bims-cagime 2022-03-06 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022‒03‒06
thirty-one papers selected by
Kıvanç Görgülü
Technical University of Munich

PP6 deficiency in mice with KRAS mutation and Trp53 loss promotes early death by PDAC with cachexia-like features.
Exploiting senescence for the treatment of cancer.
Extrinsic KRAS signaling shapes the pancreatic microenvironment through fibroblast reprogramming.
Oxygen-sensitive methylation of ULK1 is required for hypoxia-induced autophagy.
Intermittent time-restricted feeding promotes longevity through circadian autophagy.
Metabolic regulation of somatic stem cells in vivo.
Understanding and drugging RAS: 40 years to break the tip of the iceberg.
Tom70-based transcriptional regulation of mitochondrial biogenesis and aging.
Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations.
Molecular hallmarks of heterochronic parabiosis at single-cell resolution.
Neoantigen Quantity and Quality in Relation to Pancreatic Cancer Survival.
In vivo transcriptomic profiling using cell encapsulation identifieseffector pathways of systemic aging.
Selective Autophagy Receptor p62/SQSTM1, a Pivotal Player in Stress and Aging.
Radiation exposure elicits a neutrophil-driven response in healthy lung tissue that enhances metastatic colonization.
The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.
CDK/cyclin dependencies define extreme cancer cell-cycle heterogeneity and collateral vulnerabilities.
Partial p53 reactivation is sufficient to induce cancer regression.
Premature aging in mice with error-prone protein synthesis.
Signalling dynamics, cell decisions, and homeostatic control in health and disease.
Mucin 5AC-mediated CD44/ITGB1 clustering mobilizes adipose-derived mesenchymal stem cells to modulate pancreatic cancer stromal heterogeneity.
Long-lived mitochondrial proteins and why they exist.
Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes.
Nanotherapy: targeting the tumour microenvironment.
Predicting the Overall Survival in Patients with Advanced Pancreatic Cancer by Calculating L3 Skeletal Muscle Index Derived from CT.
A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence.
Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers.
Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.
Insulin and cancer: a tangled web.
Global Cancer Burden Grew From 2010 to 2019.
Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis.
Cancer proteogenomics: current impact and future prospects.

Cancer Sci. 2022 Mar 05.

PP6 deficiency in mice with KRAS mutation and Trp53 loss promotes early death by PDAC with cachexia-like features.

Katsuya Fukui, Miyuki Nomura, Kazuhiro Kishimoto, Nobuhiro Tanuma, Koreyuki Kurosawa, Kosuke Kanazawa, Hiroyuki Kato, Tomoki Sato, Shinji Miura, Koh Miura, Ikuro Sato, Hiroyuki Tsuji, Yoji Yamashita, Keiichi Tamai, Toshio Watanabe, Jun Yasuda, Takuji Tanaka, Kennichi Satoh, Toru Furukawa, Keiichi Jingu, Hiroshi Shima.

  To examine effects of PP6 gene (Ppp6c) deficiency on pancreatic tumor development, we developed pancreas-specific, tamoxifen-inducible Cre-mediated KP (KRAS(G12D) plus Trp53-deficient) mice (cKP mice) and crossed them with Ppp6cflox/flox mice. cKP mice with homozygous Ppp6c deletion developed pancreatic tumors, became emaciated and required euthanisia within 150 days of mutation induction, phenotypes not seen in heterozygous or WT mice. At 30 days, comparative analysis of genes commonly altered in homozygous versus WT Ppp6c cKP mice revealed enhanced activation of Erk and NFκB pathways in homozygotes. By 80 days, the number and size of tumors and number of precancerous lesions significantly increased in pancreas of Ppp6c homozygous relative to heterozygous or WT cKP mice. Ppp6c -/- tumors were pathologically diagnosed as pancreatic ductal adenocarcinoma (PDAC) undergoing the epithelial-mesenchymal transition (EMT), and cancer cells had invaded surrounding tissues in 3 of 6 cases. Transcriptome and metabolome analyses indicated enhanced cancer-specific glycolytic metabolism in Ppp6c-deficient cKP mice and increased expression of inflammatory cytokines. Individual Ppp6c -/- cKP mice showed weight loss, decreased skeletal muscle and adipose tissue, and increased circulating TNF-α and IL-6 levels, suggesting systemic inflammation. Overall, Ppp6c deficiency in the presence of K-ras mutations and Trp53 gene deficiency promoted pancreatic tumorigenesis with generalized cachexia and early death. This study is the first evidence that Ppp6c suppresses mouse pancreatic carcinogenesis and supports use of Ppp6c-deficient cKP mice as a model for developing treatments for cachexia associated with pancreatic cancer.

Keywords:  IL-6; K-ras; cachexia; pancreatic ductal adenocarcinoma; protein phosphatase 6

DOI:  https://doi.org/10.1111/cas.15315
Nat Rev Cancer. 2022 Mar 03.

Exploiting senescence for the treatment of cancer.

Liqin Wang, Lina Lankhorst, René Bernards.

Senescence is a cellular response to a variety of stress signals that is characterized by a stable withdrawal from the cell cycle and major changes in cell morphology and physiology. While most research on senescence has been performed on non-cancer cells, it is evident that cancer cells can also mount a senescence response. In this Review, we discuss how senescence can be induced in cancer cells. We describe the distinctive features of senescent cancer cells and how these changes in cellular physiology might be exploited for the selective eradication of these cells (senolysis). We discuss activation of the host immune system as a particularly attractive way to clear senescent cancer cells. Finally, we consider the challenges and opportunities provided by a 'one-two punch' sequential treatment of cancer with pro-senescence therapy followed by senolytic therapy.

DOI: https://doi.org/10.1038/s41568-022-00450-9
Cell Mol Gastroenterol Hepatol. 2022 Mar 01. pii: S2352-345X(22)00043-1. [Epub ahead of print]

Extrinsic KRAS signaling shapes the pancreatic microenvironment through fibroblast reprogramming.

Ashley Velez-Delgado, Katelyn L Donahue, Z Kristee L Brown, Wenting Du, Valerie Irizarry-Negron, Rosa E Menjivar, Emily L Lasse Opsahl, Nina G Steele, Stephanie The, Jenny Lazarus, Veerin R Sirihorachai, Wei Yan, Samantha B Kemp, Samuel A Kerk, Murali Bollampally, Sion Yang, Michael K Scales, Faith R Avritt, Fatima Lima, Costas A Lyssiotis, Arvind Rao, Howard C Crawford, Filip Bednar, Timothy L Frankel, Benjamin L Allen, Yaqing Zhang, Marina Pasca di Magliano.

  BACKGROUND AND AIMS: Oncogenic KRAS is the hallmark mutation of human pancreatic cancer and a driver of tumorigenesis in genetically engineered mouse models of the disease. While the tumor cell-intrinsic effects of oncogenic Kras expression have been widely studied, its role in regulating the extensive pancreatic tumor microenvironment is less understood.METHODS: Using a genetically engineered mouse model of inducible and reversible oncogenic Kras expression and a combination of approaches that include mass cytometry and single cell RNA sequencing we studied the effect of oncogenic KRAS in the tumor microenvironment.
RESULTS: We have discovered that non-cell autonomous (i.e., extrinsic) oncogenic KRAS signaling reprograms pancreatic fibroblasts, activating an inflammatory gene expression program. As a result, fibroblasts become a hub of extracellular signaling, and the main source of cytokines mediating the polarization of pro-tumorigenic macrophages while also preventing tissue repair.
CONCLUSIONS: Our study provides fundamental new knowledge on the mechanisms underlying the formation of the fibroinflammatory stroma in pancreatic cancer and highlights stromal pathways with the potential to be exploited therapeutically.

Keywords:  fibroblasts; macrophages; pancreatic cancer; transformation

DOI:  https://doi.org/10.1016/j.jcmgh.2022.02.016
Nat Commun. 2022 Mar 04. 13(1): 1172

Oxygen-sensitive methylation of ULK1 is required for hypoxia-induced autophagy.

Jingyi Li, Tao Zhang, Tao Ren, Xiaoyu Liao, Yilong Hao, Je Sun Lim, Jong-Ho Lee, Mi Li, Jichun Shao, Rui Liu.

Hypoxia is a physiological stress that frequently occurs in solid tissues. Autophagy, a ubiquitous degradation/recycling system in eukaryotic cells, renders cells tolerant to multiple stressors. However, the mechanisms underlying autophagy initiation upon hypoxia remains unclear. Here we show that protein arginine methyltransferase 5 (PRMT5) catalyzes symmetrical dimethylation of the autophagy initiation protein ULK1 at arginine 170 (R170me2s), a modification removed by lysine demethylase 5C (KDM5C). Despite unchanged PRMT5-mediated methylation, low oxygen levels decrease KDM5C activity and cause accumulation of ULK1 R170me2s. Dimethylation of ULK1 promotes autophosphorylation at T180, a prerequisite for ULK1 activation, subsequently causing phosphorylation of Atg13 and Beclin 1, autophagosome formation, mitochondrial clearance and reduced oxygen consumption. Further, expression of a ULK1 R170K mutant impaired cell proliferation under hypoxia. This study identifies an oxygen-sensitive methylation of ULK1 with an important role in hypoxic stress adaptation by promoting autophagy induction.

DOI: https://doi.org/10.1038/s41467-022-28831-6
Autophagy. 2022 Feb 27. 1-2

Intermittent time-restricted feeding promotes longevity through circadian autophagy.

Zhangyuan Yin, Daniel J Klionsky.

  Macroautophagy/autophagy plays crucial roles in aging and the pathogenesis of age-related diseases. Studies in various animal models demonstrate the conserved requirement for autophagy-related genes in multiple anti-aging interventions. A recent study from the Shirasu-Hiza lab showed that a newly designed intermittent time-restricted feeding (iTRF) dietary regimen can robustly extend fly healthspan and lifespan through circadian rhythm-dependent activation of autophagy. The night-specific induction of autophagy is both necessary and sufficient for iTRF-mediated health benefits. The study provides the intriguing possibility that novel behavioral or pharmaceutical interventions that promote night-specific autophagy can be used to promote healthy aging.

Keywords:  Aging; autophagy; circadian rhythm; lifespan; time-restricted feeding

DOI:  https://doi.org/10.1080/15548627.2022.2039524
Nat Rev Mol Cell Biol. 2022 Feb 28.

Metabolic regulation of somatic stem cells in vivo.

Corbin E Meacham, Andrew W DeVilbiss, Sean J Morrison.

Metabolism has been studied mainly in cultured cells or at the level of whole tissues or whole organisms in vivo. Consequently, our understanding of metabolic heterogeneity among cells within tissues is limited, particularly when it comes to rare cells with biologically distinct properties, such as stem cells. Stem cell function, tissue regeneration and cancer suppression are all metabolically regulated, although it is not yet clear whether there are metabolic mechanisms unique to stem cells that regulate their activity and function. Recent work has, however, provided evidence that stem cells do have a metabolic signature that is distinct from that of restricted progenitors and that metabolic changes influence tissue homeostasis and regeneration. Stem cell maintenance throughout life in many tissues depends upon minimizing anabolic pathway activation and cell division. Consequently, stem cell activation by tissue injury is associated with changes in mitochondrial function, lysosome activity and lipid metabolism, potentially at the cost of eroding self-renewal potential. Stem cell metabolism is also regulated by the environment: stem cells metabolically interact with other cells in their niches and are able to sense and adapt to dietary changes. The accelerating understanding of stem cell metabolism is revealing new aspects of tissue homeostasis with the potential to promote tissue regeneration and cancer suppression.

DOI: https://doi.org/10.1038/s41580-022-00462-1
Dis Model Mech. 2022 Feb 01. pii: dmm049519. [Epub ahead of print]15(2):

Understanding and drugging RAS: 40 years to break the tip of the iceberg.

Donita C Brady, Julija Hmeljak, Arvin C Dar.

  Several cancers and rare genetic diseases are caused by dysregulation in the RAS signaling pathway. RAS proteins serve as molecular switches that regulate pathways involved in cellular growth, differentiation and survival. These pathways have been an intense area of investigation for four decades, since the initial identification of somatic RAS mutations linked to human cancers. In the past few years, inhibitors against several RAS effectors, as well as direct inhibitors of the K-RAS mutant G12C, have been developed. This Special Issue in DMM includes original Research articles on RAS-driven cancers and RASopathies. The articles provide insights into mechanisms and biomarkers, and evaluate therapeutic targets. Several articles also present new disease models, whereas others describe technologies or approaches to evaluate the function of RAS in vivo. The collection also includes a series of Review articles on RAS biology and translational aspects of defining and treating RAS-driven diseases. In this Editorial, we summarize this collection and discuss the potential impact of the articles within this evolving area of research. We also identify areas of growth and possible future developments.

Keywords:  Cancer; Developmental disorders; RAS inhibitor; RAS pathway

DOI:  https://doi.org/10.1242/dmm.049519
Elife. 2022 Mar 02. pii: e75658. [Epub ahead of print]11

Tom70-based transcriptional regulation of mitochondrial biogenesis and aging.

Qingqing Liu, Catherine E Chang, Alexandra C Wooldredge, Benjamin Fong, Brian K Kennedy, Chuankai Zhou.

  Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.

Keywords:  S. cerevisiae; cell biology

DOI:  https://doi.org/10.7554/eLife.75658
Autophagy. 2022 Feb 28. 1-14

Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations.

Jing Xu, Kevin C Yang, Nancy Erro Go, Shane Colborne, Cally J Ho, Elham Hosseini-Beheshti, Alf H Lystad, Anne Simonsen, Emma Tomlinson Guns, Gregg B Morin, Sharon M Gorski.

  Chloroquine (CQ), a lysosomotropic agent, is commonly used to inhibit lysosomal degradation and macroautophagy/autophagy. Here we investigated the cell-extrinsic effects of CQ on secretion. We showed that lysosomal and autophagy inhibition by CQ altered the secretome, and induced the release of Atg8 orthologs and autophagy receptors. Atg8-family proteins, in particular, were secreted inside small extracellular vesicles (sEVs) in a lipidation-dependent manner. CQ treatment enhanced the release of Atg8-family proteins inside sEVs. Using full-length ATG16L1 and an ATG16L1 mutant that enables Atg8-family protein lipidation on double but not on single membranes, we demonstrated that LC3B is released in two distinct sEV populations: one enriched with SDCBP/Syntenin-1, CD63, and endosomal lipidated LC3B, and another that contains LC3B but is not enriched with SDCBP/Syntenin-1 or CD63, and which our data supports as originating from a double-membrane source. Our findings underscore the context-dependency of sEV heterogeneity and composition, and illustrate the integration of autophagy and sEV composition in response to lysosomal inhibition.Abbreviations: ACTB: actin beta; ANOVA: analysis of variance; ATG4B: autophagy related 4B cysteine peptidase; Atg8: autophagy related 8; ATG16L1: autophagy related 16 like 1; ATP5F1A/ATP5a: ATP synthase F1 subunit alpha; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CASP7: caspase 7; CQ: chloroquine; CD9: CD9 molecule; CD63: CD63 molecule; DAPI: 4',6-diamidino-2-phenylindole; DQ-BSA: dye quenched-bovine serum albumin; ER: endoplasmic reticulum; ERN1/IRE1a: endoplasmic reticulum to nucleus signaling 1; EV: extracellular vesicles; FBS: fetal bovine serum; FDR: false discovery rate; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GO: gene ontology; HCQ: hydroxychloroquine; HSP90AA1: heat shock protein 90 alpha family class A member 1; IP: immunoprecipitation; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LIR: LC3-interacting region; LMNA: lamin A/C; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MS: mass spectrometry; NBR1: NBR1 autophagy cargo receptor; NCOA4: nuclear receptor coactivator 4; NTA: nanoparticle tracking analysis; PE: phosphatidylethanolamine; PECA: probe-level expression change averaging; SDCBP/syntenin-1: syndecan binding protein; SD: standard deviation; SE: secreted; sEV: small extracellular vesicles; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TEM: transmission electron microscopy; TMT: tandem-mass tag; TSG101: tumor susceptibility 101; ULK1: unc-51 like autophagy activating kinase 1; WC: whole cell.

Keywords:  ATG16L1; Atg8; CD63; MAP1LC3B; SDCBP/syntenin-1; autophagy; chloroquine; endosome; extracellular vesicle; lysosome

DOI:  https://doi.org/10.1080/15548627.2022.2039535
Nature. 2022 Mar 02.

Molecular hallmarks of heterochronic parabiosis at single-cell resolution.

Tabula Muris Consortium

The ability to slow or reverse biological ageing would have major implications for mitigating disease risk and maintaining vitality1. Although an increasing number of interventions show promise for rejuvenation2, their effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. Here we performed single-cell RNA sequencing on 20 organs to reveal cell-type-specific responses to young and aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, haematopoietic stem cells and hepatocytes are among those cell types that are especially responsive. On the pathway level, young blood invokes new gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. We observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it in select cell types. Together, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.

DOI: https://doi.org/10.1038/s41586-022-04461-2
Front Med (Lausanne). 2021 ;8 751110

Neoantigen Quantity and Quality in Relation to Pancreatic Cancer Survival.

Iris J M Levink, Lodewijk A A Brosens, Sander S Rensen, Merel R Aberle, Steven S W Olde Damink, Djuna L Cahen, Sonja I Buschow, Gwenny M Fuhler, Maikel P Peppelenbosch, Marco J Bruno.

  Introduction: Factors underlying antitumor immunity in pancreatic cancer (PC) are poorly understood. We hypothesized that not neoantigen quantity, but quality, is related to immune cell infiltration and survival.Methodology: We performed genomic and transcriptomic profiling of paired normal, tumor tissue of 13 patients with PC with distinct survival times. Additionally, neoantigens prediction and immunological profiling were performed.
Results: The proportion of neoantigens with a low similarity-to-self score was higher in short-term survivors (p < 0.0001), while mutational load and burden, similarity-to-known-pathogens, and immunogenicity of neoantigens were not associated with immune cell infiltration or survival.
Discussion: No tumor mutational load or neoantigen quantity, but low similarity-to-self score, was associated with immune cell infiltration and survival.

Keywords:  cancer immunity; chromosomal instability disorders; mutation–genetics; neoantigen and shared-antigen vaccine; pancreatic cancer

DOI:  https://doi.org/10.3389/fmed.2021.751110
Elife. 2022 Mar 04. pii: e57393. [Epub ahead of print]11

In vivo transcriptomic profiling using cell encapsulation identifieseffector pathways of systemic aging.

Omid Mashinchian, Xiaotong Hong, Joris Michaud, Eugenia Migliavacca, Gregory Lefebvre, Christophe Boss, Filippo De Franceschi, Emmeran Le Moal, Jasmin Collerette-Tremblay, Joan Isern, Sylviane Metairon, Frederic Raymond, Patrick Descombes, Nicolas Bouche, Pura Muñoz-Cánoves, Jerome N Feige, C Florian Bentzinger.

  Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.

Keywords:  cell biology; mouse

DOI:  https://doi.org/10.7554/eLife.57393
Front Cell Dev Biol. 2022 ;10 793328

Selective Autophagy Receptor p62/SQSTM1, a Pivotal Player in Stress and Aging.

Anita V Kumar, Joslyn Mills, Louis R Lapierre.

  Efficient proteostasis is crucial for somatic maintenance, and its decline during aging leads to cellular dysfunction and disease. Selective autophagy is a form of autophagy mediated by receptors that target specific cargoes for degradation and is an essential process to maintain proteostasis. The protein Sequestosome 1 (p62/SQSTM1) is a classical selective autophagy receptor, but it also has roles in the ubiquitin-proteasome system, cellular metabolism, signaling, and apoptosis. p62 is best known for its role in clearing protein aggregates via aggrephagy, but it has recently emerged as a receptor for other forms of selective autophagy such as mitophagy and lipophagy. Notably, p62 has context-dependent impacts on organismal aging and turnover of p62 usually reflects active proteostasis. In this review, we highlight recent advances in understanding the role of p62 in coordinating the ubiquitin-proteasome system and autophagy. We also discuss positive and negative effects of p62 on proteostatic status and their implications on aging and neurodegeneration. Finally, we relate the link between defective p62 and diseases of aging and examine the utility of targeting this multifaceted protein to achieve proteostatic benefits.

Keywords:  aging; autophagy; neurodegenerative diseases; p62 (sequestosome 1(SQSTM1)); proteasome

DOI:  https://doi.org/10.3389/fcell.2022.793328
Nat Cancer. 2022 Feb;3(2): 173-187

Radiation exposure elicits a neutrophil-driven response in healthy lung tissue that enhances metastatic colonization.

Emma Nolan, Victoria Louise Bridgeman, Luigi Ombrato, Adam Karoutas, Nicolas Rabas, Celine Angeli Natascha Sewneth, Marcos Vasquez, Felipe Silva Rodrigues, Stuart Horswell, Peter Faull, Rebecca Carter, Ilaria Malanchi.

Radiotherapy is one of the most effective approaches to achieve tumor control in cancer patients, although healthy tissue injury due to off-target radiation exposure can occur. In this study, we used a model of acute radiation injury to the lung, in the context of cancer metastasis, to understand the biological link between tissue damage and cancer progression. We exposed healthy mouse lung tissue to radiation before the induction of metastasis and observed a strong enhancement of cancer cell growth. We found that locally activated neutrophils were key drivers of the tumor-supportive preconditioning of the lung microenvironment, governed by enhanced regenerative Notch signaling. Importantly, these tissue perturbations endowed arriving cancer cells with an augmented stemness phenotype. By preventing neutrophil-dependent Notch activation, via blocking degranulation, we were able to significantly offset the radiation-enhanced metastases. This work highlights a pro-tumorigenic activity of neutrophils, which is likely linked to their tissue regenerative functions.

DOI: https://doi.org/10.1038/s43018-022-00336-7
Nat Cancer. 2022 Feb;3(2): 251-261

The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.

Cancer Core Europe consortium

There is a growing need for systems that efficiently support the work of medical teams at the precision-oncology point of care. Here, we present the implementation of the Molecular Tumor Board Portal (MTBP), an academic clinical decision support system developed under the umbrella of Cancer Core Europe that creates a unified legal, scientific and technological platform to share and harness next-generation sequencing data. Automating the interpretation and reporting of sequencing results decrease the need for time-consuming manual procedures that are prone to errors. The adoption of an expert-agreed process to systematically link tumor molecular profiles with clinical actions promotes consistent decision-making and structured data capture across the connected centers. The use of information-rich patient reports with interactive content facilitates collaborative discussion of complex cases during virtual molecular tumor board meetings. Overall, streamlined digital systems like the MTBP are crucial to better address the challenges brought by precision oncology and accelerate the use of emerging biomarkers.

DOI: https://doi.org/10.1038/s43018-022-00332-x
Cell Rep. 2022 Mar 01. pii: S2211-1247(22)00175-9. [Epub ahead of print]38(9): 110448

CDK/cyclin dependencies define extreme cancer cell-cycle heterogeneity and collateral vulnerabilities.

Erik S Knudsen, Vishnu Kumarasamy, Ram Nambiar, Joel D Pearson, Paris Vail, Hanna Rosenheck, Jianxin Wang, Kevin Eng, Rod Bremner, Daniel Schramek, Seth M Rubin, Alana L Welm, Agnieszka K Witkiewicz.

  Progression through G1/S phase of the cell cycle is coordinated by cyclin-dependent kinase (CDK) activities. Here, we find that the requirement for different CDK activities and cyclins in driving cancer cell cycles is highly heterogeneous. The differential gene requirements associate with tumor origin and genetic alterations. We define multiple mechanisms for G1/S progression in RB-proficient models, which are CDK4/6 independent and elicit resistance to FDA-approved inhibitors. Conversely, RB-deficient models are intrinsically CDK4/6 independent, but exhibit differential requirements for cyclin E. These dependencies for CDK and cyclins associate with gene expression programs that denote intrinsically different cell-cycle states. Mining therapeutic sensitivities shows that there are reciprocal vulnerabilities associated with RB1 or CCND1 expression versus CCNE1 or CDKN2A. Together, these findings illustrate the complex nature of cancer cell cycles and the relevance for precision therapeutic intervention.

Keywords:  CDK; E2F; RB; cyclin; cyclin D1; cyclin E; p16; p27

DOI:  https://doi.org/10.1016/j.celrep.2022.110448
J Exp Clin Cancer Res. 2022 Mar 02. 41(1): 80

Partial p53 reactivation is sufficient to induce cancer regression.

Boris Klimovich, Laura Meyer, Nastasja Merle, Michelle Neumann, Alexander M König, Nikolaos Ananikidis, Corinna U Keber, Sabrina Elmshäuser, Oleg Timofeev, Thorsten Stiewe.

  BACKGROUND: Impaired p53 function is one of the central molecular features of a tumor cell and even a partial reduction in p53 activity can increase the cancer risk in mice and men. From a therapeutic perspective it is noteworthy that tumor cells often become addicted to the absence of p53 providing a rationale for developing p53 reactivating compounds to treat cancer patients. Unfortunately, many of the compounds that are currently undergoing preclinical and clinical testing fail to fully reactivate mutant p53 proteins, raising the crucial question: how much p53 activity is needed to elicit a therapeutic effect?METHODS: We have genetically modelled partial p53 reactivation using knock-in mice with inducible expression of the p53 variant E177R. This variant has a reduced ability to bind and transactivate target genes and consequently causes moderate cancer susceptibility. We have generated different syngeneically transplanted and autochthonous mouse models of p53-deficient acute myeloid leukemia and B or T cell lymphoma. After cancer manifestation we have activated E177R expression and analyzed the in vivo therapy response by bioluminescence or magnetic resonance imaging. The molecular response was further characterized in vitro by assays for gene expression, proliferation, senescence, differentiation, apoptosis and clonogenic growth.
RESULTS: We report the conceptually intriguing observation that the p53 variant E177R, which promotes de novo leukemia and lymphoma formation, inhibits proliferation and viability, induces immune cell infiltration and triggers cancer regression in vivo when introduced into p53-deficient leukemia and lymphomas. p53-deficient cancer cells proved to be so addicted to the absence of p53 that even the low-level activity of E177R is detrimental to cancer growth.
CONCLUSIONS: The observation that a partial loss-of-function p53 variant promotes tumorigenesis in one setting and induces regression in another, underlines the highly context-specific effects of individual p53 mutants. It further highlights the exquisite sensitivity of cancer cells to even small changes in p53 activity and reveals that changes in activity level are more important than the absolute level. As such, the study encourages ongoing research efforts into mutant p53 reactivating drugs by providing genetic proof-of-principle evidence that incomplete p53 reactivation may suffice to elicit a therapeutic response.

Keywords:  Leukemia; Lymphoma; Molecular therapy; Mouse models; Tumor suppressor gene; p53; p53 reactivation

DOI:  https://doi.org/10.1186/s13046-022-02269-6
Sci Adv. 2022 Mar 04. 8(9): eabl9051

Premature aging in mice with error-prone protein synthesis.

Dimitri Shcherbakov, Martina Nigri, Rashid Akbergenov, Margarita Brilkova, Matilde Mantovani, Patricia Isnard Petit, Amandine Grimm, Agnieszka A Karol, Youjin Teo, Adrián Cortés Sanchón, Yadhu Kumar, Anne Eckert, Kader Thiam, Petra Seebeck, David P Wolfer, Erik C Böttger.

The main source of error in gene expression is messenger RNA decoding by the ribosome. Translational accuracy has been suggested on a purely correlative basis to positively coincide with maximum possible life span among different rodent species, but causal evidence that translation errors accelerate aging in vivo and limit life span is lacking. We have now addressed this question experimentally by creating heterozygous knock-in mice that express the ribosomal ambiguity mutation RPS9 D95N, resulting in genome-wide error-prone translation. Here, we show that Rps9 D95N knock-in mice exhibit reduced life span and a premature onset of numerous aging-related phenotypes, such as reduced weight, chest deformation, hunchback posture, poor fur condition, and urinary syndrome, together with lymphopenia, increased levels of reactive oxygen species-inflicted damage, accelerated age-related changes in DNA methylation, and telomere attrition. Our results provide an experimental link between translational accuracy, life span, and aging-related phenotypes in mammals.

DOI: https://doi.org/10.1126/sciadv.abl9051
Curr Opin Cell Biol. 2022 Mar 01. pii: S0955-0674(22)00012-6. [Epub ahead of print]75 102066

Signalling dynamics, cell decisions, and homeostatic control in health and disease.

Pablo Oriol Valls, Alessandro Esposito.

Cell signalling engenders cells with the capability to receive and process information from the intracellular and extracellular environments, trigger and execute biological responses, and communicate with each other. Ultimately, cell signalling is responsible for maintaining homeostasis at the cellular, tissue and systemic level. For this reason, cell signalling is a topic of intense research efforts aimed to elucidate how cells coordinate transitions between states in developing and adult organisms in physiological and pathological conditions. Here, we review current knowledge of how cell signalling operates at multiple spatial and temporal scales, focusing on how single-cell analytical techniques reveal mechanisms underpinning cell-to-cell variability, signalling plasticity, and collective cellular responses.

DOI: https://doi.org/10.1016/j.ceb.2022.01.011
Gastroenterology. 2022 Feb 24. pii: S0016-5085(22)00198-6. [Epub ahead of print]

Mucin 5AC-mediated CD44/ITGB1 clustering mobilizes adipose-derived mesenchymal stem cells to modulate pancreatic cancer stromal heterogeneity.

Koelina Ganguly, Jesse L Cox, Dario Ghersi, Paul M Grandgenett, Michael A Hollingsworth, Maneesh Jain, Sushil Kumar, Surinder K Batra.

  BACKGROUND: Secreted mucin 5AC (MUC5AC) promotes pancreatic cancer (PC) progression and chemoresistance, suggesting its clinical association with poor prognosis. RNA sequencing analysis from the autochthonous pancreatic tumors showed a significant stromal alteration upon genetic ablation of Muc5ac. Previously, depletion or targeting the stromal fibroblasts showed an ambiguous effect on PC pathogenesis. Hence, identifying the molecular players and mechanisms driving fibroblast heterogeneity is critical for improved clinical outcomes.METHODS: Autochthonous murine models of PC [KrasG12D, Pdx1-Cre (KC); KrasG12D, Pdx1-Cre, Muc5ac-/- (KCM)] and co-implanted allografts of murine PC cell lines (Muc5ac-WT and CRISPR/Cas-KO) with adipose-derived mesenchymal stem cells (AD-MSCs) were used to assess the role of Muc5ac in stromal heterogeneity. Proliferation, migration, surface expression of cell-adhesion markers on AD-MSCs were measured using live-cell imaging and flow cytometry. MUC5AC-interactome was investigated using mass-spectrometry and ELISA.
RESULTS: The KCM tumors showed a significant decrease in the expression of α-smooth muscle actin and fibronectin compared to histology-matched KC tumors. Our study showed that MUC5AC, carrying tumor secretome, gets enriched in the adipose tissues of tumor-bearing mice and PC patients, promoting CD44/CD29 (integrin-β1) clustering that leads to Rac1 activation and migration of AD-MSCs. Further, treatment with KC-derived serum enhanced proliferation and migration of AD-MSCs, which was abolished upon Muc5ac-depletion or pharmacological inhibition of CXCR2 and Rac1, respectively. The AD-MSCs significantly contribute towards α-SMA-positive CAFs population in Muc5ac-dependent manner, as suggested by autochthonous tumors, co-implantation xenografts, and patient tumors.
CONCLUSION: MUC5AC, secreted during PC progression, enriches in adipose and enhances the mobilization of AD-MSCs. Upon recruitment to pancreatic tumors, AD-MSCs proliferate and contribute towards stromal heterogeneity.

Keywords:  MUC5AC; Mesenchymal stem cells; Pancreatic Cancer; Stroma; cancer-associated fibroblast; chemokines

DOI:  https://doi.org/10.1053/j.gastro.2022.02.032
Trends Cell Biol. 2022 Feb 24. pii: S0962-8924(22)00034-4. [Epub ahead of print]

Long-lived mitochondrial proteins and why they exist.

Ewa Bomba-Warczak, Jeffrey N Savas.

  Intracellular long-lived proteins (LLPs) provide structural support for several highly stable protein complexes and assemblies that play essential roles in ensuring cellular homeostasis and function. Recently, mitochondrial long-lived proteins (mt-LLPs) were discovered within inner mitochondria membranes (IMMs) and cristae invagination in tissues with old postmitotic cells. This observation is at odds with the fact that mitochondria are highly dynamic organelles that are continually remodeled through processes of fission, fusion, biogenesis, and multiple quality control pathways. In this opinion article, we propose that a subset of the mitochondrial proteome persists over long time frames and these mt-LLPs provide key structural support for the lifelong maintenance of mitochondrial structure.

Keywords:  cristae ultrastructure; long-lived proteins; mitochondria; mitochondrial dynamics; protein turnover; stable structures

DOI:  https://doi.org/10.1016/j.tcb.2022.02.001
Annu Rev Biophys. 2022 Feb 03.

Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes.

Pavel V Bashkirov, Peter I Kuzmin, Javier Vera Lillo, Vadim A Frolov.

Cellular membranes self-assemble from and interact with various molecular species. Each molecule locally shapes the lipid bilayer, the soft elastic core of cellular membranes. The dynamic architecture of intracellular membrane systems is based on elastic transformations and lateral redistribution of these elementary shapes, driven by chemical and curvature stress gradients. The minimization of the total elastic stress by such redistribution composes the most basic, primordial mechanism of membrane curvature-composition coupling (CCC). Although CCC is generally considered in the context of dynamic compositional heterogeneity of cellular membrane systems, in this article we discuss a broader involvement of CCC in controlling membrane deformations. We focus specifically on the mesoscale membrane transformations in open, reservoir-governed systems, such as membrane budding, tubulation, and the emergence of highly curved sites of membrane fusion and fission. We reveal that the reshuffling of molecular shapes constitutes an independent deformation mode with complex rheological properties. This mode controls effective elasticity of local deformations as well as stationary elastic stress, thus emerging as a major regulator of intracellular membrane remodeling. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-biophys-011422-100054
Nat Rev Cancer. 2022 Mar 02.

Nanotherapy: targeting the tumour microenvironment.

Santosh Kumar Singh, Rajesh Singh.

DOI: https://doi.org/10.1038/s41568-022-00461-6
Curr Med Imaging. 2022 Mar 03.

Predicting the Overall Survival in Patients with Advanced Pancreatic Cancer by Calculating L3 Skeletal Muscle Index Derived from CT.

Bahattin Özkul, Özlem Özkul Özlem Özkul, Cemil Bilir.

  Background Pancreatic cancer is mostly diagnosed in advanced stages and treatment results are not satisfactory. L3 skeletal muscle index (SMI) has emerged as a prognostic factor in pancreatic cancer patients. We aimed to assess the association between sarcopenia and overall survival in patients with pancreatic cancer in this study. Methods Patients who admitted to Department of Oncology between March 2012 and December 2019 and diagnosed as pancreatic cancer were evaluated. A total of 115 patients who had computerized tomography images and laboratory parameters were included in this retrospective single center study. We defined sarcopenia as a SMI <43,56 cm²/m² for females and <56,44 cm²/m² for males using the receiver operating characteristics (ROC) curve in the study population. Univariate and multivariate analyses were performed by using Cox-regression modelling and survival curves were constructed by using Kaplan-Meier method. Results 70% of the patients were male and the mean age was 64.9±9.9 (mean  SD). 70.6% of female patients and 67.9% of male patients were stage 4. The prevalence of sarcopenia in the whole patient group was 29.6%. By multivariate analysis, SMI (p=0.009) and advanced stage (p=0.003) were found as poor prognostic factor for overall survival (OS). The neutrophil to lymphocyte ratio (NLR) was statistically significant higher in sarcopenic patients than in non-sarcopenic patients (p=0.031). Conclusion In patients, who have sarcopenia at the time of diagnosis may be poorer overall survival of pancreas cancer and SMI may be considered as a potential prognostic factor.

Keywords:  Cancer; computed tomography; overall survival; pancreas; sarcopenia; skeletal muscle index.

DOI:  https://doi.org/10.2174/1573405618666220303105410
Autophagy. 2022 Feb 27. 1-22

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence.

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li, Ming-Qing Li.

  Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated through activation of the LPA receptors (LPAR1 and PPARG/PPARγ)-DDIT4-macroautophagy/autophagy axis, and further upregulation of multiple adhesion factors (e.g., cadherins and selectins) in a CLDN7 (claudin 7)-dependent manner. Additionally, poor trophoblast invasion and placenta development, and a high ratio of embryo loss are observed in Enpp2±, lpar1-/- or PPARG-blocked pregnant mice. Patients with unexplained spontaneous abortion display insufficient autophagy and cell residence of dMφ. In therapeutic studies, supplementation with LPA or the autophagy inducer rapamycin significantly promotes dMφ autophagy and cell residence, and improves embryo resorption in Enpp2± and spontaneous abortion mouse models, which should be dependent on the activation of DDIT4-autophagy-CLDN7-adhesion molecules axis. This observation reveals that inactivation of ENPP2-LPA metabolism and insufficient autophagy of dMφ result in resident obstacle of dMφ and further increase the risk of spontaneous abortion, and provides potential therapeutic strategies to prevent spontaneous abortion.Abbreviations: ACTB: actin beta; ADGRE1/F4/80: adhesion G protein-coupled receptor E1; Atg5: autophagy related 5; ATG13: autophagy related 13; BECN1: beclin 1; CDH1/E-cadherin: cadherin 1; CDH5/VE-cadherin: cadherin 5; CFSE: carboxyfluorescein succinimidyl ester; CLDN7: claudin 7; CSF1/M-CSF: colony stimulating factor 1; CSF2/GM-CSF: colony stimulating factor 2; Ctrl: control; CXCL10/IP-10: chemokine (C-X-C) ligand 10; DDIT4: DNA damage inducible transcript 4; dMφ: decidual macrophage; DSC: decidual stromal cells; ENPP2/ATX: ectonucleotide pyrophosphatase/phosphodiesterase 2; Enpp2±: Enpp2 heterozygous knockout mouse; ENPP2i/PF-8380: ENPP2 inhibitor; EPCAM: epithelial cell adhesion molecule; ESC: endometrial stromal cells; FGF2/b-FGF: fibroblast growth factor 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GPCPD1: glycerophosphocholine phosphodiesterase 1; HE: heterozygote; HIF1A: hypoxia inducible factor 1 subunit alpha; HNF4A: hepatocyte nuclear factor 4 alpha; HO: homozygote; ICAM2: intercellular adhesion molecule 2; IL: interleukin; ITGAV/CD51: integrin subunit alpha V; ITGAM/CD11b: integrin subunit alpha M; ITGAX/CD11b: integrin subunit alpha X; ITGB3/CD61: integrin subunit beta 3; KLRB1/NK1.1: killer cell lectin like receptor B1; KRT7/cytokeratin 7: keratin 7; LPA: lysophosphatidic acid; LPAR: lysophosphatidic acid receptor; lpar1-/-: lpar1 homozygous knockout mouse; LPAR1i/AM966: LPAR1 inhibitor; LY6C: lymphocyte antigen 6 complex, locus C1; LYPLA1: lysophospholipase 1; LYPLA2: lysophospholipase 2; Lyz2: lysozyme 2; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MARVELD2: MARVEL domain containing 2; 3-MA: 3-methyladenine; MBOAT2: membrane bound O-acyltransferase domain containing 2; MGLL: monoglyceride lipase; MRC1/CD206: mannose receptor C-type 1; MTOR: mechanistic target of rapamycin kinase; NP: normal pregnancy; PDGF: platelet derived growth factor; PLA1A: phospholipase A1 member A; PLA2G4A: phospholipase A2 group IVA; PLPP1: phospholipid phosphatase 1; pMo: peripheral blood monocytes; p-MTOR: phosphorylated MTOR; PPAR: peroxisome proliferator activated receptor; PPARG/PPARγ: peroxisome proliferator activated receptor gamma; PPARGi/GW9662: PPARG inhibitor; PTPRC/CD45: protein tyrosine phosphatase receptor type, C; Rapa: rapamycin; RHEB: Ras homolog, mTORC1 binding; SA: spontaneous abortion; SELE: selectin E; SELL: selectin L; siCLDN7: CLDN7-silenced; STAT: signal transducer and activator of transcription; SQSTM1: sequestosome 1; TJP1: tight junction protein 1; VCAM1: vascular cell adhesion molecule 1; WT: wild type.

Keywords:  Abortion; CLDN7; DDIT4; ENPP2; LPAR1; decidual macrophage; lysophosphatidic acid; trophoblast invasion

DOI:  https://doi.org/10.1080/15548627.2022.2039000
Nature. 2022 Mar 02.

Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers.

Yoshihisa Kobayashi, Chhayheng Chhoeu, Jiaqi Li, Kristin S Price, Lesli A Kiedrowski, Jamie L Hutchins, Aaron I Hardin, Zihan Wei, Fangxin Hong, Magda Bahcall, Prafulla C Gokhale, Pasi A Jänne.

RAS family members are the most frequently mutated oncogenes in human cancers. Although KRAS(G12C)-specific inhibitors show clinical activity in patients with cancer1-3, there are no direct inhibitors of NRAS, HRAS or non-G12C KRAS variants. Here we uncover the requirement of the silent KRASG60G mutation for cells to produce a functional KRAS(Q61K). In the absence of this G60G mutation in KRASQ61K, a cryptic splice donor site is formed, promoting alternative splicing and premature protein termination. A G60G silent mutation eliminates the splice donor site, yielding a functional KRAS(Q61K) variant. We detected a concordance of KRASQ61K and a G60G/A59A silent mutation in three independent pan-cancer cohorts. The region around RAS Q61 is enriched in exonic splicing enhancer (ESE) motifs and we designed mutant-specific oligonucleotides to interfere with ESE-mediated splicing, rendering the RAS(Q61) protein non-functional in a mutant-selective manner. The induction of aberrant splicing by antisense oligonucleotides demonstrated therapeutic effects in vitro and in vivo. By studying the splicing necessary for a functional KRAS(Q61K), we uncover a mutant-selective treatment strategy for RASQ61 cancer and expose a mutant-specific vulnerability, which could potentially be exploited for therapy in other genetic contexts.

DOI: https://doi.org/10.1038/s41586-022-04451-4
Science. 2022 Mar 04. 375(6584): 1000-1005

Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.

Aaron N Brooks, Amanda L Hughes, Sandra Clauder-Münster, Leslie A Mitchell, Jef D Boeke, Lars M Steinmetz.

Sequence features of genes and their flanking regulatory regions are determinants of RNA transcript isoform expression and have been used as context-independent plug-and-play modules in synthetic biology. However, genetic context-including the adjacent transcriptional environment-also influences transcript isoform expression levels and boundaries. We used synthetic yeast strains with stochastically repositioned genes to systematically disentangle the effects of sequence and context. Profiling 120 million full-length transcript molecules across 612 genomic perturbations, we observed sequence-independent alterations to gene expression levels and transcript isoform boundaries that were influenced by neighboring transcription. We identified features of transcriptional context that could predict these alterations and used these features to engineer a synthetic circuit where transcript length was controlled by neighboring transcription. This demonstrates how positional context can be leveraged in synthetic genome engineering.

DOI: https://doi.org/10.1126/science.abg0162
Biochem J. 2022 Mar 18. 479(5): 583-607

Insulin and cancer: a tangled web.

Brooks P Leitner, Stephan Siebel, Ngozi D Akingbesote, Xinyi Zhang, Rachel J Perry.

  For a century, since the pioneering work of Otto Warburg, the interwoven relationship between metabolism and cancer has been appreciated. More recently, with obesity rates rising in the U.S. and worldwide, epidemiologic evidence has supported a link between obesity and cancer. A substantial body of work seeks to mechanistically unpack the association between obesity, altered metabolism, and cancer. Without question, these relationships are multifactorial and cannot be distilled to a single obesity- and metabolism-altering hormone, substrate, or factor. However, it is important to understand the hormone-specific associations between metabolism and cancer. Here, we review the links between obesity, metabolic dysregulation, insulin, and cancer, with an emphasis on current investigational metabolic adjuncts to standard-of-care cancer treatment.

Keywords:  cancer metabolism; diabetes; immunometabolism

DOI:  https://doi.org/10.1042/BCJ20210134
JAMA. 2022 Mar 01. 327(9): 804

Global Cancer Burden Grew From 2010 to 2019.

Anita Slomski.

DOI: https://doi.org/10.1001/jama.2022.2188
Mol Cell. 2022 Feb 21. pii: S1097-2765(22)00111-3. [Epub ahead of print]

Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis.

Wenqi Xu, Chenxi He, Emily G Kaye, Jiahui Li, Mandi Mu, Geoffrey M Nelson, Li Dong, Jiahua Wang, Feizhen Wu, Yujiang Geno Shi, Karen Adelman, Fei Lan, Yang Shi, Hongjie Shen.

  N6-methyladenosine (m6A) methylation is co-transcriptionally deposited on mRNA, but a possible role of m6A on transcription remains poorly understood. Here, we demonstrate that the METTL3/METTL14/WTAP m6A methyltransferase complex (MTC) is localized to many promoters and enhancers and deposits the m6A modification on nascent transcripts, including pre-mRNAs, promoter upstream transcripts (PROMPTs), and enhancer RNAs. PRO-seq analyses demonstrate that nascent RNAs originating from both promoters and enhancers are significantly decreased in the METTL3-depleted cells. Furthermore, genes targeted by the Integrator complex for premature termination are depleted of METTL3, suggesting a potential antagonistic relationship between METTL3 and Integrator. Consistently, we found the Integrator complex component INTS11 elevated at promoters and enhancers upon loss of MTC or nuclear m6A binders. Taken together, our findings suggest that MTC-mediated m6A modification protects nascent RNAs from Integrator-mediated termination and promotes productive transcription, thus unraveling an unexpected layer of gene regulation imposed by RNA m6A modification.

Keywords:  ALKBH5; INTS11; METTL3; chromatin; enhancer; hnRNP G; m(6)A; nascent RNA; promoter

DOI:  https://doi.org/10.1016/j.molcel.2022.02.006
Nat Rev Cancer. 2022 Mar 02.

Cancer proteogenomics: current impact and future prospects.

D R Mani, Karsten Krug, Bing Zhang, Shankha Satpathy, Karl R Clauser, Li Ding, Matthew Ellis, Michael A Gillette, Steven A Carr.

Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.

DOI: https://doi.org/10.1038/s41568-022-00446-5