bims-cagime 2022-02-13 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–02–13
thirty papers selected by
Kıvanç Görgülü, Technical University of Munich

Spatially resolved isotope tracing reveals tissue metabolic activity.
RAS-mediated tumor stress adaptation and the targeting opportunities it presents.
The hallmarks of cancer metabolism: Still emerging.
Shared genetic and epigenetic changes link aging and cancer.
A short isoform of spermatogenic enzyme GAPDHS functions as a metabolic switch and limits metastasis in melanoma.
The fate of damaged mitochondrial DNA in the cell.
Liquid-liquid phase separation drives cellular function and dysfunction in cancer.
Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants.
The Lipid Droplet Knowledge Portal: A resource for systematic analyses of lipid droplet biology.
A functional genomic approach to actionable gene fusions for precision oncology.
Built to last: lysosome remodeling and repair in health and disease.
Cancer-cell-derived GABA promotes β-catenin-mediated tumour growth and immunosuppression.
A mechanistic modeling framework reveals the key principles underlying tumor metabolism.
STAMP2 suppresses autophagy in prostate cancer cells by modulating the integrated stress response pathway.
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level.
The Impact of the Rate of Weight Loss on Body Composition and Metabolism.
A noninvasive iRFP713 p53 reporter reveals dynamic p53 activity in response to irradiation and liver regeneration in vivo.
Beth Levine M.D. Prize in Autophagy Research.
Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.
CRAF dimerization with ARAF regulates KRAS-driven tumor growth.
Branching copy number evolution and parallel immune profiles across the regional tumor space of resected pancreatic cancer.
Senescence and the tumor-immune landscape: Implications for cancer immunotherapy.
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey.
p53 directs leader cell behavior, migration, and clearance during epithelial repair.
Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.
Spatial components of molecular tissue biology.
Immunogenic cell stress and death.
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution.
Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.
TISSUE CLEARING.

Nat Methods. 2022 Feb;19(2): 223-230

Spatially resolved isotope tracing reveals tissue metabolic activity.

Lin Wang, Xi Xing, Xianfeng Zeng, S RaElle Jackson, Tara TeSlaa, Osama Al-Dalahmah, Laith Z Samarah, Katharine Goodwin, Lifeng Yang, Melanie R McReynolds, Xiaoxuan Li, Jeremy J Wolff, Joshua D Rabinowitz, Shawn M Davidson.

Isotope tracing has helped to determine the metabolic activities of organs. Methods to probe metabolic heterogeneity within organs are less developed. We couple stable-isotope-labeled nutrient infusion to matrix-assisted laser desorption ionization imaging mass spectrometry (iso-imaging) to quantitate metabolic activity in mammalian tissues in a spatially resolved manner. In the kidney, we visualize gluconeogenic flux and glycolytic flux in the cortex and medulla, respectively. Tricarboxylic acid cycle substrate usage differs across kidney regions; glutamine and citrate are used preferentially in the cortex and fatty acids are used in the medulla. In the brain, we observe spatial gradations in carbon inputs to the tricarboxylic acid cycle and glutamate under a ketogenic diet. In a carbohydrate-rich diet, glucose predominates throughout but in a ketogenic diet, 3-hydroxybutyrate contributes most strongly in the hippocampus and least in the midbrain. Brain nitrogen sources also vary spatially; branched-chain amino acids contribute most in the midbrain, whereas ammonia contributes in the thalamus. Thus, iso-imaging can reveal the spatial organization of metabolic activity.

DOI: https://doi.org/10.1038/s41592-021-01378-y
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
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
Trends Cell Biol. 2022 Feb 07. pii: S0962-8924(22)00005-8. [Epub ahead of print]

Shared genetic and epigenetic changes link aging and cancer.

Daniel J Zabransky, Elizabeth M Jaffee, Ashani T Weeraratna.

  Aging is a universal biological process that increases the risk of multiple diseases including cancer. Growing evidence shows that alterations in the genome and epigenome, driven by similar mechanisms, are found in both aged cells and cancer cells. In this review, we detail the genetic and epigenetic changes associated with normal aging and the mechanisms responsible for these changes. By highlighting genetic and epigenetic alterations in the context of tumorigenesis, cancer progression, and the aging tumor microenvironment, we examine the possible impacts of the normal aging process on malignant transformation. Finally, we examine the implications of age-related genetic and epigenetic alterations in both tumors and patients for the treatment of cancer.

Keywords:  aging; cancer; epigenetics; genetics; tumor microenvironment

DOI:  https://doi.org/10.1016/j.tcb.2022.01.004
Cancer Res. 2022 Feb 11. pii: canres.2062.2021. [Epub ahead of print]

A short isoform of spermatogenic enzyme GAPDHS functions as a metabolic switch and limits metastasis in melanoma.

Jennifer G Gill, Samantha N Leef, Vijayashree Ramesh, Misty S Martin-Sandoval, Aparna D Rao, Lindsey West, Sarah Muh, Wen Gu, Zhiyu Zhao, Gregory A Hosler, Travis W Vandergriff, Alison B Durham, Thomas P Mathews, Arin B Aurora.

Despite being the leading cause of cancer deaths, metastasis remains a poorly understood process. To identify novel regulators of metastasis in melanoma, we performed a large-scale RNA-sequencing screen of 48 samples from patient-derived xenograft (PDX) subcutaneous melanomas and their associated metastases. In comparison to primary tumors, expression of glycolytic genes was frequently decreased in metastases while expression of some TCA cycle genes was increased in metastases. Consistent with these transcriptional changes, melanoma metastases underwent a metabolic switch characterized by decreased levels of glycolytic metabolites and increased abundance of TCA cycle metabolites. A short isoform of glyceraldehye-3-phosphate dehydrogenase, spermatogenic (GAPDHS) lacking the N-terminal domain suppressed metastasis and regulated this metabolic switch. GAPDHS was downregulated in metastatic nodules from PDX models as well as in human patients. Overexpression of GAPDHS was sufficient to block melanoma metastasis, while its inhibition promoted metastasis, decreased glycolysis, and increased levels of certain TCA cycle metabolites and their derivatives including citrate, fumarate, malate, and aspartate. Isotope tracing studies indicated that GADPHS mediates this shift through changes in pyruvate carboxylase activity and aspartate synthesis, both metabolic pathways critical for cancer survival and metastasis. Together these data identify a short isoform of GAPDHS that limits melanoma metastasis and regulates central carbon metabolism.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-2062
Biochim Biophys Acta Mol Cell Res. 2022 Feb 04. pii: S0167-4889(22)00024-6. [Epub ahead of print] 119233

The fate of damaged mitochondrial DNA in the cell.

Siyang Liao, Li Chen, Zhiyin Song, He He.

  Mitochondrion is a double membrane organelle that is responsible for cellular respiration and production of most of the ATP in eukaryotic cells. Mitochondrial DNA (mtDNA) is the genetic material carried by mitochondria, which encodes some essential subunits of respiratory complexes independent of nuclear DNA. Normally, mtDNA binds to certain proteins to form a nucleoid that is stable in mitochondria. Nevertheless, a variety of physiological or pathological stresses can cause mtDNA damage, and the accumulation of damaged mtDNA in mitochondria leads to mitochondrial dysfunction, which triggers the occurrence of mitochondrial diseases in vivo. In response to mtDNA damage, cell initiates multiple pathways including mtDNA repair, degradation, clearance and release, to recover mtDNA, and maintain mitochondrial quality and cell homeostasis. In this review, we provide our current understanding of the fate of damaged mtDNA, focus on the pathways and mechanisms of removing damaged mtDNA in the cell.

Keywords:  Mitochondria DNA (mtDNA); Mitocytosis; Mitophagy; mtDNA release

DOI:  https://doi.org/10.1016/j.bbamcr.2022.119233
Nat Rev Cancer. 2022 Feb 11.

Liquid-liquid phase separation drives cellular function and dysfunction in cancer.

Sohum Mehta, Jin Zhang.

Cancer is a disease of uncontrollably reproducing cells. It is governed by biochemical pathways that have escaped the regulatory bounds of normal homeostatic balance. This balance is maintained through precise spatiotemporal regulation of these pathways. The formation of biomolecular condensates via liquid-liquid phase separation (LLPS) has recently emerged as a widespread mechanism underlying the spatiotemporal coordination of biological activities in cells. Biomolecular condensates are widely observed to directly regulate key cellular processes involved in cancer cell pathology, and the dysregulation of LLPS is increasingly implicated as a previously hidden driver of oncogenic activity. In this Perspective, we discuss how LLPS shapes the biochemical landscape of cancer cells.

DOI: https://doi.org/10.1038/s41568-022-00444-7
Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00033-X. [Epub ahead of print]38(6): 110322

Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants.

Imran Khan, Akiko Koide, Mariyam Zuberi, Gayatri Ketavarapu, Eric Denbaum, Kai Wen Teng, J Matthew Rhett, Russell Spencer-Smith, G Aaron Hobbs, Ernest Ramsay Camp, Shohei Koide, John P O'Bryan.

  RAS guanosine triphosphatases (GTPases) are mutated in nearly 20% of human tumors, making them an attractive therapeutic target. Following our discovery that nucleotide-free RAS (apo RAS) regulates cell signaling, we selectively target this state as an approach to inhibit RAS function. Here, we describe the R15 monobody that exclusively binds the apo state of all three RAS isoforms in vitro, regardless of the mutation status, and captures RAS in the apo state in cells. R15 inhibits the signaling and transforming activity of a subset of RAS mutants with elevated intrinsic nucleotide exchange rates (i.e., fast exchange mutants). Intracellular expression of R15 reduces the tumor-forming capacity of cancer cell lines driven by select RAS mutants and KRAS(G12D)-mutant patient-derived xenografts (PDXs). Thus, our approach establishes an opportunity to selectively inhibit a subset of RAS mutants by targeting the apo state with drug-like molecules.

Keywords:  PDX; anti-RAS biologics; apo-RAS; colon cancer; lung cancer; monobody; multiplex imaging; pancreatic cancer; protein engineering; tumorigenesis

DOI:  https://doi.org/10.1016/j.celrep.2022.110322
Dev Cell. 2022 Feb 07. pii: S1534-5807(22)00003-X. [Epub ahead of print]57(3): 387-397.e4

The Lipid Droplet Knowledge Portal: A resource for systematic analyses of lipid droplet biology.

Niklas Mejhert, Katlyn R Gabriel, Scott Frendo-Cumbo, Natalie Krahmer, Jiunn Song, Leena Kuruvilla, Chandramohan Chitraju, Sebastian Boland, Dong-Keun Jang, Marcin von Grotthuss, Maria C Costanzo, Mikael Rydén, James A Olzmann, Jason Flannick, Noël P Burtt, Robert V Farese, Tobias C Walther.

  Lipid droplets (LDs) are organelles of cellular lipid storage with fundamental roles in energy metabolism and cell membrane homeostasis. There has been an explosion of research into the biology of LDs, in part due to their relevance in diseases of lipid storage, such as atherosclerosis, obesity, type 2 diabetes, and hepatic steatosis. Consequently, there is an increasing need for a resource that combines datasets from systematic analyses of LD biology. Here, we integrate high-confidence, systematically generated human, mouse, and fly data from studies on LDs in the framework of an online platform named the "Lipid Droplet Knowledge Portal" (https://lipiddroplet.org/). This scalable and interactive portal includes comprehensive datasets, across a variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. This resource is a powerful platform that can be utilized to identify determinants of lipid storage.

Keywords:  C16orf54; MSRB3; inflammation; proteasome; protein targeting; proximity labeling; sterol ester; triacylglycerol

DOI:  https://doi.org/10.1016/j.devcel.2022.01.003
Sci Adv. 2022 Feb 11. 8(6): eabm2382

A functional genomic approach to actionable gene fusions for precision oncology.

Jun Li, Hengyu Lu, Patrick Kwok-Shing Ng, Angeliki Pantazi, Carman Ka Man Ip, Kang Jin Jeong, Bianca Amador, Richard Tran, Yiu Huen Tsang, Lixing Yang, Xingzhi Song, Turgut Dogruluk, Xiaojia Ren, Angela Hadjipanayis, Christopher A Bristow, Semin Lee, Melanie Kucherlapati, Michael Parfenov, Jiabin Tang, Sahil Seth, Harshad S Mahadeshwar, Kamalika Mojumdar, Dong Zeng, Jianhua Zhang, Alexei Protopopov, Jonathan G Seidman, Chad J Creighton, Yiling Lu, Nidhi Sahni, Kenna R Shaw, Funda Meric-Bernstam, Andrew Futreal, Lynda Chin, Kenneth L Scott, Raju Kucherlapati, Gordon B Mills, Han Liang.

Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize ~100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology.

DOI: https://doi.org/10.1126/sciadv.abm2382
Trends Cell Biol. 2022 Feb 02. pii: S0962-8924(22)00001-0. [Epub ahead of print]

Built to last: lysosome remodeling and repair in health and disease.

Roberto Zoncu, Rushika M Perera.

  Lysosomes play major roles in growth regulation and catabolism and are recognized as critical mediators of cellular remodeling. An emerging theme is how the lysosome is itself subjected to extensive remodeling in order to perform specific tasks that meet the changing demands of the cell. Accordingly, lysosomes can sustain physical damage and undergo dramatic changes in composition following pathogen infection, accumulation of protein aggregates, or cellular transformation, necessitating dedicated pathways for their repair, remodeling, and restoration. In this review, we focus on emerging molecular mechanisms for piecemeal remodeling of lysosomal components and wholesale repair and discuss their implications in physiological and pathogenic challenges such as cancer, neurodegeneration, and pathogen infection.

Keywords:  cancer; infection; lysosome; membrane damage; neurodegeneration; repair

DOI:  https://doi.org/10.1016/j.tcb.2021.12.009
Nat Cell Biol. 2022 Feb 10.

Cancer-cell-derived GABA promotes β-catenin-mediated tumour growth and immunosuppression.

De Huang, Yan Wang, J Will Thompson, Tao Yin, Peter B Alexander, Diyuan Qin, Poorva Mudgal, Haiyang Wu, Yaosi Liang, Lianmei Tan, Christopher Pan, Lifeng Yuan, Ying Wan, Qi-Jing Li, Xiao-Fan Wang.

Many cancers have an unusual dependence on glutamine. However, most previous studies have focused on the contribution of glutamine to metabolic building blocks and the energy supply. Here, we report that cancer cells with aberrant expression of glutamate decarboxylase 1 (GAD1) rewire glutamine metabolism for the synthesis of γ-aminobutyric acid (GABA)-a prominent neurotransmitter-in non-nervous tissues. An analysis of clinical samples reveals that increased GABA levels predict poor prognosis. Mechanistically, we identify a cancer-intrinsic pathway through which GABA activates the GABAB receptor to inhibit GSK-3β activity, leading to enhanced β-catenin signalling. This GABA-mediated β-catenin activation both stimulates tumour cell proliferation and suppresses CD8+ T cell intratumoural infiltration, such that targeting GAD1 or GABABR in mouse models overcomes resistance to anti-PD-1 immune checkpoint blockade therapy. Our findings uncover a signalling role for tumour-derived GABA beyond its classic function as a neurotransmitter that can be targeted pharmacologically to reverse immunosuppression.

DOI: https://doi.org/10.1038/s41556-021-00820-9
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
Am J Cancer Res. 2022 ;12(1): 327-336

STAMP2 suppresses autophagy in prostate cancer cells by modulating the integrated stress response pathway.

Jørgen Sikkeland, Matthew Yoke Wui Ng, Hatice Zeynep Nenseth, Bilal Unal, Su Qu, Yang Jin, Anne Simonsen, Fahri Saatcioglu.

Six Transmembrane Protein of Prostate 2 (STAMP2) is critical for prostate cancer (PCa) growth. We previously showed that STAMP2 regulates the expression of stress induced transcription factor ATF4, which is implicated in starvation-induced autophagy. We therefore investigated whether STAMP2 is involved in the regulation of autophagy in PCa cells. Here we show that STAMP2 suppresses autophagy in PCa cells through modulation of the integrated stress response axis. We also find that STAMP2 regulates mitochondrial respiration. These findings suggest that STAMP2 has significant metabolic effects through mitochondrial function and autophagy, both of which support PCa growth.

Keywords: ATF4; Prostate cancer; STAMP2; autophagy; eIF2α; integrated stress response; mitochondria
Science. 2022 Feb 11. 375(6581): 681-686

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level.

Yanxiang Deng, Marek Bartosovic, Petra Kukanja, Di Zhang, Yang Liu, Graham Su, Archibald Enninful, Zhiliang Bai, Gonçalo Castelo-Branco, Rong Fan.

Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.

DOI: https://doi.org/10.1126/science.abg7216
Curr Obes Rep. 2022 Feb 08.

The Impact of the Rate of Weight Loss on Body Composition and Metabolism.

Adam Fogarasi, Katherine Gonzalez, Maria Dalamaga, Faidon Magkos.

   PURPOSE OF REVIEW: Weight loss has multiple beneficial effects on body composition and metabolism, but whether these depend on the rate at which body weight is lost is not clear. We analyzed data from studies in which the same amount of weight loss was induced rapidly or gradually.
RECENT FINDINGS: Thirteen studies were included in which the same percentage weight loss was achieved at slow or fast rates (range: 0.2 to 3.2 kg/week) by means of dietary calorie restriction, exercise, and bariatric surgery. Faster rates of weight loss may result in more fat-free mass and less fat mass being lost during the dynamic phase of weight reduction compared with slower rates of weight loss, in conjunction with greater declines in resting energy expenditure. However, these differences are attenuated after 2-4 weeks of stabilization at the new, lower body weight, and do not affect the rate and amount of weight regain 9-33 months later (nor the tissue composition of regained weight). Differences in waist circumference, visceral and liver fat contents, resting blood pressure, fasting blood lipid profile, and insulin and adipokine concentrations in response to different rates of weight loss are trivial. The decline in fasting glucose concentration and the improvement in insulin sensitivity after 6-11% weight loss are both greater with rapid than gradual weight loss, but not different after 18-20% weight loss. Changes in body composition and metabolism after losing the same amount of body weight at different rates are largely similar, and occasional differences are likely not meaningful clinically for the long-term management of obesity and cardiometabolic diseases.

Keywords:  Body composition; Fast; Gradual; Insulin sensitivity; Metabolic risk factors; Obesity; Rapid; Slow

DOI:  https://doi.org/10.1007/s13679-022-00470-4
Sci Signal. 2022 Feb 08. 15(720): eabd9099

A noninvasive iRFP713 p53 reporter reveals dynamic p53 activity in response to irradiation and liver regeneration in vivo.

Timothy J Humpton, Andreas K Hock, Christos Kiourtis, Marco De Donatis, Frédéric Fercoq, Colin Nixon, Sheila Bryson, Douglas Strathdee, Leo M Carlin, Thomas G Bird, Karen Blyth, Karen H Vousden.

Genetically encoded probes are widely used to visualize cellular processes in vitro and in vivo. Although effective in cultured cells, fluorescent protein tags and reporters are suboptimal in vivo because of poor tissue penetration and high background signal. Luciferase reporters offer improved signal-to-noise ratios but require injections of luciferin that can lead to variable responses and that limit the number and timing of data points that can be gathered. Such issues in studying the critical transcription factor p53 have limited insight on its activity in vivo during development and tissue injury responses. Here, by linking the expression of the near-infrared fluorescent protein iRFP713 to a synthetic p53-responsive promoter, we generated a knock-in reporter mouse that enabled noninvasive, longitudinal analysis of p53 activity in vivo in response to various stimuli. In the developing embryo, this model revealed the timing and localization of p53 activation. In adult mice, the model monitored p53 activation in response to irradiation and paracetamol- or CCl4-induced liver regeneration. After irradiation, we observed potent and sustained activation of p53 in the liver, which limited the production of reactive oxygen species (ROS) and promoted DNA damage resolution. We propose that this new reporter may be used to further advance our understanding of various physiological and pathophysiological p53 responses.

DOI: https://doi.org/10.1126/scisignal.abd9099
Autophagy. 2021 Sep;17(9): 2053

Beth Levine M.D. Prize in Autophagy Research.

Ellen S Vitetta, Melanie H Cobb, Helen H Hobbs, Lora Hooper, Sean J Morrison, Kim Orth, Julie Pfeiffer, Michael K Rosen, Joseph S Takahashi, Thomas Wang.

DOI: https://doi.org/10.1080/15548627.2021.1962170
Dev Cell. 2022 Feb 07. pii: S1534-5807(22)00006-5. [Epub ahead of print]57(3): 310-328.e9

Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.

Preetish Kadur Lakshminarasimha Murthy, Rui Xi, Diana Arguijo, Jeffrey I Everitt, Dewran D Kocak, Yoshihiko Kobayashi, Aline Bozec, Silvestre Vicent, Shengli Ding, Gregory E Crawford, David Hsu, Purushothama Rao Tata, Timothy Reddy, Xiling Shen.

  Oncogenic Kras induces a hyper-proliferative state that permits cells to progress to neoplasms in diverse epithelial tissues. Depending on the cell of origin, this also involves lineage transformation. Although a multitude of downstream factors have been implicated in these processes, the precise chronology of molecular events controlling them remains elusive. Using mouse models, primary human tissues, and cell lines, we show that, in Kras-mutant alveolar type II cells (AEC2), FOSL1-based AP-1 factor guides the mSWI/SNF complex to increase chromatin accessibility at genomic loci controlling the expression of genes necessary for neoplastic transformation. We identified two orthogonal processes in Kras-mutant distal airway club cells. The first promoted their transdifferentiation into an AEC2-like state through NKX2.1, and the second controlled oncogenic transformation through the AP-1 complex. Our results suggest that neoplasms retain an epigenetic memory of their cell of origin through cell-type-specific transcription factors. Our analysis showed that a cross-tissue-conserved AP-1-dependent chromatin remodeling program regulates carcinogenesis.

Keywords:  ATAC-seq; Fosl1; KRAS; NSCLC; adenocarcinoma; alveolar type II cell; club cell; epigenetics; intestinal stem cell; lung

DOI:  https://doi.org/10.1016/j.devcel.2022.01.006
Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00067-5. [Epub ahead of print]38(6): 110351

CRAF dimerization with ARAF regulates KRAS-driven tumor growth.

Avinashnarayan Venkatanarayan, Jason Liang, Ivana Yen, Frances Shanahan, Benjamin Haley, Lilian Phu, Erik Verschueren, Trent B Hinkle, David Kan, Ehud Segal, Jason E Long, Tony Lima, Nicholas P D Liau, Jawahar Sudhamsu, Jason Li, Christiaan Klijn, Robert Piskol, Melissa R Junttila, Andrey S Shaw, Mark Merchant, Matthew T Chang, Donald S Kirkpatrick, Shiva Malek.

  KRAS, which is mutated in ∼30% of all cancers, activates the RAF-MEK-ERK signaling cascade. CRAF is required for growth of KRAS mutant lung tumors, but the requirement for CRAF kinase activity is unknown. Here, we show that subsets of KRAS mutant tumors are dependent on CRAF for growth. Kinase-dead but not dimer-defective CRAF rescues growth inhibition, suggesting that dimerization but not kinase activity is required. Quantitative proteomics demonstrates increased levels of CRAF:ARAF dimers in KRAS mutant cells, and depletion of both CRAF and ARAF rescues the CRAF-loss phenotype. Mechanistically, CRAF depletion causes sustained ERK activation and induction of cell-cycle arrest, while treatment with low-dose MEK or ERK inhibitor rescues the CRAF-loss phenotype. Our studies highlight the role of CRAF in regulating MAPK signal intensity to promote tumorigenesis downstream of mutant KRAS and suggest that disrupting CRAF dimerization or degrading CRAF may have therapeutic benefit.

Keywords:  ARAF; BRAF; CRAF; ERK; KRAS; MAPK; MEK; cancer; dimerization; kinase

DOI:  https://doi.org/10.1016/j.celrep.2022.110351
Mol Cancer Res. 2022 Feb 11. pii: molcanres.MCR-21-0986-E.2021. [Epub ahead of print]

Branching copy number evolution and parallel immune profiles across the regional tumor space of resected pancreatic cancer.

Alexandra Petersson, Natalie Andersson, Sofie Olsson Hau, Jakob Eberhard, Jenny Karlsson, Subhayan Chattopadhyay, Anders Valind, Jacob Elebro, Bjorn Nodin, Karin Leandersson, David Gisselsson, Karin Jirstrom.

Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double immunohistochemical staining. Copy number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, a FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated PDAC patients. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected. Implications: Evolutionary copy number patterns may be associated with survival in patients with resected PDAC.

DOI: https://doi.org/10.1158/1541-7786.MCR-21-0986
Semin Cancer Biol. 2022 Feb 07. pii: S1044-579X(22)00026-8. [Epub ahead of print]

Senescence and the tumor-immune landscape: Implications for cancer immunotherapy.

Loretah Chibaya, Jarin Snyder, Marcus Ruscetti.

  Cancer therapies, including conventional chemotherapy, radiation, and molecularly targeted agents, can lead to tumor eradication through a variety of mechanisms. In addition to their effects on tumor cell growth and survival, these regimens can also influence the surrounding tumor-immune microenvironment in ways that ultimately impact therapy responses. A unique biological outcome of cancer therapy is induction of cellular senescence. Senescence is a damage-induced stress program that leads to both the durable arrest of tumor cells and remodeling the tumor-immune microenvironment through activation of a collection pleiotropic cytokines, chemokines, growth factors, and proteinases known as the senescence-associated secretory phenotype (SASP). Depending on the cancer context and the mechanism of action of the therapy, the SASP produced following therapy-induced senescence (TIS) can promote anti-tumor immunity that enhances therapeutic efficacy, or alternatively chronic inflammation that leads to therapy failure and tumor relapse. Thus, a deeper understanding of the mechanisms regulating the SASP and components necessary for robust anti-immune surveillance in different cancer and therapy contexts are key to harnessing senescence for tumor control. Here we draw a roadmap to modulate TIS and its immune-stimulating features for cancer immunotherapy.

Keywords:  Cellular senescence; Immunotherapy; Senescence-associated secretory phenotype; Senotherapeutics; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.semcancer.2022.02.005
F1000Res. 2022 ;pii: ISCB Comm J-98. [Epub ahead of print]11

Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey.

Yasin Kaya, Tülay Karakulak, Cemil Can Saylan, E Ravza Gür, Engin Tatlıdil, Sevilay Güleşen, Fatma Betül Dinçaslan, Handan Melike Dönertaş.

  The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.

Keywords:  10 years; iscb; student council; turkey

DOI:  https://doi.org/10.12688/f1000research.107886.1
Science. 2022 Feb 11. 375(6581): eabl8876

p53 directs leader cell behavior, migration, and clearance during epithelial repair.

Kasia Kozyrska, Giulia Pilia, Medhavi Vishwakarma, Laura Wagstaff, Maja Goschorska, Silvia Cirillo, Saad Mohamad, Kelli Gallacher, Rafael E Carazo Salas, Eugenia Piddini.

Epithelial cells migrate across wounds to repair injured tissue. Leader cells at the front of migrating sheets often drive this process. However, it is unclear how leaders emerge from an apparently homogeneous epithelial cell population. We characterized leaders emerging from epithelial monolayers in cell culture and found that they activated the stress sensor p53, which was sufficient to initiate leader cell behavior. p53 activated the cell cycle inhibitor p21WAF1/CIP1, which in turn induced leader behavior through inhibition of cyclin-dependent kinase activity. p53 also induced crowding hypersensitivity in leader cells such that, upon epithelial closure, they were eliminated by cell competition. Thus, mechanically induced p53 directs emergence of a transient population of leader cells that drive migration and ensures their clearance upon epithelial repair.

DOI: https://doi.org/10.1126/science.abl8876
Heliyon. 2022 Jan;8(1): e08762

Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.

Pekka Ruusuvuori, Masi Valkonen, Kimmo Kartasalo, Mira Valkonen, Tapio Visakorpi, Matti Nykter, Leena Latonen.

  Histological changes in tissue are of primary importance in pathological research and diagnosis. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue. Conventional histopathological assessments are performed from individual tissue sections, leading to the loss of three-dimensional context of the tissue. Yet, the tissue context and spatial determinants are critical in several pathologies, such as in understanding growth patterns of cancer in its local environment. Here, we develop computational methods for visualization and quantitative assessment of histopathological alterations in three dimensions. First, we reconstruct the 3D representation of the whole organ from serial sectioned tissue. Then, we proceed to analyze the histological characteristics and regions of interest in 3D. As our example cases, we use whole slide images representing hematoxylin-eosin stained whole mouse prostates in a Pten+/- mouse prostate tumor model. We show that quantitative assessment of tumor sizes, shapes, and separation between spatial locations within the organ enable characterizing and grouping tumors. Further, we show that 3D visualization of tissue with computationally quantified features provides an intuitive way to observe tissue pathology. Our results underline the heterogeneity in composition and cellular organization within individual tumors. As an example, we show how prostate tumors have nuclear density gradients indicating areas of tumor growth directions and reflecting varying pressure from the surrounding tissue. The methods presented here are applicable to any tissue and different types of pathologies. This work provides a proof-of-principle for gaining a comprehensive view from histology by studying it quantitatively in 3D.

Keywords:  3D reconstruction; Histology; Image analysis; Quantitative imaging; Spatial analysis; Tissue analysis; Visualization

DOI:  https://doi.org/10.1016/j.heliyon.2022.e08762
Nat Biotechnol. 2022 Feb 07.

Spatial components of molecular tissue biology.

Giovanni Palla, David S Fischer, Aviv Regev, Fabian J Theis.

Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly evolving, making it possible to comprehensively characterize cells and tissues in health and disease. To maximize the biological insights obtained using these techniques, it is critical to both clearly articulate the key biological questions in spatial analysis of tissues and develop the requisite computational tools to address them. Developers of analytical tools need to decide on the intrinsic molecular features of each cell that need to be considered, and how cell shape and morphological features are incorporated into the analysis. Also, optimal ways to compare different tissue samples at various length scales are still being sought. Grouping these biological problems and related computational algorithms into classes across length scales, thus characterizing common issues that need to be addressed, will facilitate further progress in spatial transcriptomics and proteomics.

DOI: https://doi.org/10.1038/s41587-021-01182-1
Nat Immunol. 2022 Feb 10.

Immunogenic cell stress and death.

Guido Kroemer, Claudia Galassi, Laurence Zitvogel, Lorenzo Galluzzi.

Dying mammalian cells emit numerous signals that interact with the host to dictate the immunological correlates of cellular stress and death. In the absence of reactive antigenic determinants (which is generally the case for healthy cells), such signals may drive inflammation but cannot engage adaptive immunity. Conversely, when cells exhibit sufficient antigenicity, as in the case of infected or malignant cells, their death can culminate with adaptive immune responses that are executed by cytotoxic T lymphocytes and elicit immunological memory. Suggesting a key role for immunogenic cell death (ICD) in immunosurveillance, both pathogens and cancer cells evolved strategies to prevent the recognition of cell death as immunogenic. Intriguingly, normal cells succumbing to conditions that promote the formation of post-translational neoantigens (for example, oxidative stress) can also drive at least some degree of antigen-specific immunity, pointing to a novel implication of ICD in the etiology of non-infectious, non-malignant disorders linked to autoreactivity.

DOI: https://doi.org/10.1038/s41590-022-01132-2
Nat Commun. 2022 Feb 09. 13(1): 781

A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution.

Michele Bortolomeazzi, Lucia Montorsi, Damjan Temelkovski, Mohamed Reda Keddar, Amelia Acha-Sagredo, Michael J Pitcher, Gianluca Basso, Luigi Laghi, Manuel Rodriguez-Justo, Jo Spencer, Francesca D Ciccarelli.

Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires multiple tools, restricting analytical scalability and result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPLexed Images), a flexible and technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After raw image processing, SIMPLI performs a spatially resolved, single-cell analysis of the tissue slide as well as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for large datasets. SIMPLI produces multiple tabular and graphical outputs at each step of the analysis. Its containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis. Software is available at "SIMPLI [ https://github.com/ciccalab/SIMPLI ]".

DOI: https://doi.org/10.1038/s41467-022-28470-x
Structure. 2022 Feb 02. pii: S0969-2126(22)00006-5. [Epub ahead of print]

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.

Valentina Loconte, Jitin Singla, Angdi Li, Jian-Hua Chen, Axel Ekman, Gerry McDermott, Andrej Sali, Mark Le Gros, Kate L White, Carolyn A Larabell.

  Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.

Keywords:  3D cell mapping; mesoscale analysis; organelle interaction; pancreatic β cell; soft X-ray tomography

DOI:  https://doi.org/10.1016/j.str.2022.01.006
Nat Rev Methods Primers. 2021 ;pii: 84. [Epub ahead of print]1(1):

TISSUE CLEARING.

Douglas S Richardson, Webster Guan, Katsuhiko Matsumoto, Chenchen Pan, Kwanghun Chung, Ali Ertürk, Hiroki R Ueda, Jeff W Lichtman.

Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.

DOI: https://doi.org/10.1038/s43586-021-00080-9