoride ions originate from their strong interactions with molecular steps.

Radiative electron capture to the continuum and the short-wavelength limit of electron-nucleus bremsstrahlung in 90A MeV U88 + ((1s2)(2s2))+N2 Collisions

We have measured the continuum momentum distribution for radiative electron capture to the continuum (RECC) cusp electrons in 90A MeV U88+ + N2-->U88+ + N2 +* + ecusp(0 degrees ) + hnu (RECC) collisions. We demonstrate that x rays coincident with RECC cusp electrons originate from the short-wavelength limit of the electron-nucleus bremsstrahlung and explain the asymmetric cusp shape by comparison with theory within the relativistic impulse approximation.

Supporting cancer care in the developing countries: role of IAEA/WHO

Cancer management can be expensive and constitutes a major problem in many developing countries where management standards are poor due to many factors, including non-availability of sufficient funds, equipment, and trained personnel. The incidence of cancer is rising worldwide. This is more so in the developing countries, many of whom are less equipped to deal with the problems. Radiation therapy is one of the major treatment modalities for cancer, and it is estimated that about 60% of all cancer patients require this treatment at one time or another during the course of their disease. Unfortunately, radiotherapy facilities are lacking or grossly inadequate in many developing countries. Over the past 8 years the IAEA and WHO have shown more interest in the problem and treatment of cancer in the developing countries. This paper reviews the role of these international organizations, with emphasis on research activities, education (seminars, workshops, training courses), and technical assistance programs. These include establishment or upgrading of radiotherapy facilities, provision of experts, etc. Scientific papers are published with a view to disseminating current information and research findings in the developing countries. The achievements up to date are assessed and discussed.

An overview of the situation in radiotherapy with emphasis on the developing countries

Radiotherapy services are closely linked to the level of medical care which, in turn, is an important component of the overall health care program, with its development related to social, economic, and educational factors. As a basis for understanding the situation regarding adequate coverage of the population by radiotherapy services, general information about the world population (currently 5 billion), age distribution, frequency of cancer occurrence, and causes of death is presented. For an appreciation of the obstacles that must be overcome, the situation with regard to Gross National Product (GNP), transfer of economic resources, and per capita expenditures for health services is shown. For example, in the developing world, most countries spend less than 5% of their GNP for health, and on a macro scale at least 20 billion U.S. dollars per year are being transferred from the poor nations of the southern hemisphere to the northern hemisphere. Information about the wide range of population coverage with radiotherapy resources and the trend regarding high-energy radiotherapy machines is presented. For example, in North America (USA) there are six high-energy machines for each one million persons, and each machine is used to treat about 230 new patients per year. In other parts of the world, such as large areas of Africa and South-East Asia, there may only be one high-energy radiotherapy machine for 20 to 40 million people, and one machine may be used to treat more than 600 new patients per year. Many cancer patients have no access to radiotherapy services. When estimates of the need for radiotherapy services in the developing world as a consequence of cancer incidence are compared with the current health expenditures, it is concluded that a combined effort of national authorities, donor and financial institutions, professional and scientific societies, and international organizations is required. The knowledge, skills, and technology are available in many excellent radiotherapy centers throughout the world. The key issues are priority and the commitment of sufficient resources.

Optimization of nuclear medicine procedures for the diagnosis and management of thyroid disorders: report of a research coordination meeting held in Vienna, 15-17 December 1986 under the auspices of the International Atomic Energy Agency

The third and final meeting of a coordinated research programme on the diagnosis and management of thyroid disorders was held in Vienna from 15 to 17 December 1986. The participants were from Czechoslovakia, Egypt, Israel, Malaysia and Thailand. Each participant had studied between 500 and 1000 patients for thyroid function evaluation by performing T3, T4 and TSH radioimmunoassays. Each had also used the newly available supersensitive immunoradiometric (IRMA) assay in a group of patients to compare the efficiency of the new assay with that of the conventional assay. A microcomputer was provided to each participant for data analysis. Internal quality control was studied by establishing precision profiles and external quality control was on the basis of pooled standard sera in different ranges. Recommendation for the strategy suggested T4 RIA as the test of first choice in each category of thyroid function. IRMA TSH was suggested as a second test in borderline cases.

The optimization of nuclear medicine procedures for the diagnosis and management of thyroid disorders in developing countries

Thyroid disease is common in developing countries and its management is based on the measurement of thyroid function and the investigation of thyroid masses. This report discusses techniques and outlines a strategy for the measurement of thyroid function using radioimmunoassays of thyroid-related hormones in the blood. It makes proposals for the evaluation of thyroid morphology using echography, pertechnetate imaging and fine needle biopsy. Note is taken of the difficulties facing laboratories in developing countries and the International Atomic Energy Agency is concerned with the practical assessment of these recommendations and of any alternative proposals in this field.

Cell mediated immune (CMI) responsiveness to soluble egg antigen (SEA) and its relation to the occurrence of schistosomal hepatosplenic disease in patients with schistosomiasis mansoni

The delayed intradermal test and migration inhibition tests were used to assess the delayed hypersensitivity in patients with BHF and simple intestinal bilharziasis using SEA. All bilharzial patients gave a positive intradermal test. The specificity of the intradermal test using SEA is demonstrated clearly by the negative response in all control groups.