bims-cagime 2022-12-18 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–12–18
forty papers selected by
Kıvanç Görgülü, Technical University of Munich

Diversity of mitophagy pathways at a glance.
NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.
p21 induces a senescence program and skeletal muscle dysfunction.
Targeting the bicarbonate transporter SLC4A4 overcomes immunosuppression and immunotherapy resistance in pancreatic cancer.
Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery.
Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma.
Adjuvant nab-Paclitaxel + Gemcitabine in Resected Pancreatic Ductal Adenocarcinoma: Results From a Randomized, Open-Label, Phase III Trial.
Emerging roles of intratumor microbiota in cancer metastasis.
Metabolic modulation of transcription: The role of one-carbon metabolism.
Quantitative imaging of single-cell phenotypes in cancer cells cultured on hydrogel surfaces.
Lysosome signaling in cell survival and programmed cell death for cellular homeostasis.
A Genetically Encoded Magnetic Resonance Imaging Reporter Enables Sensitive Detection and Tracking of Spontaneous Metastases in Deep Tissues.
Protein import into peroxisomes occurs through a nuclear pore-like phase.
Furnishing the cachexia landscape: A year of research in JCSM.
Estimating Metastatic Risk of Pancreatic Ductal Adenocarcinoma at Single-Cell Resolution.
Laser Capture Microdissection: A Gear for Pancreatic Cancer Research.
Modeling cancer metabolism in vitro: current improvements and future challenges.
Perineural Invasion in Pancreatic Ductal Adenocarcinoma: From Molecules towards Drugs of Clinical Relevance.
A transcriptomic-based tool to predict gemcitabine sensitivity in advanced pancreatic adenocarcinoma.
Proteome diversification by mRNA translation in cancer.
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.
DisGUVery: A Versatile Open-Source Software for High-Throughput Image Analysis of Giant Unilamellar Vesicles.
Protocol to isolate immune cells from mouse pancreatic lymph nodes and whole pancreas for mass cytometric analyses.
Protein Phase Separation: New Insights into Carcinogenesis.
Lactate dehydrogenase: relationship with the diagnostic GLIM criterion for cachexia in patients with advanced cancer.
A biopolymer to fight pancreatic cancer.
Single-cell analysis of senescent epithelia reveals targetable mechanisms promoting fibrosis.
The Aging-Cancer Cycle: Mechanisms and Opportunities for Intervention.
Immediate surgery compared with short-course neoadjuvant gemcitabine plus capecitabine, FOLFIRINOX, or chemoradiotherapy in patients with borderline resectable pancreatic cancer (ESPAC5): a four-arm, multicentre, randomised, phase 2 trial.
Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function.
In vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma.
The war on pancreatic cancer: progress and promise.
Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies.
Membrane Contact Sites in Autophagy.
CPPA: A Web Tool for Exploring Proteomic and Phosphoproteomic Data in Cancer.
Tipping the balance: New insights into stromal regulation of cancer.
Emerging current trends and research focus related to pancreatic cancer metabolism: A bibliometric and visualized analysis.
An open access, machine learning pipeline for high-throughput quantification of cell morphology.
Plasma proteome profiling of healthy subjects undergoing bed rest reveals unloading-dependent changes linked to muscle atrophy.
Protocol for detecting macrophage-mediated cancer cell phagocytosis in vitro and in vivo.

J Cell Sci. 2022 Dec 01. pii: jcs259748. [Epub ahead of print]135(23):

Diversity of mitophagy pathways at a glance.

Ian G Ganley, Anne Simonsen.

  Mitochondria are crucial organelles that play a central role in various cell signaling and metabolic pathways. A healthy mitochondrial population is maintained through a series of quality control pathways and requires a fine-tuned balance between mitochondrial biogenesis and degradation. Defective targeting of dysfunctional mitochondria to lysosomes through mitophagy has been linked to several diseases, but the underlying mechanisms and the relative importance of distinct mitophagy pathways in vivo are largely unknown. In this Cell Science at a Glance and the accompanying poster, we describe our current understanding of how parts of, or whole, mitochondria are recognized by the autophagic machinery and targeted to lysosomes for degradation. We also discuss how this might be regulated under different physiological conditions to maintain mitochondrial and cellular health.

Keywords:  BNIP3; HIF1; Mitochondria; Mitophagy; NIX; PINK1; Parkin; SLR; Selective autophagy

DOI:  https://doi.org/10.1242/jcs.259748
EMBO J. 2022 Dec 14. e111372

NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.

Tetsushi Kataura, Elsje G Otten, Yoana Rabanal-Ruiz, Elias Adriaenssens, Francesca Urselli, Filippo Scialo, Lanyu Fan, Graham R Smith, William M Dawson, Xingxiang Chen, Wyatt W Yue, Agnieszka K Bronowska, Bernadette Carroll, Sascha Martens, Michael Lazarou, Viktor I Korolchuk.

  Mitophagy, the elimination of mitochondria via the autophagy-lysosome pathway, is essential for the maintenance of cellular homeostasis. The best characterised mitophagy pathway is mediated by stabilisation of the protein kinase PINK1 and recruitment of the ubiquitin ligase Parkin to damaged mitochondria. Ubiquitinated mitochondrial surface proteins are recognised by autophagy receptors including NDP52 which initiate the formation of an autophagic vesicle around the mitochondria. Damaged mitochondria also generate reactive oxygen species (ROS) which have been proposed to act as a signal for mitophagy, however the mechanism of ROS sensing is unknown. Here we found that oxidation of NDP52 is essential for the efficient PINK1/Parkin-dependent mitophagy. We identified redox-sensitive cysteine residues involved in disulphide bond formation and oligomerisation of NDP52 on damaged mitochondria. Oligomerisation of NDP52 facilitates the recruitment of autophagy machinery for rapid mitochondrial degradation. We propose that redox sensing by NDP52 allows mitophagy to function as a mechanism of oxidative stress response.

Keywords:  NDP52; autophagy; mitophagy; p62; redox

DOI:  https://doi.org/10.15252/embj.2022111372
Mol Metab. 2022 Dec 09. pii: S2212-8778(22)00221-6. [Epub ahead of print] 101652

p21 induces a senescence program and skeletal muscle dysfunction.

Davis A Englund, Alyssa Jolliffe, Zaira Aversa, Xu Zhang, Ines Sturmlechner, Ayumi E Sakamoto, Julianna D Zeidler, Gina M Warner, Colton McNinch, Thomas A White, Eduardo N Chini, Darren J Baker, Jan M van Deursen, Nathan K LeBrasseur.

  Recent work has established associations between elevated p21, the accumulation of senescent cells, and skeletal muscle dysfunction in mice and humans. Using a mouse model of p21 overexpression (p21OE), we examined if p21 mechanistically contributes to cellular senescence and pathological features in skeletal muscle. We show that p21 induces several core properties of cellular senescence in skeletal muscle, including an altered transcriptome, DNA damage, mitochondrial dysfunction, and the senescence-associated secretory phenotype (SASP). Furthermore, p21OE mice exhibit manifestations of skeletal muscle pathology, such as atrophy, fibrosis, and impaired physical function when compared to age-matched controls. These findings suggest p21 alone is sufficient to drive a cellular senescence program and reveal a novel source of skeletal muscle loss and dysfunction.

Keywords:  Aging; Cellular senescence; DNA damage; Fibrosis; Physical function; Sarcopenia; Senescence-associated secretory phenotype

DOI:  https://doi.org/10.1016/j.molmet.2022.101652
Nat Cancer. 2022 Dec 15.

Targeting the bicarbonate transporter SLC4A4 overcomes immunosuppression and immunotherapy resistance in pancreatic cancer.

Federica Cappellesso, Marie-Pauline Orban, Niranjan Shirgaonkar, Emanuele Berardi, Jens Serneels, Marie-Aline Neveu, Daria Di Molfetta, Francesca Piccapane, Rosa Caroppo, Lucantonio Debellis, Tessa Ostyn, Nicolas Joudiou, Lionel Mignion, Elena Richiardone, Bénédicte F Jordan, Bernard Gallez, Cyril Corbet, Tania Roskams, Ramanuj DasGupta, Sabine Tejpar, Mario Di Matteo, Daniela Taverna, Stephan J Reshkin, Baki Topal, Federico Virga, Massimiliano Mazzone.

Solid tumors are generally characterized by an acidic tumor microenvironment (TME) that favors cancer progression, therapy resistance and immune evasion. By single-cell RNA-sequencing analysis in individuals with pancreatic ductal adenocarcinoma (PDAC), we reveal solute carrier family 4 member 4 (SLC4A4) as the most abundant bicarbonate transporter, predominantly expressed by epithelial ductal cells. Functionally, SLC4A4 inhibition in PDAC cancer cells mitigates the acidosis of the TME due to bicarbonate accumulation in the extracellular space and a decrease in lactate production by cancer cells as the result of reduced glycolysis. In PDAC-bearing mice, genetic or pharmacological SLC4A4 targeting improves T cell-mediated immune response and breaches macrophage-mediated immunosuppression, thus inhibiting tumor growth and metastases. In addition, Slc4a4 targeting in combination with immune checkpoint blockade is able to overcome immunotherapy resistance and prolong survival. Overall, our data propose SLC4A4 as a therapeutic target to unleash an antitumor immune response in PDAC.

DOI: https://doi.org/10.1038/s43018-022-00470-2
Sci Adv. 2022 Dec 14. 8(50): eadd1436

Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery.

Liv E Jensen, Shanlin Rao, Martina Schuschnig, A King Cada, Sascha Martens, Gerhard Hummer, James H Hurley.

How the highly curved phagophore membrane is stabilized during autophagy initiation is a major open question in autophagosome biogenesis. Here, we use in vitro reconstitution on membrane nanotubes and molecular dynamics simulations to investigate how core autophagy proteins in the LC3 (Microtubule-associated proteins 1A/1B light chain 3) lipidation cascade interact with curved membranes, providing insight into their possible roles in regulating membrane shape during autophagosome biogenesis. ATG12(Autophagy-related 12)-ATG5-ATG16L1 was up to 100-fold enriched on highly curved nanotubes relative to flat membranes. At high surface density, ATG12-ATG5-ATG16L1 binding increased the curvature of the nanotubes. While WIPI2 (WD repeat domain phosphoinositide-interacting protein 2) binding directs membrane recruitment, the amphipathic helix α2 of ATG16L1 is responsible for curvature sensitivity. Molecular dynamics simulations revealed that helix α2 of ATG16L1 inserts shallowly into the membrane, explaining its curvature-sensitive binding to the membrane. These observations show how the binding of the ATG12-ATG5-ATG16L1 complex to the early phagophore rim could stabilize membrane curvature and facilitate autophagosome growth.

DOI: https://doi.org/10.1126/sciadv.add1436
Cell Rep. 2022 Dec 13. pii: S2211-1247(22)01710-7. [Epub ahead of print]41(11): 111818

Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma.

Dane T Sessions, Kee-Beom Kim, Jennifer A Kashatus, Nikolas Churchill, Kwon-Sik Park, Marty W Mayo, Hiromi Sesaki, David F Kashatus.

  Oncogenic KRas activates mitochondrial fission through Erk-mediated phosphorylation of the mitochondrial fission GTPase Drp1. Drp1 deletion inhibits tumorigenesis of KRas-driven pancreatic cancer, but the role of mitochondrial dynamics in other Ras-driven malignancies is poorly defined. Here we show that in vitro and in vivo growth of KRas-driven lung adenocarcinoma is unaffected by deletion of Drp1 but is inhibited by deletion of Opa1, the GTPase that regulates inner membrane fusion and proper cristae morphology. Mechanistically, Opa1 knockout disrupts cristae morphology and inhibits electron transport chain (ETC) assembly and activity, which inhibits tumor cell proliferation through loss of NAD+ regeneration. Simultaneous inactivation of Drp1 and Opa1 restores cristae morphology, ETC activity, and cell proliferation indicating that mitochondrial fission activity drives ETC dysfunction induced by Opa1 knockout. Our results support a model in which mitochondrial fission events disrupt cristae structure, and tumor cells with hyperactive fission activity require Opa1 activity to maintain ETC function.

Keywords:  CP: Cancer; Drp1; ETC; KRas; NAD; Opa1; cancer; cristae; fission; fusion; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2022.111818
J Clin Oncol. 2022 Dec 15. JCO2201134

Adjuvant nab-Paclitaxel + Gemcitabine in Resected Pancreatic Ductal Adenocarcinoma: Results From a Randomized, Open-Label, Phase III Trial.

APACT Investigators

PURPOSE: This randomized, open-label trial compared the efficacy and safety of adjuvant nab-paclitaxel + gemcitabine with those of gemcitabine for resected pancreatic ductal adenocarcinoma (ClinicalTrials.gov identifier: NCT01964430).
METHODS: We assigned 866 treatment-naive patients with pancreatic ductal adenocarcinoma to nab-paclitaxel (125 mg/m2) + gemcitabine (1,000 mg/m2) or gemcitabine alone to one 30-40 infusion on days 1, 8, and 15 of six 28-day cycles. The primary end point was independently assessed disease-free survival (DFS). Additional end points included investigator-assessed DFS, overall survival (OS), and safety.
RESULTS: Two hundred eighty-seven of 432 patients and 310 of 434 patients completed nab-paclitaxel + gemcitabine and gemcitabine treatment, respectively. At primary data cutoff (December 31, 2018; median follow-up, 38.5 [interquartile range [IQR], 33.8-43 months), the median independently assessed DFS was 19.4 (nab-paclitaxel + gemcitabine) versus 18.8 months (gemcitabine; hazard ratio [HR], 0.88; 95% CI, 0.729 to 1.063; P = .18). The median investigator-assessed DFS was 16.6 (IQR, 8.4-47.0) and 13.7 (IQR, 8.3-44.1) months, respectively (HR, 0.82; 95% CI, 0.694 to 0.965; P = .02). The median OS (427 events; 68% mature) was 40.5 (IQR, 20.7 to not reached) and 36.2 (IQR, 17.7-53.3) months, respectively (HR, 0.82; 95% CI, 0.680 to 0.996; P = .045). At a 16-month follow-up (cutoff, April 3, 2020; median follow-up, 51.4 months [IQR, 47.0-57.0]), the median OS (511 events; 81% mature) was 41.8 (nab-paclitaxel + gemcitabine) versus 37.7 months (gemcitabine; HR, 0.82; 95% CI, 0.687 to 0.973; P = .0232). At the 5-year follow-up (cutoff, April 9, 2021; median follow-up, 63.2 months [IQR, 60.1-68.7]), the median OS (555 events; 88% mature) was 41.8 versus 37.7 months, respectively (HR, 0.80; 95% CI, 0.678 to 0.947; P = .0091). Eighty-six percent (nab-paclitaxel + gemcitabine) and 68% (gemcitabine) of patients experienced grade ≥ 3 treatment-emergent adverse events. Two patients per study arm died of treatment-emergent adverse events.
CONCLUSION: The primary end point (independently assessed DFS) was not met despite favorable OS seen with nab-paclitaxel + gemcitabine.

DOI: https://doi.org/10.1200/JCO.22.01134
Trends Cell Biol. 2022 Dec 13. pii: S0962-8924(22)00258-6. [Epub ahead of print]

Emerging roles of intratumor microbiota in cancer metastasis.

Aikun Fu, Bingqing Yao, Tingting Dong, Shang Cai.

  Cancer metastasis is the leading cause of mortality in patients with cancer. Theories have been developed to explain the causes and principles of metastasis. Metastasis is attributed to cancer cell-intrinsic properties and the extrinsic cellular environment. In recent years, the intratumor microbiota has been identified as an integral tumor component and may functionally regulate various aspects of metastasis. These novel discoveries in intratumor microbiota reshape the framework of our understanding of metastasis and reveal a new path for studies on cancer progression and clinical cancer management. Here, we summarize recent advances in the emerging roles of intratumor microbiota in cancer metastasis and discuss the challenges and implications for cancer treatment.

Keywords:  bacteria invasion; cancer ecosystem; cancer metastasis; intracellular bacteria; intratumor microbiota

DOI:  https://doi.org/10.1016/j.tcb.2022.11.007
Cell Chem Biol. 2022 Dec 01. pii: S2451-9456(22)00415-9. [Epub ahead of print]

Metabolic modulation of transcription: The role of one-carbon metabolism.

Jung-Ming G Lin, Savvas Kourtis, Ritobrata Ghose, Natalia Pardo Lorente, Stefan Kubicek, Sara Sdelci.

  While it is well known that expression levels of metabolic enzymes regulate the metabolic state of the cell, there is mounting evidence that the converse is also true, that metabolite levels themselves can modulate gene expression via epigenetic modifications and transcriptional regulation. Here we focus on the one-carbon metabolic pathway, which provides the essential building blocks of many classes of biomolecules, including purine nucleotides, thymidylate, serine, and methionine. We review the epigenetic roles of one-carbon metabolic enzymes and their associated metabolites and introduce an interactive computational resource that places enzyme essentiality in the context of metabolic pathway topology. Therefore, we briefly discuss examples of metabolic condensates and higher-order complexes of metabolic enzymes downstream of one-carbon metabolism. We speculate that they may be required to the formation of transcriptional condensates and gene expression control. Finally, we discuss new ways to exploit metabolic pathway compartmentalization to selectively target these enzymes in cancer.

Keywords:  cancer; chromatin; epigenetics; folate metabolism; metabolic condensates; nuclear condensates; nuclear metabolism; nucleotides; one-carbon metabolism; phase separation; purinergic signaling; transcription regulation; transcriptional condensates

DOI:  https://doi.org/10.1016/j.chembiol.2022.11.009
STAR Protoc. 2022 Dec 15. pii: S2666-1667(22)00822-X. [Epub ahead of print]4(1): 101942

Quantitative imaging of single-cell phenotypes in cancer cells cultured on hydrogel surfaces.

Vicky Bousgouni, Chris Bakal.

  Small interfering RNA (siRNA) screening approaches used with quantitative single-cell analysis can uncover the roles of genes in cell morphogenesis. Here, we present a high-throughput automated phenotypic screening technique to quantify a single cell shape in cancer cells cultured on top of soft 3D hydrogels. We describe reverse transfection of cells with siRNAs and seeding of these cells on top of collagen, followed by image analysis to quantify morphology of a single cell and population levels in low-elasticity matrices. For complete details on the use and execution of this protocol, please refer to Bousgouni et al. (2022).1.

Keywords:  Cancer; Cell Biology; Cell culture; Cell-based Assays; High Throughput Screening; Single Cell

DOI:  https://doi.org/10.1016/j.xpro.2022.101942
J Cell Physiol. 2022 Dec 11.

Lysosome signaling in cell survival and programmed cell death for cellular homeostasis.

Srimanta Patra, Shankargouda Patil, Daniel J Klionsky, Sujit K Bhutia.

  Recent developments in lysosome biology have transformed our view of lysosomes from static garbage disposals that can also act as suicide bags to decidedly dynamic multirole adaptive operators of cellular homeostasis. Lysosome-governed signaling pathways, proteins, and transcription factors equilibrate the rate of catabolism and anabolism (autophagy to lysosomal biogenesis and metabolite pool maintenance) by sensing cellular metabolic status. Lysosomes also interact with other organelles by establishing contact sites through which they exchange cellular contents. Lysosomal function is critically assessed by lysosomal positioning and motility for cellular adaptation. In this setting, mechanistic target of rapamycin kinase (MTOR) is the chief architect of lysosomal signaling to control cellular homeostasis. Notably, lysosomes can orchestrate explicit cell death mechanisms, such as autophagic cell death and lysosomal membrane permeabilization-associated regulated necrotic cell death, to maintain cellular homeostasis. These lines of evidence emphasize that the lysosomes serve as a central signaling hub for cellular homeostasis.

Keywords:  autophagy; lysosomal biogenesis; lysosomal membrane permeabilization; lysosome; mechanistic target of rapamycin kinase

DOI:  https://doi.org/10.1002/jcp.30928
Cancer Res. 2022 Dec 13. pii: CAN-22-2770. [Epub ahead of print]

A Genetically Encoded Magnetic Resonance Imaging Reporter Enables Sensitive Detection and Tracking of Spontaneous Metastases in Deep Tissues.

Nivin N Nyström, Sean W McRae, Francisco M Martinez, John J Kelly, Timothy J Scholl, John A Ronald.

Metastasis is the leading cause of cancer-related death. However, it remains a poorly understood aspect of cancer biology, and most preclinical cancer studies do not examine metastasis, focusing solely on the primary tumor. One major factor contributing to this paradox is a gap in available tools for accurate spatiotemporal measurements of metastatic spread in vivo. Here, our objective was to develop an imaging reporter system that offers sensitive three-dimensional detection of cancer cells at high resolutions in live mice. An organic anion-transporting polypeptide 1b3 (oatp1b3) was utilized as a magnetic resonance imaging (MRI) reporter gene, and its sensitivity was systematically optimized for in vivo tracking of viable cancer cells in a spontaneous metastasis model. Metastases with oatp1b3-MRI could be observed at the single lymph node level and tracked over time as cancer cells spread to multiple lymph nodes and different organ systems in individual animals. While initial single lesions were successfully imaged in parallel via bioluminescence, later metastases were largely obscured by light scatter from the initial node. Importantly, MRI could detect micro-metastases in lung tissue estimated to comprise of as few as 1000 cancer cells. In summary, oatp1b3-MRI enables longitudinal tracking of cancer cells with combined high resolution and high sensitivity that provides 3D spatial information and the surrounding anatomical context.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2770
Science. 2022 Dec 16. 378(6625): eadf3971

Protein import into peroxisomes occurs through a nuclear pore-like phase.

Yuan Gao, Michael L Skowyra, Peiqiang Feng, Tom A Rapoport.

Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal proteins are imported from the cytosol in a folded state by the soluble receptor PEX5. How folded cargo crosses the membrane is unknown. Here, we show that peroxisomal import is similar to nuclear transport. The peroxisomal membrane protein PEX13 contains a conserved tyrosine (Y)- and glycine (G)-rich YG domain, which forms a selective phase resembling that formed by phenylalanine-glycine (FG) repeats within nuclear pores. PEX13 resides in the membrane in two orientations that oligomerize and suspend the YG meshwork within the lipid bilayer. Purified YG domains form hydrogels into which PEX5 selectively partitions, by using conserved aromatic amino acid motifs, bringing cargo along. The YG meshwork thus forms an aqueous conduit through which PEX5 delivers folded proteins into peroxisomes.

DOI: https://doi.org/10.1126/science.adf3971
J Cachexia Sarcopenia Muscle. 2022 Dec;13(6): 2763-2771

Furnishing the cachexia landscape: A year of research in JCSM.

Ann-Kathrin Fröhlich, Monika Diek, Stephan von Haehling, Markus S Anker.



Keywords:  cachexia; muscle wasting; sarcopenia

DOI:  https://doi.org/10.1002/jcsm.13151
Int J Mol Sci. 2022 Nov 30. pii: 15020. [Epub ahead of print]23(23):

Estimating Metastatic Risk of Pancreatic Ductal Adenocarcinoma at Single-Cell Resolution.

Sina Chen, Shunheng Zhou, Yu-E Huang, Mengqin Yuan, Wanyue Lei, Jiahao Chen, Kongxuan Lin, Wei Jiang.

  Pancreatic ductal adenocarcinoma (PDAC) is characterized by intra-tumoral heterogeneity, and patients are always diagnosed after metastasis. Thus, finding out how to effectively estimate metastatic risk underlying PDAC is necessary. In this study, we proposed scMetR to evaluate the metastatic risk of tumor cells based on single-cell RNA sequencing (scRNA-seq) data. First, we identified diverse cell types, including tumor cells and other cell types. Next, we grouped tumor cells into three sub-populations according to scMetR score, including metastasis-featuring tumor cells (MFTC), transitional metastatic tumor cells (TransMTC), and conventional tumor cells (ConvTC). We identified metastatic signature genes (MSGs) through comparing MFTC and ConvTC. Functional enrichment analysis showed that up-regulated MSGs were enriched in multiple metastasis-associated pathways. We also found that patients with high expression of up-regulated MSGs had worse prognosis. Spatial mapping of MFTC showed that they are preferentially located in the cancer and duct epithelium region, which was enriched with the ductal cells' associated inflammation. Further, we inferred cell-cell interactions, and observed that interactions of the ADGRE5 signaling pathway, which is associated with metastasis, were increased in MFTC compared to other tumor sub-populations. Finally, we predicted 12 candidate drugs that had the potential to reverse expression of MSGs. Taken together, we have proposed scMetR to estimate metastatic risk in PDAC patients at single-cell resolution which might facilitate the dissection of tumor heterogeneity.

Keywords:  drug prediction; metastasis; pancreatic ductal adenocarcinoma; single-cell RNA sequencing; spatial transcriptomics

DOI:  https://doi.org/10.3390/ijms232315020
Int J Mol Sci. 2022 Nov 23. pii: 14566. [Epub ahead of print]23(23):

Laser Capture Microdissection: A Gear for Pancreatic Cancer Research.

Bhavana Hemantha Rao, Pavel Souček, Viktor Hlaváč.

  The advancement in molecular techniques has been attributed to the quality and significance of cancer research. Pancreatic cancer (PC) is one of the rare cancers with aggressive behavior and a high mortality rate. The asymptomatic nature of the disease until its advanced stage has resulted in late diagnosis as well as poor prognosis. The heterogeneous character of PC has complicated cancer development and progression studies. The analysis of bulk tissues of the disease was insufficient to understand the disease, hence, the introduction of the single-cell separating technique aided researchers to decipher more about the specific cell population of tumors. This review gives an overview of the Laser Capture Microdissection (LCM) technique, one of the single-cell separation methods used in PC research.

Keywords:  Laser Capture Microdissection (LCM); hypoxia; intraductal papillary mucinous neoplasm (IPMN); metastasis; pancreatic cancer; single-cell separation

DOI:  https://doi.org/10.3390/ijms232314566
FEBS J. 2022 Dec 14.

Modeling cancer metabolism in vitro: current improvements and future challenges.

Helena Dragic, Cedric Chaveroux, Erika Cosset, Serge N Manie.

  Advances in cancer biology over the past decades have revealed that metabolic adaptation of cancer cells is an essential aspect of tumorigenesis. However, recent insights into tumor metabolism in vivo have revealed dissimilarities with results obtained in vitro. This is partly due to the reductionism of in vitro cancer models that struggle to reproduce the complexity of tumor tissues. This review describes some of the discrepancies in cancer cell metabolism between in vitro and in vivo conditions, and presents current methodological approaches and tools used to bridge the gap with the clinically relevant microenvironment. As such, these approaches should generate new knowledge that could be more effectively translated into therapeutic opportunities.

Keywords:  3D models; metabolic heterogeneity; metabolic sensors; tissue culture media; tumor cell metabolism

DOI:  https://doi.org/10.1111/febs.16704
Cancers (Basel). 2022 Nov 24. pii: 5793. [Epub ahead of print]14(23):

Perineural Invasion in Pancreatic Ductal Adenocarcinoma: From Molecules towards Drugs of Clinical Relevance.

Federico Selvaggi, Eugenia Melchiorre, Ilaria Casari, Sebastiano Cinalli, Massimiliano Cinalli, Gitana Maria Aceto, Roberto Cotellese, Ingrid Garajova, Marco Falasca.

  Pancreatic ductal adenocarcinoma is one of the most threatening solid malignancies. Molecular and cellular mediators that activate paracrine signalling also regulate the dynamic interaction between pancreatic cancer cells and nerves. This reciprocal interface leads to perineural invasion (PNI), defined as the ability of cancer cells to invade nerves, similar to vascular and lymphatic metastatic cascade. Targeting PNI in pancreatic cancer might help ameliorate prognosis and pain relief. In this review, the modern knowledge of PNI in pancreatic cancer has been analysed and critically presented. We focused on molecular pathways promoting cancer progression, with particular emphasis on neuropathic pain generation, and we reviewed the current knowledge of pharmacological inhibitors of the PNI axis. PNI represents a common hallmark of PDAC and correlates with recurrence, poor prognosis and pain in pancreatic cancer patients. The interaction among pancreatic cancer cells, immune cells and nerves is biologically relevant in each stage of the disease and stimulates great interest, but the real impact of the administration of novel agents in clinical practice is limited. It is still early days for PNI-targeted treatments, and further advanced studies are needed to understand whether they could be effective tools in the clinical setting.

Keywords:  neuropathic pain; pancreas; pancreatic ductal adenocarcinoma; perineural invasion; tumour microenvironment

DOI:  https://doi.org/10.3390/cancers14235793
Gastroenterology. 2022 Dec 07. pii: S0016-5085(22)01373-7. [Epub ahead of print]

A transcriptomic-based tool to predict gemcitabine sensitivity in advanced pancreatic adenocarcinoma.

PDAC Chemo sensitivity prediction working group



Keywords:  Pancreatic cancer; RNA signature; chemosensitivity prediction; gemcitabine; precision medicine

DOI:  https://doi.org/10.1053/j.gastro.2022.11.035
Mol Cell. 2022 Dec 07. pii: S1097-2765(22)01103-0. [Epub ahead of print]

Proteome diversification by mRNA translation in cancer.

Adva Kochavi, Domenica Lovecchio, William James Faller, Reuven Agami.

  mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.

Keywords:  aberrant protein production; mRNA translation; ribosomal heterogeneity; transfer RNA

DOI:  https://doi.org/10.1016/j.molcel.2022.11.014
J Comput Biol. 2022 Dec;29(12): 1305-1323

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.

Uthsav Chitra, Tae Yoon Park, Benjamin J Raphael.

  A standard paradigm in computational biology is to leverage interaction networks as prior knowledge in analyzing high-throughput biological data, where the data give a score for each vertex in the network. One classical approach is the identification of altered subnetworks, or subnetworks of the interaction network that have both outlier vertex scores and a defined network topology. One class of algorithms for identifying altered subnetworks search for high-scoring subnetworks in subnetwork families with simple topological constraints, such as connected subnetworks, and have sound statistical guarantees. A second class of algorithms employ network propagation-the smoothing of vertex scores over the network using a random walk or diffusion process-and utilize the global structure of the network. However, network propagation algorithms often rely on ad hoc heuristics that lack a rigorous statistical foundation. In this work, we unify the subnetwork family and network propagation approaches by deriving the propagation family, a subnetwork family that approximates the sets of vertices ranked highly by network propagation approaches. We introduce NetMix2, a principled algorithm for identifying altered subnetworks from a wide range of subnetwork families. When using the propagation family, NetMix2 combines the advantages of the subnetwork family and network propagation approaches. NetMix2 outperforms other methods, including network propagation on simulated data, pan-cancer somatic mutation data, and genome-wide association data from multiple human diseases.

Keywords:  GWAS; altered subnetworks; anomaly detection; cancer; interaction network; network analysis; network propagation

DOI:  https://doi.org/10.1089/cmb.2022.0336
ACS Synth Biol. 2022 Dec 12.

DisGUVery: A Versatile Open-Source Software for High-Throughput Image Analysis of Giant Unilamellar Vesicles.

Lennard van Buren, Gijsje Hendrika Koenderink, Cristina Martinez-Torres.

  Giant unilamellar vesicles (GUVs) are cell-sized aqueous compartments enclosed by a phospholipid bilayer. Due to their cell-mimicking properties, GUVs have become a widespread experimental tool in synthetic biology to study membrane properties and cellular processes. In stark contrast to the experimental progress, quantitative analysis of GUV microscopy images has received much less attention. Currently, most analysis is performed either manually or with custom-made scripts, which makes analysis time-consuming and results difficult to compare across studies. To make quantitative GUV analysis accessible and fast, we present DisGUVery, an open-source, versatile software that encapsulates multiple algorithms for automated detection and analysis of GUVs in microscopy images. With a performance analysis, we demonstrate that DisGUVery's three vesicle detection modules successfully identify GUVs in images obtained with a wide range of imaging sources, in various typical GUV experiments. Multiple predefined analysis modules allow the user to extract properties such as membrane fluorescence, vesicle shape, and internal fluorescence from large populations. A new membrane segmentation algorithm facilitates spatial fluorescence analysis of nonspherical vesicles. Altogether, DisGUVery provides an accessible tool to enable high-throughput automated analysis of GUVs, and thereby to promote quantitative data analysis in synthetic cell research.

Keywords:  bottom-up reconstitution; giant unilamellar vesicles; image analysis; object detection; open-source software; synthetic cell

DOI:  https://doi.org/10.1021/acssynbio.2c00407
STAR Protoc. 2022 Dec 14. pii: S2666-1667(22)00818-8. [Epub ahead of print]4(1): 101938

Protocol to isolate immune cells from mouse pancreatic lymph nodes and whole pancreas for mass cytometric analyses.

Titli Nargis, Annie R Piñeros, Sarah C May, Sarah A Tersey, Raghavendra G Mirmira.

  Investigating the immune attack on β cells is critical to understanding autoimmune diabetes. Here, we present a protocol to isolate immune cells from mouse pancreatic lymph nodes and whole pancreas, followed by mass cytometric analyses. This protocol can be used to analyze subsets of innate and adaptive immune cells that play critical roles in autoimmune diabetes, with as few as 5 × 105 cells. This protocol can also be adapted to study resident immune cells from other tissues. For complete details on the use and execution of this protocol, please refer to Piñeros et al. (2022).1.

Keywords:  Cell Biology; Cell isolation; Cell-based Assays; Flow Cytometry/Mass Cytometry; Immunology

DOI:  https://doi.org/10.1016/j.xpro.2022.101938
Cancers (Basel). 2022 Dec 02. pii: 5971. [Epub ahead of print]14(23):

Protein Phase Separation: New Insights into Carcinogenesis.

Yan Luo, Shasha Xiang, Jianbo Feng.

  Phase separation is now acknowledged as an essential biologic mechanism wherein distinct activated molecules assemble into a different phase from the surrounding constituents of a cell. Condensates formed by phase separation play an essential role in the life activities of various organisms under normal physiological conditions, including the advanced structure and regulation of chromatin, autophagic degradation of incorrectly folded or unneeded proteins, and regulation of the actin cytoskeleton. During malignant transformation, abnormally altered condensate assemblies are often associated with the abnormal activation of oncogenes or inactivation of tumor suppressors, resulting in the promotion of the carcinogenic process. Thus, understanding the role of phase separation in various biological evolutionary processes will provide new ideas for the development of drugs targeting specific condensates, which is expected to be an effective cancer therapy strategy. However, the relationship between phase separation and cancer has not been fully elucidated. In this review, we mainly summarize the main processes and characteristics of phase separation and the main methods for detecting phase separation. In addition, we summarize the cancer proteins and signaling pathways involved in phase separation and discuss their promising future applications in addressing the unmet clinical therapeutic needs of people with cancer. Finally, we explain the means of targeted phase separation and cancer treatment.

Keywords:  biomolecular condensates; membraneless organelle; oncogenic mutation; oncology therapy; phase separation

DOI:  https://doi.org/10.3390/cancers14235971
Br J Cancer. 2022 Dec 14.

Lactate dehydrogenase: relationship with the diagnostic GLIM criterion for cachexia in patients with advanced cancer.

Josh McGovern, Ross D Dolan, Claribel P L Simmons, Louise E Daly, Aoife M Ryan, Derek G Power, Donogh Maguire, Marie T Fallon, Barry J Laird, Donald C McMillan.

BACKGROUND: Although suggestive of dysregulated metabolism, the relationship between serum LDH level, phenotypic/aetiologic diagnostic Global Leadership Initiative on Malnutrition (GLIM) criteria and survival in patients with advanced cancer has yet to examined.
METHODS: Prospectively collected data from patients with advanced cancer, undergoing anti-cancer therapy with palliative intent, across nine sites in the UK and Ireland between 2011-2016, was retrospectively analysed. LDH values were grouped as <250/250-500/>500 Units/L. Relationships were examined using χ2 test for linear-by-linear association and binary logistics regression analysis.
RESULTS: A total of 436 patients met the inclusion criteria. 46% (n = 200) were male and 59% (n = 259) were ≥65 years of age. The median serum LDH was 394 Units/L and 33.5% (n = 146) had an LDH > 500 Units/L. LDH was significantly associated with ECOG-PS (p < 0.001), NLR (p < 0.05), mGPS (p < 0.05) and 3-month survival (p < 0.001). LDH was significantly associated with 3-month survival independent of weight loss (p < 0.01), BMI (p < 0.05), skeletal muscle mass (p < 0.01), metastatic disease (p < 0.05), NLR (p < 0.05) and mGPS (p < 0.01).
DISCUSSION: LDH was associated with performance status, systemic inflammation and survival in patients with advanced cancer. LDH measurement may be considered as an aetiologic criteria and become a potential therapeutic target in the treatment of cancer cachexia.

DOI: https://doi.org/10.1038/s41416-022-02099-5
Nat Mater. 2022 Dec 14.

A biopolymer to fight pancreatic cancer.

Cristina Lo Giudice.

DOI: https://doi.org/10.1038/s41563-022-01443-7
JCI Insight. 2022 11 22. pii: e154124. [Epub ahead of print]7(22):

Single-cell analysis of senescent epithelia reveals targetable mechanisms promoting fibrosis.

Eoin D O'Sullivan, Katie J Mylonas, Rachel Bell, Cyril Carvalho, David P Baird, Carolynn Cairns, Kevin M Gallagher, Ross Campbell, Marie Docherty, Alexander Laird, Neil C Henderson, Tamir Chandra, Kristina Kirschner, Bryan Conway, Gry H Dihazi, Michael Zeisberg, Jeremy Hughes, Laura Denby, Hassan Dihazi, David A Ferenbach.

  Progressive fibrosis and maladaptive organ repair result in significant morbidity and millions of premature deaths annually. Senescent cells accumulate with aging and after injury and are implicated in organ fibrosis, but the mechanisms by which senescence influences repair are poorly understood. Using 2 murine models of injury and repair, we show that obstructive injury generated senescent epithelia, which persisted after resolution of the original injury, promoted ongoing fibrosis, and impeded adaptive repair. Depletion of senescent cells with ABT-263 reduced fibrosis in reversed ureteric obstruction and after renal ischemia/reperfusion injury. We validated these findings in humans, showing that senescence and fibrosis persisted after relieved renal obstruction. We next characterized senescent epithelia in murine renal injury using single-cell RNA-Seq. We extended our classification to human kidney and liver disease and identified conserved profibrotic proteins, which we validated in vitro and in human disease. We demonstrated that increased levels of protein disulfide isomerase family A member 3 (PDIA3) augmented TGF-β-mediated fibroblast activation. Inhibition of PDIA3 in vivo significantly reduced kidney fibrosis during ongoing renal injury and as such represented a new potential therapeutic pathway. Analysis of the signaling pathways of senescent epithelia connected senescence to organ fibrosis, permitting rational design of antifibrotic therapies.

Keywords:  Bioinformatics; Cell Biology; Cellular senescence; Fibrosis; Nephrology

DOI:  https://doi.org/10.1172/jci.insight.154124
J Gerontol A Biol Sci Med Sci. 2022 Dec 13. pii: glac247. [Epub ahead of print]

The Aging-Cancer Cycle: Mechanisms and Opportunities for Intervention.

Mina S Sedrak, Harvey Jay Cohen.

  Aging is the largest risk factor for the development of cancer. A a growing body of literature indicates that aging and cancer often play a somewhat reciprocal relationship at various times. On the one hand, aging is a "driver" of cancer, and on the other, cancer is a "disease driver" of aging. Here, we synthesize our reflections on the current literature linking cancer and aging, with an eye on fundamental aging processes, such as cellular senescence. Additionally, we consider how interventions that target fundamental aging processes can potentially transform cancer care, from preventing cancer development and progression to reducing the burden of accelerated aging in cancer survivors. Finally, we conclude with a reflection highlighting our vision for future directions to advance the science of cancer and aging and its applicability to improve the care of older adults with cancer.

Keywords:  aging; aging biology; cancer; geroscience; hallmarks

DOI:  https://doi.org/10.1093/gerona/glac247
Lancet Gastroenterol Hepatol. 2022 Dec 12. pii: S2468-1253(22)00348-X. [Epub ahead of print]

Immediate surgery compared with short-course neoadjuvant gemcitabine plus capecitabine, FOLFIRINOX, or chemoradiotherapy in patients with borderline resectable pancreatic cancer (ESPAC5): a four-arm, multicentre, randomised, phase 2 trial.

European Study Group for Pancreatic Cancer

BACKGROUND: Patients with borderline resectable pancreatic ductal adenocarcinoma have relatively low resection rates and poor survival despite the use of adjuvant chemotherapy. The aim of our study was to establish the feasibility and efficacy of three different types of short-course neoadjuvant therapy compared with immediate surgery.
METHODS: ESPAC5 (formerly known as ESPAC-5f) was a multicentre, open label, randomised controlled trial done in 16 pancreatic centres in two countries (UK and Germany). Eligible patients were aged 18 years or older, with a WHO performance status of 0 or 1, biopsy proven pancreatic ductal adenocarcinoma in the pancreatic head, and were staged as having a borderline resectable tumour by contrast-enhanced CT criteria following central review. Participants were randomly assigned by means of minimisation to one of four groups: immediate surgery; neoadjuvant gemcitabine and capecitabine (gemcitabine 1000 mg/m2 on days 1, 8, and 15, and oral capecitabine 830 mg/m2 twice a day on days 1-21 of a 28-day cycle for two cycles); neoadjuvant FOLFIRINOX (oxaliplatin 85 mg/m2, irinotecan 180 mg/m2, folinic acid given according to local practice, and fluorouracil 400 mg/m2 bolus injection on days 1 and 15 followed by 2400 mg/m2 46 h intravenous infusion given on days 1 and 15, repeated every 2 weeks for four cycles); or neoadjuvant capecitabine-based chemoradiation (total dose 50·4 Gy in 28 daily fractions over 5·5 weeks [1·8 Gy per fraction, Monday to Friday] with capecitabine 830 mg/m2 twice daily [Monday to Friday] throughout radiotherapy). Patients underwent restaging contrast-enhanced CT at 4-6 weeks after neoadjuvant therapy and underwent surgical exploration if the tumour was still at least borderline resectable. All patients who had their tumour resected received adjuvant therapy at the oncologist's discretion. Primary endpoints were recruitment rate and resection rate. Analyses were done on an intention-to-treat basis. This trial is registered with ISRCTN, 89500674, and is complete.
FINDINGS: Between Sept 3, 2014, and Dec 20, 2018, from 478 patients screened, 90 were randomly assigned to a group (33 to immediate surgery, 20 to gemcitabine plus capecitabine, 20 to FOLFIRINOX, and 17 to capecitabine-based chemoradiation); four patients were excluded from the intention-to-treat analysis (one in the capecitabine-based chemoradiotherapy withdrew consent before starting therapy and three [two in the immediate surgery group and one in the gemcitabine plus capecitabine group] were found to be ineligible after randomisation). 44 (80%) of 55 patients completed neoadjuvant therapy. The recruitment rate was 25·92 patients per year from 16 sites; 21 (68%) of 31 patients in the immediate surgery and 30 (55%) of 55 patients in the combined neoadjuvant therapy groups underwent resection (p=0·33). R0 resection was achieved in three (14%) of 21 patients in the immediate surgery group and seven (23%) of 30 in the neoadjuvant therapy groups combined (p=0·49). Surgical complications were observed in 29 (43%) of 68 patients who underwent surgery; no patients died within 30 days. 46 (84%) of 55 patients receiving neoadjuvant therapy were available for restaging. Six (13%) of 46 had a partial response. Median follow-up time was 12·2 months (95% CI 12·0-12·4). 1-year overall survival was 39% (95% CI 24-61) for immediate surgery, 78% (60-100) for gemcitabine plus capecitabine, 84% (70-100) for FOLFIRINOX, and 60% (37-97) for capecitabine-based chemoradiotherapy (p=0·0028). 1-year disease-free survival from surgery was 33% (95% CI 19-58) for immediate surgery and 59% (46-74) for the combined neoadjuvant therapies (hazard ratio 0·53 [95% CI 0·28-0·98], p=0·016). Three patients reported local disease recurrence (two in the immediate surgery group and one in the FOLFIRINOX group). 78 (91%) patients were included in the safety set and assessed for toxicity events. 19 (24%) of 78 patients reported a grade 3 or worse adverse event (two [7%] of 28 patients in the immediate surgery group and 17 [34%] of 50 patients in the neoadjuvant therapy groups combined), the most common of which were neutropenia, infection, and hyperglycaemia.
INTERPRETATION: Recruitment was challenging. There was no significant difference in resection rates between patients who underwent immediate surgery and those who underwent neoadjuvant therapy. Short-course (8 week) neoadjuvant therapy had a significant survival benefit compared with immediate surgery. Neoadjuvant chemotherapy with either gemcitabine plus capecitabine or FOLFIRINOX had the best survival compared with immediate surgery. These findings support the use of short-course neoadjuvant chemotherapy in patients with borderline resectable pancreatic ductal adenocarcinoma.
FUNDING: Cancer Research UK.

DOI: https://doi.org/10.1016/S2468-1253(22)00348-X
Science. 2022 Dec 16. 378(6625): eabq5209

Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function.

Wonyul Jang, Dmytro Puchkov, Paula Samsó, YongTian Liang, Michal Nadler-Holly, Stephan J Sigrist, Ulrich Kintscher, Fan Liu, Kamel Mamchaoui, Vincent Mouly, Volker Haucke.

Cells respond to fluctuating nutrient supply by adaptive changes in organelle dynamics and in metabolism. How such changes are orchestrated on a cell-wide scale is unknown. We show that endosomal signaling lipid turnover by MTM1, a phosphatidylinositol 3-phosphate [PI(3)P] 3-phosphatase mutated in X-linked centronuclear myopathy in humans, controls mitochondrial morphology and function by reshaping the endoplasmic reticulum (ER). Starvation-induced endosomal recruitment of MTM1 impairs PI(3)P-dependent contact formation between tubular ER membranes and early endosomes, resulting in the conversion of ER tubules into sheets, the inhibition of mitochondrial fission, and sustained oxidative metabolism. Our results unravel an important role for early endosomal lipid signaling in controlling ER shape and, thereby, mitochondrial form and function to enable cells to adapt to fluctuating nutrient environments.

DOI: https://doi.org/10.1126/science.abq5209
Sci Adv. 2022 Dec 16. 8(50): eabp8293

In vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma.

Akash K Kaushik, Amy Tarangelo, Lindsey K Boroughs, Mukundan Ragavan, Yuanyuan Zhang, Cheng-Yang Wu, Xiangyi Li, Kristen Ahumada, Jui-Chung Chiang, Vanina T Tcheuyap, Faeze Saatchi, Quyen N Do, Cissy Yong, Tracy Rosales, Christina Stevens, Aparna D Rao, Brandon Faubert, Panayotis Pachnis, Lauren G Zacharias, Hieu Vu, Feng Cai, Thomas P Mathews, Giannicola Genovese, Barbara S Slusher, Payal Kapur, Xiankai Sun, Matthew Merritt, James Brugarolas, Ralph J DeBerardinis.

Targeting metabolic vulnerabilities has been proposed as a therapeutic strategy in renal cell carcinoma (RCC). Here, we analyzed the metabolism of patient-derived xenografts (tumorgrafts) from diverse subtypes of RCC. Tumorgrafts from VHL-mutant clear cell RCC (ccRCC) retained metabolic features of human ccRCC and engaged in oxidative and reductive glutamine metabolism. Genetic silencing of isocitrate dehydrogenase-1 or isocitrate dehydrogenase-2 impaired reductive labeling of tricarboxylic acid (TCA) cycle intermediates in vivo and suppressed growth of tumors generated from tumorgraft-derived cells. Glutaminase inhibition reduced the contribution of glutamine to the TCA cycle and resulted in modest suppression of tumorgraft growth. Infusions with [amide-15N]glutamine revealed persistent amidotransferase activity during glutaminase inhibition, and blocking these activities with the amidotransferase inhibitor JHU-083 also reduced tumor growth in both immunocompromised and immunocompetent mice. We conclude that ccRCC tumorgrafts catabolize glutamine via multiple pathways, perhaps explaining why it has been challenging to achieve therapeutic responses in patients by inhibiting glutaminase.

DOI: https://doi.org/10.1126/sciadv.abp8293
Nat Rev Gastroenterol Hepatol. 2022 Dec 16.

The war on pancreatic cancer: progress and promise.

Christine A Iacobuzio-Donahue.

DOI: https://doi.org/10.1038/s41575-022-00728-1
Elife. 2022 Dec 16. pii: e80981. [Epub ahead of print]11

Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies.

CRUK IMAXT Grand Challenge Team

  Tumour heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here, we utilise clonal transcriptomics with WILD-seq; Wholistic Interrogation of Lineage Dynamics by sequencing, in mouse models of triple-negative breast cancer (TNBC) to understand response and resistance to therapy, including BET bromodomain inhibition and taxane-based chemotherapy. These analyses revealed oxidative stress protection by NRF2 as a major mechanism of taxane resistance and led to the discovery that our tumour models are collaterally sensitive to asparagine deprivation therapy using the clinical stage drug L-asparaginase after frontline treatment with docetaxel. In summary, clonal transcriptomics with WILD-seq identifies mechanisms of resistance to chemotherapy that are also operative in patients and pin points asparagine bioavailability as a druggable vulnerability of taxane-resistant lineages.

Keywords:  cancer biology; cancer therapy; chromosomes; gene expression; lineage tracing; mouse; single cell genomics; tumor heterogeneity

DOI:  https://doi.org/10.7554/eLife.80981
Cells. 2022 Nov 28. pii: 3813. [Epub ahead of print]11(23):

Membrane Contact Sites in Autophagy.

Emma Zwilling, Fulvio Reggiori.

  Eukaryotes utilize different communication strategies to coordinate processes between different cellular compartments either indirectly, through vesicular transport, or directly, via membrane contact sites (MCSs). MCSs have been implicated in lipid metabolism, calcium signaling and the regulation of organelle biogenesis in various cell types. Several studies have shown that MCSs play a crucial role in the regulation of macroautophagy, an intracellular catabolic transport route that is characterized by the delivery of cargoes (proteins, protein complexes or aggregates, organelles and pathogens) to yeast and plant vacuoles or mammalian lysosomes, for their degradation and recycling into basic metabolites. Macroautophagy is characterized by the de novo formation of double-membrane vesicles called autophagosomes, and their biogenesis requires an enormous amount of lipids. MCSs appear to have a central role in this supply, as well as in the organization of the autophagy-related (ATG) machinery. In this review, we will summarize the evidence for the participation of specific MCSs in autophagosome formation, with a focus on the budding yeast and mammalian systems.

Keywords:  MAMs; autophagosome; endoplasmic reticulum; lipid droplets; lipid transfer; mitochondria; phagophore; plasma membrane; vacuole

DOI:  https://doi.org/10.3390/cells11233813
J Proteome Res. 2022 Dec 12.

CPPA: A Web Tool for Exploring Proteomic and Phosphoproteomic Data in Cancer.

Guo-Sheng Hu, Zao-Zao Zheng, Yao-Hui He, Du-Chuang Wang, Wen Liu.

  A tremendous amount of proteomic and phosphoproteomic data has been produced over the years with the development of mass spectrometry techniques, providing us with new opportunities to explore and understand the proteome and phosphoproteome as well as the function of proteins and protein phosphorylation sites. However, a lack of powerful tools that we can utilize to explore these valuable data limits our understanding of the proteome and phosphoproteome, particularly in diseases such as cancer. To address these unmet needs, we established CPPA (Cancer Proteome and Phosphoproteome Atlas), a web tool to mine abnormalities of the proteome and phosphoproteome in cancer based on published data sets. All analysis results are presented in CPPA with a flexible web interface to provide key customization utilities, including general analysis, differential expression profiling, statistical analysis of protein phosphorylation sites, correlation analysis, similarity analysis, survival analysis, pathological stage analysis, etc. CPPA greatly facilitates the process of data mining and therapeutic target discovery by providing a comprehensive analysis of proteomic and phosphoproteomic data in normal and tumor tissues with a simple click, which helps to unlock the precious value of mass spectrometry data by bridging the gap between raw data and experimental biologists. CPPA is currently available at https://cppa.site/cppa.

Keywords:  cancer; phosphoproteome; proteome; web tool

DOI:  https://doi.org/10.1021/acs.jproteome.2c00512
Cancer Cell. 2022 Dec 12. pii: S1535-6108(22)00558-X. [Epub ahead of print]40(12): 1467-1469

Tipping the balance: New insights into stromal regulation of cancer.

Joana Leitão Castro, Janine Terra Erler.

Desmoplastic extracellular matrix (ECM) exerts a seemingly paradoxical role in cancer, restricting or promoting progression. Two recent back-to-back Nature reports shed light on this conundrum, revealing the role of different hepatic stellate cell (HSC) populations and different collagen I cleavage states in directing the progression of cancer.

DOI: https://doi.org/10.1016/j.ccell.2022.11.011
Front Oncol. 2022 ;12 1009700

Emerging current trends and research focus related to pancreatic cancer metabolism: A bibliometric and visualized analysis.

Qian Shen, Chuanlong Zhang, Xiaochen Jiang, Junchen Li, Fudong Liu, Xiyuan Zhang, Ge'er En, Bo Pang.

   Background: As a malignant digestive system tumor, pancreatic cancer has unique metabolic characteristics. In recent years, the study of pancreatic cancer metabolism is in full swing, which provides a new direction for the treatment of pancreatic cancer patients. However, there is no systematic report of pancreatic cancer metabolism. In this paper, bibliometrics and visualization methods were used to analyze the number of publications, countries/regions, authors, institutions, journals, co-cited references, and keywords of pancreatic cancer metabolism articles, to summarize the research trends and predict research hotspots.
Methods: We searched, screened and downloaded articles on pancreatic cancer metabolism through the Web of Science Core Collection (WoSCC). Using CiteSpace, VOSviewer and Bibliometrix Package to analyze publications, countries/regions, authors, institutions, journals, co-cited references, and keywords of pancreatic cancer metabolism to identify research trends and predict research hotspots.
Results: According to the inclusion and exclusion criteria, a total of 5,255 articles were retrieved during the period 1943-2022. The number of publications on pancreatic cancer metabolism is increasing year by year. The United States (n=1602, 30.49%), China (n=1074, 20.44%), and Italy (n=313, 5.96%) are the three countries with the largest number of publications and citations, and there is close cooperation between countries. LI J (n=55) is the most prolific author. FUDAN UNIV (n=348) is the most published institution. CANCERS (n=118), PLOS ONE (n=93), and CANCER RESEARCH (n=80) are the most popular journals in this field. "Nutriment-deficient environment", "cancer chemoprevention" and "targeting cancer stem cell" are the main areas of focus. "immunotherapy", "ferroptosis" and "targeted therapy" are hot keywords in recent years. Taking pancreatic cancer metabolism as an entry point to study the role of traditional Chinese medicine (TCM) mainly focuses on curcumin and resveratrol, lack of broader and deeper research on TCM.
Conclusions: The number of publications on pancreatic cancer metabolism has generally increased, and scholars have generally paid more attention to this field. "immunotherapy", "ferroptosis" and "targeted therapy" are the current research hotspots. The in-depth study of pancreatic cancer metabolism will provide new ideas for the treatment of pancreatic cancer.

Keywords:  CiteSpace; VOSviewer; bibliometric analysis; metabolism; pancreatic cancer

DOI:  https://doi.org/10.3389/fonc.2022.1009700
STAR Protoc. 2022 Dec 15. pii: S2666-1667(22)00827-9. [Epub ahead of print]4(1): 101947

An open access, machine learning pipeline for high-throughput quantification of cell morphology.

Emma M Welter, Oksana Kosyk, Anthony S Zannas.

  Cell morphology is influenced by many factors and can be used as a phenotypic marker. Here we describe a machine-learning-based protocol for high-throughput morphological measurement of human fibroblasts using a standard fluorescence microscope and the pre-existing, open access software ilastik for cell body identification, ImageJ/Fiji for image overlay, and CellProfiler for morphological quantification. Because this protocol overlays nuclei with their cell bodies and relies on coloration differences, it can be broadly applied to other cell types beyond fibroblasts. For details on the use and execution of this protocol, please also refer to Leung et al. (2022).1.

Keywords:  Cell Biology; Cell culture; Computer sciences; Microscopy

DOI:  https://doi.org/10.1016/j.xpro.2022.101947
J Cachexia Sarcopenia Muscle. 2022 Dec 14.

Plasma proteome profiling of healthy subjects undergoing bed rest reveals unloading-dependent changes linked to muscle atrophy.

Marta Murgia, Lorenza Brocca, Elena Monti, Martino V Franchi, Maximilian Zwiebel, Sophia Steigerwald, Emiliana Giacomello, Roberta Sartori, Sandra Zampieri, Giovanni Capovilla, Mladen Gasparini, Gianni Biolo, Marco Sandri, Matthias Mann, Marco V Narici.

   BACKGROUND: Inactivity and unloading induce skeletal muscle atrophy, loss of strength and detrimental metabolic effects. Bed rest is a model to study the impact of inactivity on the musculoskeletal system. It not only provides information for bed-ridden patients care, but it is also a ground-based spaceflight analogue used to mimic the challenges of long space missions for the human body. In both cases, it would be desirable to develop a panel of biomarkers to monitor muscle atrophy in a minimally invasive way at point of care to limit the onset of muscle loss in a personalized fashion.
METHODS: We applied mass spectrometry-based proteomics to measure plasma protein abundance changes in response to 10 days of bed rest in 10 young males. To validate the correlation between muscle atrophy and the significant hits emerging from our study, we analysed in parallel, with the same pipeline, a cohort of cancer patients with or without cachexia and age-matched controls. Our analysis resulted in the quantification of over 500 proteins.
RESULTS: Unloading affected plasma concentration of proteins of the complement cascade, lipid carriers and proteins derived from tissue leakage. Among the latter, teneurin-4 increased 1.6-fold in plasma at bed rest day 10 (BR10) compared with BR0 (6.E9 vs. 4.3E9, P = 0.02) and decreased to 0.6-fold the initial abundance after 2 days of recovery at normal daily activity (R + 2, 2.7E9, P = 3.3E-4); the extracellular matrix protein lumican was decreased to 0.7-fold (1.2E9 vs. 8.5E8, P = 1.5E-4) at BR10 and remained as low at R + 2. We identified six proteins distinguishing subjects developing unloading-mediated muscle atrophy (decrease of >4% of quadriceps cross-sectional area) from those largely maintaining their initial muscle mass. Among them, transthyretin, a thyroid hormone-binding protein, was significantly less abundant at BR10 in the plasma of subjects with muscle atrophy compared with those with no atrophy (1.6E10 vs. 2.6E10, P = 0.001). Haptoglobin-related protein was also significantly reduced in the serum of cancer patients with cachexia compared with that of controls.
CONCLUSIONS: Our findings highlight a combination or proteomic changes that can be explored as potential biomarkers of muscle atrophy occurring under different conditions. The panel of significant proteomic differences distinguishing atrophy-prone and atrophy-resistant subjects after 10 days of bed rest need to be tested in a larger cohort to validate their potential to predict inactivity-triggered muscle loss in humans.

Keywords:  Atrophy; Bed rest; Cachexia; Plasma; Proteomics; Skeletal muscle

DOI:  https://doi.org/10.1002/jcsm.13146
STAR Protoc. 2022 Dec 14. pii: S2666-1667(22)00820-6. [Epub ahead of print]4(1): 101940

Protocol for detecting macrophage-mediated cancer cell phagocytosis in vitro and in vivo.

Chuan Xu, Hong Wu, Yiqiang Liu, Feifei Li, Rajesh Kumar Manne, Hui-Kuan Lin.

  Here, we present optimized approaches to identify the efficiency of cancer cell phagocytosis by macrophages in vitro and in vivo. We describe the preparation and co-culture of macrophages and cancer cells, followed by in vitro phagocytosis assay using flow cytometry and confocal microscopy, respectively. We then detail the establishment of xenograft tumor mouse model and the in vivo detecting of phagocytosis efficiency by flow cytometry and qRT-PCR. This protocol provides a convenient way to assess macrophage-mediated phagocytosis of cancer cells. For complete details on the use and execution of this protocol, please refer to Xu et al.1.

Keywords:  Cancer; Cell Biology; Cell culture; Flow Cytometry/Mass Cytometry; Immunology; Microscopy; Model Organisms; Molecular Biology

DOI:  https://doi.org/10.1016/j.xpro.2022.101940