bims-cagime 2022-05-08 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–05–08
33 papers selected by
Kıvanç Görgülü, Technical University of Munich

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.
Sex specificity of pancreatic cancer cachexia phenotypes, mechanisms, and treatment in mice and humans: role of Activin.
CDC7-independent G1/S transition revealed by targeted protein degradation.
The Mettl3 epitranscriptomic writer amplifies p53 stress responses.
Adiponectin receptors sustain haematopoietic stem cells throughout adulthood by protecting them from inflammation.
Neutrophil phenotypes and functions in cancer: A consensus statement.
Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice.
High tumor mutational burden (TMB) identifies a microsatellite stable pancreatic cancer subset with prolonged survival and strong anti-tumor immunity.
ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer.
STING controls energy stress-induced autophagy and energy metabolism via STX17.
Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer.
Short senolytic or senostatic interventions rescue progression of radiation-induced frailty and premature ageing in mice.
A non-canonical cGAS-STING-PERK pathway facilitates the translational program critical for senescence and organ fibrosis.
Glycine decarboxylase maintains mitochondrial protein lipoylation to support tumor growth.
Tumor cell anabolism and host tissue catabolism-energetic inefficiency during cancer cachexia.
Pharmaceutical Shp2 inhibition suppresses primary and metastasized liver tumors by provoking hepatic innate immunity.
Cancer cachexia: a nutritional or a systemic inflammatory syndrome?
The V-ATPases in cancer and cell death.
Genetic ablation of p62/SQSTM1 demonstrates little effect on pancreatic β-cell function under autophagy deficiency.
Genetic Susceptibility in Understanding of Pancreatic Ductal Adenocarcinoma Risk: A Decade-Long Effort of the PANDORA Consortium.
Prmt5 determines the pattern of polyploidization and prevents liver from cirrhosis and carcinogenesis.
Establishment of patient-derived organoids and a characterization-based drug discovery platform for treatment of pancreatic cancer.
Autophagy and pluripotency: self-eating your way to eternal youth.
Comprehensive molecular profiling of pancreatic ductal adenocarcinoma in FNA, biopsy, and resection specimens.
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools.
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context.
A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane.
Cellular point-of-care diagnostics using an inexpensive layer-stack microfluidic device.
Limiting Dilution Tumor Initiation Assay: An In Vivo Approach for the Study of Cancer Stem Cells.
Proteotoxic stress disrupts epithelial integrity by inducing MTOR sequestration and autophagy overactivation.
A live-imaging protocol for tracking receptor dynamics in single cells.
V-ATPase is a universal regulator of LC3-associated phagocytosis and non-canonical autophagy.
Biomanufacturing human tissues via organ building blocks.

Cell. 2022 Apr 28. pii: S0092-8674(22)00462-7. [Epub ahead of print]

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.

Dian Yang, Matthew G Jones, Santiago Naranjo, William M Rideout, Kyung Hoi Joseph Min, Raymond Ho, Wei Wu, Joseph M Replogle, Jennifer L Page, Jeffrey J Quinn, Felix Horns, Xiaojie Qiu, Michael Z Chen, William A Freed-Pastor, Christopher S McGinnis, David M Patterson, Zev J Gartner, Eric D Chow, Trever G Bivona, Michelle M Chan, Nir Yosef, Tyler Jacks, Jonathan S Weissman.

  Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.

Keywords:  fitness; genetically engineered mouse model; lineage tracing; lung cancer; phylogenetics; plasticity; single cell; transcriptome heterogeneity; tumor evolution

DOI:  https://doi.org/10.1016/j.cell.2022.04.015
J Cachexia Sarcopenia Muscle. 2022 May 05.

Sex specificity of pancreatic cancer cachexia phenotypes, mechanisms, and treatment in mice and humans: role of Activin.

Xiaoling Zhong, Ashok Narasimhan, Libbie M Silverman, Andrew R Young, Safi Shahda, Sheng Liu, Jun Wan, Yunlong Liu, Leonidas G Koniaris, Teresa A Zimmers.

   BACKGROUND: Cachexia is frequent, deadly, and untreatable for patients with pancreatic ductal adenocarcinoma (PDAC). The reproductive hormone and cytokine Activin is a mediator of PDAC cachexia, and Activin receptor targeting was clinically tested for cancer cachexia therapy. However, sex-specific manifestations and mechanisms are poorly understood, constraining development of effective treatments.
METHODS: Cachexia phenotypes, muscle gene/protein expression, and effects of the Activin blocker ACVR2B/Fc were assessed in LSL-KrasG12D/+ , LSL-Trp53R172H/+ , and Pdx-1-Cre (KPC) mice with autochthonic PDAC. Effects of PDAC and sex hormones were modelled by treating C2C12 myotubes with KPC-cell conditioned medium (CM) and estradiol. Muscle gene expression by RNAseq and change in muscle from serial CT scans were measured in patients with PDAC.
RESULTS: Despite equivalent tumour latency (median 17 weeks) and mortality (24.5 weeks), male KPC mice showed earlier and more severe cachexia than females. In early PDAC, male gastrocnemius, quadriceps, and tibialis anterior muscles were reduced (-21.7%, -18.9%, and -20.8%, respectively, all P < 0.001), with only gastrocnemius reduced in females (-16%, P < 0.01). Sex differences disappeared in late PDAC. Plasma Activin A was similarly elevated between sexes throughout, while oestrogen and testosterone levels suggested a virilizing effect of PDAC in females. Estradiol partially protected myotubes from KPC-CM induced atrophy and promoted expression of the potential Activin inhibitor Fstl1. Early-stage female mice showed greater muscle expression of Activin inhibitors Fst, Fstl1, and Fstl3; this sex difference disappeared by late-stage PDAC. ACVR2B/Fc initiated in early PDAC preserved muscle and fat only in male KPC mice, with increases of 41.2%, 52.6%, 39.3%, and 348.8%, respectively, in gastrocnemius, quadriceps, tibialis, and fat pad weights vs. vehicle controls, without effect on tumour. No protection was observed in females. At protein and RNA levels, pro-atrophy pathways were induced more strongly in early-stage males, with sex differences less evident in late-stage disease. As with mass, ACVR2B/Fc blunted atrophy-associated pathways only in males. In patients with resectable PDAC, muscle expression of Activin inhibitors FSTL1, FSLT3, and WFIKKN2/GASP2 were higher in women than men. Overall, among 124 patients on first-line gemcitabine/nab-paclitaxel for PDAC, only men displayed muscle loss (P < 0.001); average muscle wasting in men was greater (-6.63 ± 10.70% vs. -1.62 ± 12.00% mean ± SD, P = 0.038) and more rapid (-0.0098 ± 0.0742%/day vs. -0.0466 ± 0.1066%/day, P = 0.017) than in women.
CONCLUSIONS: Pancreatic ductal adenocarcinoma cachexia displays sex-specific phenotypes in mice and humans, with Activin a preferential driver of muscle wasting in males. Sex is a major modulator of cachexia mechanisms. Consideration of sexual dimorphism is essential for discovery and development of effective treatments.

Keywords:  ACVR2B; Activin; Cachexia; Estradiol; Muscle wasting; Pancreatic cancer; Sexual dimorphism; Weight loss

DOI:  https://doi.org/10.1002/jcsm.12998
Nature. 2022 May 04.

CDC7-independent G1/S transition revealed by targeted protein degradation.

Jan M Suski, Nalin Ratnayeke, Marcin Braun, Tian Zhang, Vladislav Strmiska, Wojciech Michowski, Geylani Can, Antoine Simoneau, Konrad Snioch, Mikolaj Cup, Caitlin M Sullivan, Xiaoji Wu, Joanna Nowacka, Timothy B Branigan, Lindsey R Pack, James A DeCaprio, Yan Geng, Lee Zou, Steven P Gygi, Johannes C Walter, Tobias Meyer, Piotr Sicinski.

The entry of mammalian cells into the DNA synthesis phase (S phase) represents a key event in cell division1. According to current models of the cell cycle, the kinase CDC7 constitutes an essential and rate-limiting trigger of DNA replication, acting together with the cyclin-dependent kinase CDK2. Here we show that CDC7 is dispensable for cell division of many different cell types, as determined using chemical genetic systems that enable acute shutdown of CDC7 in cultured cells and in live mice. We demonstrate that another cell cycle kinase, CDK1, is also active during G1/S transition both in cycling cells and in cells exiting quiescence. We show that CDC7 and CDK1 perform functionally redundant roles during G1/S transition, and at least one of these kinases must be present to allow S-phase entry. These observations revise our understanding of cell cycle progression by demonstrating that CDK1 physiologically regulates two distinct transitions during cell division cycle, whereas CDC7 has a redundant function in DNA replication.

DOI: https://doi.org/10.1038/s41586-022-04698-x
Mol Cell. 2022 Apr 27. pii: S1097-2765(22)00321-5. [Epub ahead of print]

The Mettl3 epitranscriptomic writer amplifies p53 stress responses.

Nitin Raj, Mengxiong Wang, Jose A Seoane, Richard L Zhao, Alyssa M Kaiser, Nancie A Moonie, Janos Demeter, Anthony M Boutelle, Craig H Kerr, Abigail S Mulligan, Clare Moffatt, Shelya X Zeng, Hua Lu, Maria Barna, Christina Curtis, Howard Y Chang, Peter K Jackson, Laura D Attardi.

  The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in in vivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.

Keywords:  DNA damage; METTL14; METTL3; N(6)-methyladenosine (m6A) modification; epitranscriptomics; lung cancer; mass spectrometry; methyltransferase complex; p53; tumor suppressor

DOI:  https://doi.org/10.1016/j.molcel.2022.04.010
Nat Cell Biol. 2022 May 05.

Adiponectin receptors sustain haematopoietic stem cells throughout adulthood by protecting them from inflammation.

Corbin E Meacham, Elise C Jeffery, Rebecca J Burgess, Charukesi D Sivakumar, Madison A Arora, Anne Marie Stanley, Emily M Colby, Genevieve M Crane, Zhiyu Zhao, Sean J Morrison.

How are haematopoietic stem cells (HSCs) protected from inflammation, which increases with age and can deplete HSCs? Adiponectin, an anti-inflammatory factor that is not required for HSC function or haematopoiesis, promotes stem/progenitor cell proliferation after bacterial infection and myeloablation. Adiponectin binds two receptors, AdipoR1 and AdipoR2, which have ceramidase activity that increases upon adiponectin binding. Here we found that adiponectin receptors are non-cell-autonomously required in haematopoietic cells to promote HSC quiescence and self-renewal. Adiponectin receptor signalling suppresses inflammatory cytokine expression by myeloid cells and T cells, including interferon-γ and tumour necrosis factor. Without adiponectin receptors, the levels of these factors increase, chronically activating HSCs, reducing their self-renewal potential and depleting them during ageing. Pathogen infection accelerates this loss of HSC self-renewal potential. Blocking interferon-γ or tumour necrosis factor signalling partially rescues these effects. Adiponectin receptors are thus required in immune cells to sustain HSC quiescence and to prevent premature HSC depletion by reducing inflammation.

DOI: https://doi.org/10.1038/s41556-022-00909-9
J Exp Med. 2022 Jun 06. pii: e20220011. [Epub ahead of print]219(6):

Neutrophil phenotypes and functions in cancer: A consensus statement.

Daniela F Quail, Borko Amulic, Monowar Aziz, Betsy J Barnes, Evgeniy Eruslanov, Zvi G Fridlender, Helen S Goodridge, Zvi Granot, Andrés Hidalgo, Anna Huttenlocher, Mariana J Kaplan, Ilaria Malanchi, Taha Merghoub, Etienne Meylan, Vivek Mittal, Mikael J Pittet, Andrea Rubio-Ponce, Irina A Udalova, Timo K van den Berg, Denisa D Wagner, Ping Wang, Arturo Zychlinsky, Karin E de Visser, Mikala Egeblad, Paul Kubes.

Neutrophils are the first responders to infection and inflammation and are thus a critical component of innate immune defense. Understanding the behavior of neutrophils as they act within various inflammatory contexts has provided insights into their role in sterile and infectious diseases; however, the field of neutrophils in cancer is comparatively young. Here, we summarize key concepts and current knowledge gaps related to the diverse roles of neutrophils throughout cancer progression. We discuss sources of neutrophil heterogeneity in cancer and provide recommendations on nomenclature for neutrophil states that are distinct in maturation and activation. We address discrepancies in the literature that highlight a need for technical standards that ought to be considered between laboratories. Finally, we review emerging questions in neutrophil biology and innate immunity in cancer. Overall, we emphasize that neutrophils are a more diverse population than previously appreciated and that their role in cancer may present novel unexplored opportunities to treat cancer.

DOI: https://doi.org/10.1084/jem.20220011
Science. 2022 May 05. e

Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice.

Victoria Acosta-Rodríguez, Filipa Rijo-Ferreira, Mariko Izumo, Pin Xu, Mary Wight-Carter, Carla B Green, Joseph S Takahashi.

Caloric restriction (CR) prolongs lifespan, yet the mechanisms by which it does so remain poorly understood. Under CR, mice self-impose chronic cycles of 2-hour-feeding and 22-hour-fasting, raising the question whether calories, fasting, or time of day are causal. We show that 30%-CR is sufficient to extend lifespan 10%; however, a daily fasting interval and circadian-alignment of feeding act together to extend lifespan 35% in male C57BL/6J mice. These effects are independent of body weight. Aging induces widespread increases in gene expression associated with inflammation and decreases in expression of genes encoding components of metabolic pathways in liver from ad lib fed mice. CR at night ameliorates these aging-related changes. Thus, circadian interventions promote longevity and provide a perspective to further explore mechanisms of aging.

DOI: https://doi.org/10.1126/science.abk0297
Eur J Cancer. 2022 May 02. pii: S0959-8049(22)00181-2. [Epub ahead of print]169 64-73

High tumor mutational burden (TMB) identifies a microsatellite stable pancreatic cancer subset with prolonged survival and strong anti-tumor immunity.

Eva Karamitopoulou, Andreas Andreou, Anna Silvia Wenning, Beat Gloor, Aurel Perren.

   AIM: Tumor mutational burden (TMB: somatic mutations per megabase, mut/Mb) predicts the efficacy of immunotherapy. Here, we link TMB levels with the activation of immune pathways and intratumoral immune responses in pancreatic adenocarcinoma (PDAC) to explore immunoarchitectural patterns associated with high TMB.
METHODS: We assessed TMB in 161 resected, microsatellite stable (MSS) PDACs, including 41 long-term survivors (LTS). Five microsatellite instable (MSI-high) cases were also assessed. Cases were classified into TMB-high (≥10 mut/Mb), TMB-intermediate (>5 < 10 mut/Mb), and TMB-low (≤5 mut/Mb) categories. Tumors additionally underwent mRNA in situ hybridization for immune pathway genes and were immunoprofiled by multiplex immunofluorescence followed by automated image analysis.
RESULTS: We detected 12 TMB-high, 28 TMB-intermediate, and 121 TMB-low cases. TMB-high tumors comprised ten LTSs (10/41; 24%) and two conventional PDACs (2/120; 1.7%). They exhibited the highest T cell density with significantly increased CD3+CD4+T helper and CD208+dendritic cell (DC) counts, compared to all other cases. CD3+CD8+cytotoxic T cells were significantly closer to tumor cells and T helper cells closer to DCs in TMB-high PDACs. Immune pathways involved in T cell activation, immune cell adhesion/migration, antigen presentation, and cytokine signaling were upregulated in most TMB-high and many TMB-intermediate tumors. ARID1A and ERBB4 alterations were more frequent in TMB-high PDACs. All MSI-high PDACs were TMB-high.
CONCLUSIONS: TMB-high cases frequently belong to specific PDAC subsets with prolonged survival such as LTSs and MSI-high PDACs. They display strong anti-tumor immune responses fueled by a T helper cell/DC-mediated priming of the cytotoxic T cells. Moreover, they frequently harbor further actionable alterations.

Keywords:  Immune response; Immunotherapy; Microsatellite instability; Pancreatic cancer; Tumor mutational burden

DOI:  https://doi.org/10.1016/j.ejca.2022.03.033
Dev Cell. 2022 Apr 22. pii: S1534-5807(22)00254-4. [Epub ahead of print]

ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer.

Harun Ozturk, Harun Cingoz, Turan Tufan, Jiekun Yang, Sara J Adair, Krishna Seshu Tummala, Cem Kuscu, Meric Kinali, Gamze Comertpay, Sarbajeet Nagdas, Bernadette J Goudreau, Husnu Umit Luleyap, Yagmur Bingul, Timothy B Ware, Wiliam L Hwang, Ku-Lung Hsu, David F Kashatus, David T Ting, Navdeep S Chandel, Nabeel Bardeesy, Todd W Bauer, Mazhar Adli.

  Pancreatic ductal adenocarcinoma (PDA) cells reprogram their transcriptional and metabolic programs to survive the nutrient-poor tumor microenvironment. Through in vivo CRISPR screening, we discovered islet-2 (ISL2) as a candidate tumor suppressor that modulates aggressive PDA growth. Notably, ISL2, a nuclear and chromatin-associated transcription factor, is epigenetically silenced in PDA tumors and high promoter DNA methylation or its reduced expression correlates with poor patient survival. The exogenous ISL2 expression or CRISPR-mediated upregulation of the endogenous loci reduces cell proliferation. Mechanistically, ISL2 regulates the expression of metabolic genes, and its depletion increases oxidative phosphorylation (OXPHOS). As such, ISL2-depleted human PDA cells are sensitive to the inhibitors of mitochondrial complex I in vitro and in vivo. Spatial transcriptomic analysis shows heterogeneous intratumoral ISL2 expression, which correlates with the expression of critical metabolic genes. These findings nominate ISL2 as a putative tumor suppressor whose inactivation leads to increased mitochondrial metabolism that may be exploitable therapeutically.

Keywords:  CRISPR; ISL2; pancreatic cancer; tumor suppressor

DOI:  https://doi.org/10.1016/j.devcel.2022.04.014
J Cell Biol. 2022 Jul 04. pii: e202202060. [Epub ahead of print]221(7):

STING controls energy stress-induced autophagy and energy metabolism via STX17.

Yueguang Rong, Shen Zhang, Nilay Nandi, Zhe Wu, Linsen Li, Yang Liu, Yuehan Wei, Yuan Zhao, Weigang Yuan, Chuchu Zhou, Guanghua Xiao, Beth Levine, Nan Yan, Shan Mou, Liufu Deng, Zaiming Tang, Xiaoxia Liu, Helmut Kramer, Qing Zhong.

The stimulator of interferon genes (STING) plays a critical role in innate immunity. Emerging evidence suggests that STING is important for DNA or cGAMP-induced non-canonical autophagy, which is independent of a large part of canonical autophagy machineries. Here, we report that, in the absence of STING, energy stress-induced autophagy is upregulated rather than downregulated. Depletion of STING in Drosophila fat cells enhances basal- and starvation-induced autophagic flux. During acute exercise, STING knockout mice show increased autophagy flux, exercise endurance, and altered glucose metabolism. Mechanistically, these observations could be explained by the STING-STX17 interaction. STING physically interacts with STX17, a SNARE that is essential for autophagosome biogenesis and autophagosome-lysosome fusion. Energy crisis and TBK1-mediated phosphorylation both disrupt the STING-STX17 interaction, allow different pools of STX17 to translocate to phagophores and mature autophagosomes, and promote autophagic flux. Taken together, we demonstrate a heretofore unexpected function of STING in energy stress-induced autophagy through spatial regulation of autophagic SNARE STX17.

DOI: https://doi.org/10.1083/jcb.202202060
Cancer Cell. 2022 Apr 26. pii: S1535-6108(22)00173-8. [Epub ahead of print]

Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer.

Huocong Huang, Zhaoning Wang, Yuqing Zhang, Rachana N Pradhan, Debolina Ganguly, Raghav Chandra, Gilbert Murimwa, Steven Wright, Xiaowu Gu, Ravikanth Maddipati, Sören Müller, Shannon J Turley, Rolf A Brekken.

  Recent studies have identified a unique cancer-associated fibroblast (CAF) population termed antigen-presenting CAFs (apCAFs), characterized by the expression of major histocompatibility complex class II molecules, suggesting a function in regulating tumor immunity. Here, by integrating multiple single-cell RNA-sequencing studies and performing robust lineage-tracing assays, we find that apCAFs are derived from mesothelial cells. During pancreatic cancer progression, mesothelial cells form apCAFs by downregulating mesothelial features and gaining fibroblastic features, a process induced by interleukin-1 and transforming growth factor β. apCAFs directly ligate and induce naive CD4+ T cells into regulatory T cells (Tregs) in an antigen-specific manner. Moreover, treatment with an antibody targeting the mesothelial cell marker mesothelin can effectively inhibit mesothelial cell to apCAF transition and Treg formation induced by apCAFs. Taken together, our study elucidates how mesothelial cells may contribute to immune evasion in pancreatic cancer and provides insight on strategies to enhance cancer immune therapy.

Keywords:  cancer-associated fibroblast; mesothelial cell; mesothelin; pancreatic cancer; regulatory T cell

DOI:  https://doi.org/10.1016/j.ccell.2022.04.011
Elife. 2022 May 04. pii: e75492. [Epub ahead of print]11

Short senolytic or senostatic interventions rescue progression of radiation-induced frailty and premature ageing in mice.

Edward Fielder, Tengfei Wan, Ghazaleh Alimohammadiha, Abbas Ishaq, Evon Low, B Melanie Weigand, George Kelly, Craig Parker, Brigid Griffin, Diana Jurk, Viktor I Korolchuk, Thomas von Zglinicki, Satomi Miwa.

  Cancer survivors suffer from progressive frailty, multimorbidity and premature morbidity. We hypothesize that therapy-induced senescence and senescence progression via bystander effects is a significant cause of this premature ageing phenotype. Accordingly, the study addresses the question whether a short anti-senescence intervention is able to block progression of radiation-induced frailty and disability in a pre-clinical setting. Male mice were sub-lethally irradiated at 5 months of age and treated (or not) with either a senolytic drug (Navitoclax or dasatinib + quercetin) for 10 days or with the senostatic metformin for 10 weeks. Follow up was for one year. Treatments commencing within a month after irradiation effectively reduced frailty progression (p<0.05) and improved muscle (p<0.01) and liver (p<0.05) function as well as short-term memory (p<0.05) until advanced age with no need for repeated interventions. Senolytic interventions that started late, after radiation-induced premature frailty was manifest, still had beneficial effects on frailty (p<0.05) and short-term memory (p<0.05). Metformin was similarly effective as senolytics. At therapeutically achievable concentrations metformin acted as a senostatic neither via inhibition of mitochondrial complex I, nor via improvement of mitophagy or mitochondrial function, but by reducing non-mitochondrial ROS production via NOX4 inhibition in senescent cells. Our study suggests that the progression of adverse long-term health and quality-of-life effects of radiation exposure, as experienced by cancer survivors, might be rescued by short-term adjuvant anti-senescence interventions.

Keywords:  cancer biology; cell biology; mouse

DOI:  https://doi.org/10.7554/eLife.75492
Nat Cell Biol. 2022 May 02.

A non-canonical cGAS-STING-PERK pathway facilitates the translational program critical for senescence and organ fibrosis.

Dan Zhang, Yutong Liu, Yezhang Zhu, Qian Zhang, Hongxing Guan, Shengduo Liu, Shasha Chen, Chen Mei, Chen Chen, Zhiyong Liao, Ying Xi, Songying Ouyang, Xin-Hua Feng, Tingbo Liang, Li Shen, Pinglong Xu.

Innate DNA sensing via the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) mechanism surveys microbial invasion and cellular damage and thus participates in various human infectious diseases, autoimmune diseases and cancers. However, how DNA sensing rapidly and adaptively shapes cellular physiology is incompletely known. Here we identify the STING-PKR-like endoplasmic reticulum kinase (PERK)-eIF2α pathway, a previously unknown cGAS-STING mechanism, enabling an innate immunity control of cap-dependent messenger RNA translation. Upon cGAMP binding, STING at the ER binds and directly activates the ER-located kinase PERK via their intracellular domains, which precedes TBK1-IRF3 activation and is irrelevant to the unfolded protein response. The activated PERK phosphorylates eIF2α, forming an inflammatory- and survival-preferred translation program. Notably, this STING-PERK-eIF2α pathway is evolutionarily primitive and physiologically critical to cellular senescence and organ fibrosis. Pharmacologically or genetically targeting this non-canonical cGAS-STING pathway attenuated lung and kidney fibrosis. Collectively, the findings identify an alternative innate immune pathway and its critical role in organ fibrosis, report an innate immunity-directed translation program and suggest the therapeutic potential for targeting the STING-PERK pathway in treating fibrotic diseases.

DOI: https://doi.org/10.1038/s41556-022-00894-z
Cell Metab. 2022 May 03. pii: S1550-4131(22)00133-4. [Epub ahead of print]34(5): 775-782.e9

Glycine decarboxylase maintains mitochondrial protein lipoylation to support tumor growth.

Dzmitry Mukha, Mariam Fokra, Alona Feldman, Boris Sarvin, Nikita Sarvin, Keren Nevo-Dinur, Elazar Besser, Elior Hallo, Elina Aizenshtein, Zachary T Schug, Tomer Shlomi.

  The folic acid cycle mediates the transfer of one-carbon (1C) units to support nucleotide biosynthesis. While the importance of serine as a mitochondrial and cytosolic donor of folate-mediated 1C units in cancer cells has been thoroughly investigated, a potential role of glycine oxidation remains unclear. We developed an approach for quantifying mitochondrial glycine cleavage system (GCS) flux by combining stable and radioactive isotope tracing with computational flux decomposition. We find high GCS flux in hepatocellular carcinoma (HCC), supporting nucleotide biosynthesis. Surprisingly, other than supplying 1C units, we found that GCS is important for maintaining protein lipoylation and mitochondrial activity. Genetic silencing of glycine decarboxylase inhibits the lipoylation and activity of pyruvate dehydrogenase and impairs tumor growth, suggesting a novel drug target for HCC. Considering the physiological role of liver glycine cleavage, our results support the notion that tissue of origin plays an important role in tumor-specific metabolic rewiring.

Keywords:  GCS; GLDC; PDH; glycine cleavage system; glycine decarboxylase; hepatocellular carcinoma; one-carbon metabolism; protein P; protein lipoylation; pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.cmet.2022.04.006
Exp Biol Med (Maywood). 2022 May 06. 15353702221087962

Tumor cell anabolism and host tissue catabolism-energetic inefficiency during cancer cachexia.

Mangala Hegde, Uzini Devi Daimary, Sosmitha Girisa, Aviral Kumar, Ajaikumar B Kunnumakkara.

  Cancer-associated cachexia (CC) is a pathological condition characterized by sarcopenia, adipose tissue depletion, and progressive weight loss. CC is driven by multiple factors such as anorexia, excessive catabolism, elevated energy expenditure by growing tumor mass, and inflammatory mediators released by cancer cells and surrounding tissues. In addition, endocrine system, systemic metabolism, and central nervous system (CNS) perturbations in combination with cachexia mediators elicit exponential elevation in catabolism and reduced anabolism in skeletal muscle, adipose tissue, and cardiac muscle. At the molecular level, mechanisms of CC include inflammation, reduced protein synthesis, and lipogenesis, elevated proteolysis and lipolysis along with aggravated toxicity and complications of chemotherapy. Furthermore, CC is remarkably associated with intolerance to anti-neoplastic therapy, poor prognosis, and increased mortality with no established standard therapy. In this context, we discuss the spatio-temporal changes occurring in the various stages of CC and highlight the imbalance of host metabolism. We provide how multiple factors such as proteasomal pathways, inflammatory mediators, lipid and protein catabolism, glucocorticoids, and in-depth mechanisms of interplay between inflammatory molecules and CNS can trigger and amplify the cachectic processes. Finally, we highlight current diagnostic approaches and promising therapeutic interventions for CC.

Keywords:  Glycolysis; anabolism; anorexia; cachexia; catabolism; gluconeogenesis

DOI:  https://doi.org/10.1177/15353702221087962
Hepatology. 2022 May 03.

Pharmaceutical Shp2 inhibition suppresses primary and metastasized liver tumors by provoking hepatic innate immunity.

Jacey J Liu, Bing Xin, Li Du, Lydia Chen, Yanyan Long, Gen-Sheng Feng.

   BACKGROUND AND AIMS: Shp2 is the first identified pro-oncogenic tyrosine phosphatase that acts downstream of receptor tyrosine kinases (RTK) to promote Ras-Erk signaling. However, this phosphatase was also shown to be anti-tumorigenic in hepatocellular cancer (HCC). This study is aimed at deciphering paradoxical Shp2 functions and mechanisms in hepatocarcinogenesis and also at exploring its value as a pharmaceutical target in HCC therapy.
APPROACHES AND RESULTS: We took both genetic and pharmaceutical approaches, to examine the effects of Shp2 inhibition on primary liver cancers driven by various oncogenes and also on metastasized liver tumors. We show here that the catalytic activity of Shp2 was essential for relay of oncogenic signals from RTK in HCC and that chemical inhibition of Shp2 robustly suppressed HCC driven by RTK. However, in contrast to a tumor-promoting hepatic niche generated by genetically deleting Shp2 in hepatocytes, treatment with a specific Shp2 inhibitor had a tumor-suppressing effect on metastasized liver tumor progression. Mechanistically, the Shp2 inhibitor enhanced anti-tumor innate immunity by downregulating inflammatory cytokines, suppressing the CCR5 signaling axis but upregulating interferon-β secretion.
CONCLUSIONS: These results unveil complex mechanisms for the tumor-suppressing effect of pharmaceutical Shp2 inhibition in the liver immune environment. We provide a proof of principle for clinical trial with specific Shp2 inhibitors in primary and metastasized liver cancer patients.

Keywords:  anti-tumor immunity; oncogenic signaling; oncological treatment; small-molecule therapeutics; tumor microenvironment

DOI:  https://doi.org/10.1002/hep.32555
Br J Cancer. 2022 May 06.

Cancer cachexia: a nutritional or a systemic inflammatory syndrome?

Josh McGovern, Ross D Dolan, Richard J Skipworth, Barry J Laird, Donald C McMillan.

Cancer cachexia has long been perceived as a nutritional syndrome. However, nutritional interventions have continued to be ineffective. With the recent recognition of the importance of systemic inflammation in the definition of this syndrome and treatment, has the time come to consider whether this syndrome is primarily a manifestation of systemic inflammation with the consequent implications for future treatment?

DOI: https://doi.org/10.1038/s41416-022-01826-2
Cancer Gene Ther. 2022 May 03.

The V-ATPases in cancer and cell death.

Fangquan Chen, Rui Kang, Jiao Liu, Daolin Tang.

Transmembrane ATPases are membrane-bound enzyme complexes and ion transporters that can be divided into F-, V-, and A-ATPases according to their structure. The V-ATPases, also known as H+-ATPases, are large multi-subunit protein complexes composed of a peripheral domain (V1) responsible for the hydrolysis of ATP and a membrane-integrated domain (V0) that transports protons across plasma membrane or organelle membrane. V-ATPases play a fundamental role in maintaining pH homeostasis through lysosomal acidification and are involved in modulating various physiological and pathological processes, such as macropinocytosis, autophagy, cell invasion, and cell death (e.g., apoptosis, anoikis, alkaliptosis, ferroptosis, and lysosome-dependent cell death). In addition to participating in embryonic development, V-ATPase pathways, when dysfunctional, are implicated in human diseases, such as neurodegenerative diseases, osteopetrosis, distal renal tubular acidosis, and cancer. In this review, we summarize the structure and regulation of isoforms of V-ATPase subunits and discuss their context-dependent roles in cancer biology and cell death. Updated knowledge about V-ATPases may enable us to design new anticancer drugs or strategies.

DOI: https://doi.org/10.1038/s41417-022-00477-y
Biochem Biophys Res Commun. 2022 Apr 25. pii: S0006-291X(22)00634-9. [Epub ahead of print]612 99-104

Genetic ablation of p62/SQSTM1 demonstrates little effect on pancreatic β-cell function under autophagy deficiency.

Toshinaru Fukae, Takeshi Miyatsuka, Miwa Himuro, Yuka Wakabayashi, Hitoshi Iida, Shuhei Aoyama, Tomoya Mita, Fuki Ikeda, Hidenori Haruna, Noriyuki Takubo, Yuya Nishida, Toshiaki Shimizu, Hirotaka Watada.

  Autophagy is known to play an essential role in intracellular quality control through the degradation of damaged organelles and components. We previously demonstrated that β-cell-specific autophagy deficient mice, which lack Atg7, exhibited impaired glucose tolerance, accompanied by the accumulation of sequestosome 1/p62 (hereafter referred to as p62). Whereas p62 has been reported to play essential roles in regulating cellular homeostasis in the liver and adipose tissue, we previously showed that β-cell-specific p62 deficiency does not cause any apparent impairment in glucose metabolism. In the present study, we investigated the roles of p62 in β cells under autophagy-deficient conditions, by simultaneously inactivating both Atg7 and p62 in a β-cell specific manner. Whereas p62 accumulation was substantially reduced in the islets of Atg7 and p62 double-deficient mice, glucose tolerance and insulin secretion were comparable to Atg7 single-deficient mice. Taken together, these findings suggest that the p62 accumulation appears to have little effect on β-cell function under conditions of autophagy inhibition.

Keywords:  Atg7; Autophagy; Diabetes; p62/SQSTM1; β cell

DOI:  https://doi.org/10.1016/j.bbrc.2022.04.092
Cancer Epidemiol Biomarkers Prev. 2022 May 04. 31(5): 942-948

Genetic Susceptibility in Understanding of Pancreatic Ductal Adenocarcinoma Risk: A Decade-Long Effort of the PANDORA Consortium.

Ludmila Vodickova, Josef Horak, Pavel Vodicka.

Pancreatic cancer, a complex disease, emerges as a severe health problem worldwide and it exhibits a poor prognosis and high mortality. Risk factors associated with sporadic pancreatic cancer remain poorly understood, even less is known about disease prognosis due to its rapid progression. The PANcreatic Disease ReseArch (PANDoRA) consortium, of which the authors are members, was established to coordinate the efforts of different research groups to uncover new genetic factors for pancreatic cancer risk, response to treatment, and patient survival. PANDoRA consortium has contributed to the identification of several low-penetrance risk loci for the disease both by candidate variants approach and genome-wide association studies, including those in cell-cycle and DNA damage response, telomere homeostasis, SCL and ABC transporters, ABO locus variability, mitochondrial metabolism and it participated on collaborative genome-wide association study approach and implementation of a search for functional-based pancreatic cancer risk loci and long noncoding RNAs. Complex studies covering genetic, environmental and microenvironmental factors in the pancreatic cancer onset, progression and its prognosis are warranted.

DOI: https://doi.org/10.1158/1055-9965.EPI-21-1340
J Genet Genomics. 2022 Apr 29. pii: S1673-8527(22)00128-X. [Epub ahead of print]

Prmt5 determines the pattern of polyploidization and prevents liver from cirrhosis and carcinogenesis.

Jincheng Wang, Xiang Huang, Daoshan Zheng, Qiuling Li, Mei Mei, Shilai Bao.

  Human hepatocellular carcinoma (HCC) occurs almost exclusively in cirrhotic livers. Here we report that hepatic loss of PRMT5 is sufficient to cause cirrhosis and HCC in a clinically relevant way. Furthermore, pathological polyploidization induced by hepatic loss of PRMT5 promotes liver cirrhosis and hepatic tumorigenesis in aged liver. The loss of PRMT5 leads to hyper-accumulation of P21 and endoreplication-dependent formation of pathological mono-nuclear polyploid hepatocytes. PRMT5 and symmetric dimethylation at histone H4 arginine 3 (H4R3me2s) directly associate with chromatin of P21 to suppress its transcription. More importantly, loss of P21 rescues the pathological mono-nuclear polyploidy and prevents PRMT5-deficiency-induced liver cirrhosis and HCC. Thus, our results indicate that PRMT5 mediated symmetric dimethylation at histone H4 arginine 3 (H4R3me2s) is crucial for preventing pathological polyploidization, liver cirrhosis and tumorigenesis in mouse liver.

Keywords:  PRMT5; Pathological polyploidizaion; aging; cirrhosis; hepatocellular carcinoma

DOI:  https://doi.org/10.1016/j.jgg.2022.04.008
BMC Cancer. 2022 May 03. 22(1): 489

Establishment of patient-derived organoids and a characterization-based drug discovery platform for treatment of pancreatic cancer.

Sadanori Watanabe, Akitada Yogo, Tsuguteru Otsubo, Hiroki Umehara, Jun Oishi, Toru Kodo, Toshihiko Masui, Shigeo Takaishi, Hiroshi Seno, Shinji Uemoto, Etsuro Hatano.

   BACKGROUND: Pancreatic cancer is one of the most lethal tumors. The aim of this study is to provide an effective therapeutic discovery platform for pancreatic cancer by establishing and characterizing patient-derived organoids (PDOs).
METHODS: PDOs were established from pancreatic tumor surgical specimens, and the mutations were examined using a panel sequence. Expression of markers was assessed by PCR, immunoblotting, and immunohistochemistry; tumorigenicity was examined using immunodeficient mice, and drug responses were examined in vitro and in vivo.
RESULTS: PDOs were established from eight primary and metastatic tumors, and the characteristic mutations and expression of cancer stem cell markers and CA19-9 were confirmed. Tumorigenicity of the PDOs was confirmed in subcutaneous transplantation and in the peritoneal cavity in the case of PDOs derived from disseminated nodules. Gemcitabine-sensitive/resistant PDOs showed consistent responses in vivo. High throughput screening in PDOs identified a compound effective for inhibiting tumor growth of a gemcitabine-resistant PDO xenograft model.
CONCLUSIONS: This PDO-based platform captures important aspects of treatment-resistant pancreatic cancer and its metastatic features, suggesting that this study may serve as a tool for the discovery of personalized therapies.

Keywords:  Compound screening; Organoid; Pancreatic cancer; Peritoneal dissemination; Xenograft model

DOI:  https://doi.org/10.1186/s12885-022-09619-9
Trends Cell Biol. 2022 Apr 27. pii: S0962-8924(22)00089-7. [Epub ahead of print]

Autophagy and pluripotency: self-eating your way to eternal youth.

Yi Xu, Xiaolu Yang.

  Pluripotent stem cells (PSCs) can self-renew indefinitely in culture while retaining the potential to differentiate into virtually all normal cell types in the adult animal. Due to these remarkable properties, PSCs not only provide a superb system to investigate mammalian development and model diseases, but also hold promise for regenerative therapies. Autophagy is a self-digestive process that targets proteins, organelles, and other cellular contents for lysosomal degradation. Here, we review recent literature on the mechanistic role of different types of autophagy in embryonic development, embryonic stem cells (ESCs), and induced PSCs (iPSCs), focusing on their remodeling functions on protein, metabolism, and epigenetics. We present a perspective on unsolved issues and propose that autophagy is a promising target to modulate acquisition, maintenance, and directed differentiation of PSCs.

Keywords:  autophagy; chaperone-mediated autophagy; differentiation; embryonic stem cells; induced pluripotent stem cells; macroautophagy; microautophagy; self-renewal

DOI:  https://doi.org/10.1016/j.tcb.2022.04.001
Cancer Cytopathol. 2022 May 05.

Comprehensive molecular profiling of pancreatic ductal adenocarcinoma in FNA, biopsy, and resection specimens.

Dana Razzano, Soumar J Bouza, Patricia V Hernandez, Minhua Wang, Marie E Robert, Zenta Walther, Guoping Cai.

   BACKGROUND: Molecular testing to identify molecular alterations in pancreatic ductal adenocarcinoma (PDAC) has been increasingly requested because of potential therapeutic implications. In this study, we compared the performance of PDAC fine-needle aspiration (FNA), fine-needle biopsy (FNB), and resection specimens for comprehensive molecular analysis.
METHODS: A next-generation sequencing-based Oncomine Comprehensive Assay (OCA) was used to analyze molecular alterations in FNA, FNB, or resection specimens. We examined adequacy and success rates for completion of molecular testing and catalogued molecular alterations in these specimen types.
RESULTS: The cohort included 23 FNA, 20 FNB, and 27 resection cases. Gene mutation or amplification analysis was successful in 18 (78%) FNA and 16 (80%) FNB specimens, whereas gene fusion assessment succeeded in 12 (52%) FNA and 12 (60%) FNB samples. All 27 (100%) resection specimens were adequate for complete OCA. There were significant differences in success rates for mutation and amplification analysis between resection and FNA or FNB specimens (P < .01) but not between FNA and FNB samples (P > .05). Manual microdissection was less likely to be performed for FNA specimens than FNB or resection specimens (P < .01). KRAS mutation was the most common mutation identified (90%), followed by mutations in TP53 (64%), CDKN2A (25%), and SMAD4 (15%) genes.
CONCLUSIONS: Our study demonstrated similar success rates for comprehensive molecular analysis using FNA and FNB specimens of PDAC, suggesting that FNA material could serve as an alternative source for comprehensive molecular testing. The molecular alterations identified in these specimens may have potential diagnostic and therapeutic implications.

Keywords:  Oncomine assay; fine-needle aspiration; fine-needle biopsy; molecular testing; next-generation sequencing; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1002/cncy.22589
Bioinformatics. 2022 May 05. pii: btac306. [Epub ahead of print]

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools.

Carlos A Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo.

MOTIVATION: The analysis of cancer genomes provides fundamental information about its aetiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i.e., those that have been acquired during their evolution). For that purpose, a wide range of computational tools have been developed in recent years to detect somatic mutations in sequencing data from tumor samples. While there have been some efforts to benchmark somatic variant calling tools and strategies, the extent to which variant calling decisions impact the results of downstream analyses of tumor genomes remains unknown.
RESULTS: Here we quantify the impact of variant calling decisions by comparing the results obtained in three important analyses of cancer genomics data (identification of cancer driver genes, quantification of mutational signatures and detection of clinically actionable variants) when changing the somatic variant caller (MuSE, MuTect2, SomaticSniper, VarScan2) or the strategy to combine them (Consensus of two, Consensus of three and Union) across all 33 cancer types from The Cancer Genome Atlas. Our results show that variant calling decisions have a significant impact on these analyses, creating important differences that could even impact treatment decisions for some patients. Moreover, the Consensus of three calling strategy to combine the output of multiple variant calling tools, a very widely used strategy by the research community, can lead to the loss of some cancer driver genes and actionable mutations. Overall, our results highlight the limitations of widespread practices within the cancer genomics community and point to important differences in critical analyses of tumor sequencing data depending on variant calling, affecting even the identification of clinically actionable variants.
AVAILABILITY: Code is available at https://github.com/carlosgarciaprieto/VariantCallingClinicalBenchmark.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac306
Nucleic Acids Res. 2022 May 07. pii: gkac306. [Epub ahead of print]

The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context.

Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann.

Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterized by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It, however, lacked functions aimed at integrating mitochondria in the cellular context and thus identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade, we implemented two novel integrative functions, network analysis and transcription factor enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualization, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species and an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.

DOI: https://doi.org/10.1093/nar/gkac306
Proc Natl Acad Sci U S A. 2022 May 10. 119(19): e2122531119

A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane.

Chun-Wei Lin, Laura M Nocka, Brittany L Stinger, Joseph B DeGrandchamp, L J Nugent Lew, Steven Alvarez, Henry T Phan, Yasushi Kondo, John Kuriyan, Jay T Groves.

  SignificanceTwo-dimensional condensates of proteins on the membrane surface, driven by tyrosine phosphorylation, are beginning to emerge as important players in signal transduction. This work describes discovery of a protein condensation phase transition of EGFR and Grb2 on membrane surfaces, which is poised to have a significant impact on how we understand EGFR signaling and misregulation in disease. EGFR condensation is mediated through a Grb2-Grb2 crosslinking element, which itself is regulatable through a specific phosphotyrosine site on Grb2. Furthermore, the EGFR condensate exerts significant control over the ability of SOS to activate Ras, thus implicating the EGFR condensate as a regulator of signal propagation from EGFR to Ras and the MAPK pathway.

Keywords:  EGFR; Ras; condensation phase transition; membrane; protein condensate

DOI:  https://doi.org/10.1073/pnas.2122531119
Lab Chip. 2022 May 06.

Cellular point-of-care diagnostics using an inexpensive layer-stack microfluidic device.

Kilean Lucas, Juhyun Oh, Jan Hoelzl, Ralph Weissleder.

Cellular analyses are increasingly used to diagnose diseases at point-of-care and global healthcare settings. Some analyses are simple as they rely on chromogenic stains (blood counts, malaria) but others often require higher multiplexing to define and quantitate cell populations (cancer diagnosis, immunoprofiling). Simplifying the latter with inexpensive solutions represents a current bottleneck in designing start-end pipelines. Based on the hypothesis that novel film adhesives could be used to create inexpensive disposable devices, we tested a number of different designs and materials, to rapidly perform 12-15 channel single-cell imaging. Using an optimized passive pumping layer-stack microfluidic (PLASMIC) device (<1 $ in supplies) we show that rapid, inexpensive cellular analysis is feasible.

DOI: https://doi.org/10.1039/d2lc00162d
Methods Mol Biol. 2022 ;2429 547-554

Limiting Dilution Tumor Initiation Assay: An In Vivo Approach for the Study of Cancer Stem Cells.

Petra den Hollander, Robiya Joseph, Suhas Vasaikar, Nick A Kuburich, Abhijeet P Deshmukh, Sendurai A Mani.

  Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. Calculating the frequency of tumor-initiating cells is important in the assessment of the number of CSCs present in a cell population. In this chapter, we present a protocol developed for quantification of CSCs from breast cancer tumors that can be adapted to CSCs from other types of tumors.

Keywords:  Cancer stem cells; In vivo; Limiting dilution tumor initiation; Tumor-initiating cell frequency

DOI:  https://doi.org/10.1007/978-1-0716-1979-7_38
Autophagy. 2022 May 06. 1-15

Proteotoxic stress disrupts epithelial integrity by inducing MTOR sequestration and autophagy overactivation.

Xiaoxiang Cheng, Pei Zhang, Hongyu Zhao, Hui Zheng, Kai Zheng, Hong Zhang, Hongjie Zhang.

  Macroautophagy/autophagy, an evolutionarily conserved degradation system, serves to clear intracellular components through the lysosomal pathway. Mounting evidence has revealed cytoprotective roles of autophagy; however, the intracellular causes of overactivated autophagy, which has cytotoxic effects, remain elusive. Here we show that sustained proteotoxic stress induced by loss of the RING and Kelch repeat-containing protein C53A5.6/RIKE-1 induces sequestration of LET-363/MTOR complex and overactivation of autophagy, and consequently impairs epithelial integrity in C. elegans. In C53A5.6/RIKE-1-deficient animals, blocking autophagosome formation effectively prevents excessive endosomal degradation, mitigates mislocalization of intestinal membrane components and restores intestinal lumen morphology. However, autophagy inhibition does not affect LET-363/MTOR aggregation in animals with compromised C53A5.6/RIKE-1 function. Improving proteostasis capacity by reducing DAF-2 insulin/IGF1 signaling markedly relieves the aggregation of LET-363/MTOR and alleviates autophagy overactivation, which in turn reverses derailed endosomal trafficking and rescues epithelial morphogenesis defects in C53A5.6/RIKE-1-deficient animals. Hence, our studies reveal that C53A5.6/RIKE-1-mediated proteostasis is critical for maintaining the basal level of autophagy and epithelial integrity.Abbreviations: ACT-5: actin 5; ACTB: actin beta; ALs: autolysosomes; APs: autophagosomes; AJM-1: apical junction molecule; ATG: autophagy related; C. elegans: Caenorhabditis elegans; CPL-1: cathepsin L family; DAF: abnormal dauer formation; DLG-1: Drosophila discs large homolog; ERM-1: ezrin/radixin/moesin; EPG: ectopic P granule; GFP: freen fluorescent protein; HLH-30: helix loop helix; HSP: heat shock protein; LAAT-1: lysosome associated amino acid transporter; LET: lethal; LGG-1: LC3, GABARAP and GATE-16 family; LMP-1: LAMP (lysosome-associated membrane protein) homolog; MTOR: mechanistic target of rapamycin kinase; NUC-1: abnormal nuclease; PEPT-1/OPT-2: Peptide transporter family; PGP-1: P-glycoprotein related; RAB: RAB family; RIKE-1: RING and Kelch repeat-containing protein; SLCF-1: solute carrier family; SQST-1: sequestosome related; SPTL-1: serine palmitoyl transferase family.

Keywords:  Autophagy; C. elegans; LET-363/MTOR; endosomal degradation; epithelial morphogenesis; proteostasis

DOI:  https://doi.org/10.1080/15548627.2022.2071381
STAR Protoc. 2022 Jun 17. 3(2): 101347

A live-imaging protocol for tracking receptor dynamics in single cells.

Yibin Huang, Toshimasa Takahashi, Herbert Gaisano, Hiromi Rakugi, Koichi Yamamoto.

  Adjacent membrane receptors can show different cellular responses to ligand stimulation. Here, we describe a super-resolution microscopy imaging protocol for tracking the dynamics of two different membrane-bound receptors in single cells. We describe the transfection protocol by electroporation. We detail the imaging procedure for receptors in a single cell. We then outline the data analysis pipeline. We have applied this protocol to imaging of endocytosis of the LOX-1 and AT1 in CHO-K1 cells, but the protocol can be applied to a variety of membrane receptors in other cell lines. For complete details on the use and execution of this protocol, please refer to Takahashi et al. (2021).

Keywords:  Cell Biology; Cell culture; Microscopy; Signal Transduction; Single Cell

DOI:  https://doi.org/10.1016/j.xpro.2022.101347
J Cell Biol. 2022 Jun 06. pii: e202105112. [Epub ahead of print]221(6):

V-ATPase is a universal regulator of LC3-associated phagocytosis and non-canonical autophagy.

Kirsty M Hooper, Elise Jacquin, Taoyingnan Li, Jonathan M Goodwin, John H Brumell, Joanne Durgan, Oliver Florey.

Non-canonical autophagy is a key cellular pathway in immunity, cancer, and neurodegeneration, characterized by conjugation of ATG8 to endolysosomal single membranes (CASM). CASM is activated by engulfment (endocytosis, phagocytosis), agonists (STING, TRPML1), and infection (influenza), dependent on K490 in the ATG16L1 WD40-domain. However, factors associated with non-canonical ATG16L1 recruitment and CASM induction remain unknown. Here, using pharmacological inhibitors, we investigate a role for V-ATPase during non-canonical autophagy. We report that increased V0-V1 engagement is associated with, and sufficient for, CASM activation. Upon V0-V1 binding, V-ATPase recruits ATG16L1, via K490, during LC3-associated phagocytosis (LAP), STING- and drug-induced CASM, indicating a common mechanism. Furthermore, during LAP, key molecular players, including NADPH oxidase/ROS, converge on V-ATPase. Finally, we show that LAP is sensitive to Salmonella SopF, which disrupts the V-ATPase-ATG16L1 axis and provide evidence that CASM contributes to the Salmonella host response. Together, these data identify V-ATPase as a universal regulator of CASM and indicate that SopF evolved in part to evade non-canonical autophagy.

DOI: https://doi.org/10.1083/jcb.202105112
Cell Stem Cell. 2022 May 05. pii: S1934-5909(22)00165-5. [Epub ahead of print]29(5): 667-677

Biomanufacturing human tissues via organ building blocks.

Kayla J Wolf, Jonathan D Weiss, Sebastien G M Uzel, Mark A Skylar-Scott, Jennifer A Lewis.

The construction of human organs on demand remains a tantalizing vision to solve the organ donor shortage. Yet, engineering tissues that recapitulate the cellular and architectural complexity of native organs is a grand challenge. The use of organ building blocks (OBBs) composed of multicellular spheroids, organoids, and assembloids offers an important pathway for creating organ-specific tissues with the desired cellular-to-tissue-level organization. Here, we review the differentiation, maturation, and 3D assembly of OBBs into functional human tissues and, ultimately, organs for therapeutic repair and replacement. We also highlight future challenges and areas of opportunity for this nascent field.

DOI: https://doi.org/10.1016/j.stem.2022.04.012