bims-cagime 2022-12-04 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–12–04
28 papers selected by
Kıvanç Görgülü, Technical University of Munich

Metabolic determinants of tumour initiation.
Epithelial and stromal co-evolution and complicity in pancreatic cancer.
Association between a polymorphic variant in the CDKN2B-AS1/ANRIL gene and pancreatic cancer risk.
Spatially-resolved single-cell assessment of pancreatic cancer expression subtypes reveals co-expressor phenotypes and extensive intra-tumoral heterogeneity.
Reducing the aneuploid cell burden - cell competition and the ribosome connection.
Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
Assessment of spatial transcriptomics for oncology discovery.
Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.
Hand grip strength-based cachexia index as a predictor of cancer cachexia and prognosis in patients with cancer.
MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells.
3-deazaadenosine (3DA) alleviates senescence to promote cellular fitness and cell therapy efficiency in mice.
Understanding and targeting anoikis in metastasis for cancer therapies.
Elevated FSP1 protects KRAS-mutated cells from ferroptosis during tumor initiation.
A Time and Place for Inhibiting Autophagy.
Therapeutic silencing of p120 in fascia fibroblasts ameliorate tissue repair.
Decellularized extracellular matrix as scaffold for cancer organoid cultures of colorectal peritoneal metastases.
Epigenetic modulation enhances immunotherapy for pancreatic ductal adenocarcinoma.
Cachexia staging score predicts survival in patients with cancer who receive palliative care.
Spatial statistics is a comprehensive tool for quantifying cell neighbor relationships and biological processes via tissue image analysis.
p62/Sqstm1 rescue in muscle retards the progression of steatohepatitis in p62/Sqstm1-null mice fed a high-fat diet.
POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells.
The human signal peptidase complex acts as a quality control enzyme for membrane proteins.
Dexamethasone for cancer-related dyspnoea - Authors' reply.
Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane.
Fixation can change the appearance of phase separation in living cells.
Metabolomics in Cell Biology.
Lipid Droplets: A Cellular Organelle Vital for Thermogenesis.
Alteration of cholesterol distribution at the plasma membrane of cancer cells: From evidence to pathophysiological implication and promising therapy strategy.

Nat Rev Endocrinol. 2022 Nov 29.

Metabolic determinants of tumour initiation.

Julia S Brunner, Lydia W S Finley.

Tumours exhibit notable metabolic alterations compared with their corresponding normal tissue counterparts. These metabolic alterations can support anabolic growth, enable survival in hostile environments and regulate gene expression programmes that promote malignant progression. Whether these metabolic changes are selected for during malignant transformation or can themselves be drivers of tumour initiation is unclear. However, intriguingly, many of the major bottlenecks for tumour initiation - control of cell fate, survival and proliferation - are all amenable to metabolic regulation. In this article, we review evidence demonstrating a critical role for metabolic pathways in processes that support the earliest stages of tumour development. We discuss how cell-intrinsic factors, such as the cell of origin or transforming oncogene, and cell-extrinsic factors, such as local nutrient availability, promote or restrain tumour initiation. Deeper insight into how metabolic pathways control tumour initiation will improve our ability to design metabolic interventions to limit tumour incidence.

DOI: https://doi.org/10.1038/s41574-022-00773-5
Nat Rev Cancer. 2022 Nov 29.

Epithelial and stromal co-evolution and complicity in pancreatic cancer.

Sunil R Hingorani.

Pancreatic ductal adenocarcinomas are distinguished by their robust desmoplasia, or fibroinflammatory response. Dominated by non-malignant cells, the mutated epithelium must therefore combat, cooperate with or co-opt the surrounding cells and signalling processes in its microenvironment. It is proposed that an invasive pancreatic ductal adenocarcinoma represents the coordinated evolution of malignant and non-malignant cells and mechanisms that subvert and repurpose normal tissue composition, architecture and physiology to foster tumorigenesis. The complex kinetics and stepwise development of pancreatic cancer suggests that it is governed by a discrete set of organizing rules and principles, and repeated attempts to target specific components within the microenvironment reveal self-regulating mechanisms of resistance. The histopathological and genetic progression models of the transforming ductal epithelium must therefore be considered together with a programme of stromal progression to create a comprehensive picture of pancreatic cancer evolution. Understanding the underlying organizational logic of the tumour to anticipate and pre-empt the almost inevitable compensatory mechanisms will be essential to eradicate the disease.

DOI: https://doi.org/10.1038/s41568-022-00530-w
Int J Cancer. 2022 Nov 30.

Association between a polymorphic variant in the CDKN2B-AS1/ANRIL gene and pancreatic cancer risk.

Matteo Giaccherini, Riccardo Farinella, Manuel Gentiluomo, Beatrice Mohelnikova-Duchonova, Emanuele Federico Kauffmann, Matteo Palmeri, Faik Uzunoglu, Pavel Soucek, Dalius Petrauskas, Giulia Martina Cavestro, Romanas Zykus, Silvia Carrara, Raffaele Pezzilli, Marta Puzzono, Andrea Szentesi, John Neoptolemos, Livia Archibugi, Orazio Palmieri, Anna Caterina Milanetto, Gabriele Capurso, Casper H J van Eijck, Hannah Stocker, Rita T Lawlor, Pavel Vodicka, Martin Lovecek, Jakob R Izbicki, Francesco Perri, Rita Kupcinskaite-Noreikiene, Mara Götz, Juozas Kupcinskas, Tamás Hussein, Péter Hegyi, Olivier R Busch, Thilo Hackert, Andrea Mambrini, Hermann Brenner, Maurizio Lucchesi, Daniela Basso, Francesca Tavano, Ben Schöttker, Giuseppe Vanella, Stefania Bunduc, Ágota Petrányi, Stefano Landi, Luca Morelli, Federico Canzian, Daniele Campa.

  Genes carrying high-penetrance germline mutations may also be associated with cancer susceptibility through common low-penetrance genetic variants. To increase the knowledge on genetic pancreatic ductal adenocarcinoma (PDAC) aetiology, the common genetic variability of PDAC familial genes was analysed in this study. We conducted a multi-phase study analysing 7,745 single nucleotide polymorphisms (SNPs) from 29 genes reported to harbour a high-penetrance PDAC-associated mutation in at least one published study. To assess the effect of the SNPs on PDAC risk, a total of 14,666 PDAC cases and 221,897 controls across five different studies were analysed. The T allele of the rs1412832 polymorphism, that is situated in the CDKN2B-AS1/ANRIL, showed a genome-wide significant association with increased risk of developing PDAC (OR=1.11, 95%CI=1.07-1.15, P=5.25×10-9 ). CDKN2B-AS1/ANRIL is a long non-coding RNA, situated in 9p21.3, and regulates many target genes, among which CDKN2A (p16) that frequently shows deleterious somatic and germline mutations and deregulation in PDAC. Our results strongly support the role of the genetic variability of the 9p21.3 region in PDAC aetiopathogenesis and highlight the importance of secondary analysis as a tool for discovering new risk loci in complex human diseases. This article is protected by copyright. All rights reserved.

Keywords:  Pancreatic ductal adenocarcinoma; association study; genetic susceptibility; single nucleotide polymorphisms

DOI:  https://doi.org/10.1002/ijc.34383
Cancer Res. 2022 Dec 02. pii: CAN-22-3050. [Epub ahead of print]

Spatially-resolved single-cell assessment of pancreatic cancer expression subtypes reveals co-expressor phenotypes and extensive intra-tumoral heterogeneity.

Hannah L Williams, Andressa Dias Costa, Jinming Zhang, Srivatsan Raghavan, Peter S Winter, Kevin S Kapner, Scott P Ginebaugh, Sara A Väyrynen, Juha P Väyrynen, Chen Yuan, Andrew W Navia, Junning Wang, Annan Yang, Timothy L Bosse, Radha L Kalekar, Kristen E Lowder, Mai Chan Lau, Dalia Elganainy, Vicente Morales-Oyarvide, Douglas A Rubinson, Harshabad Singh, Kimberly Perez, James M Cleary, Thomas E Clancy, Jiping Wang, Joseph D Mancias, Lauren K Brais, Emma R Hill, Margaret M Kozak, David C Linehan, Richard F Dunne, Daniel T Chang, Albert C Koong, Aram F Hezel, William C Hahn, Alex K Shalek, Andrew J Aguirre, Jonathan A Nowak, Brian M Wolpin.

Pancreatic ductal adenocarcinoma (PDAC) has been classified into classical and basal-like transcriptional subtypes by bulk RNA measurements. However, recent work has uncovered greater complexity to transcriptional subtypes than was initially appreciated using bulk RNA expression profiling. To provide a deeper understanding of PDAC subtypes, we developed a multiplex immunofluorescence (mIF) pipeline that quantifies protein expression of six PDAC subtype markers (CLDN18.2, TFF1, GATA6, KRT17, KRT5, and S100A2) and permits spatially resolved, single-cell interrogation of pancreatic tumors from resection specimens and core needle biopsies. Both primary and metastatic tumors displayed striking intra-tumoral subtype heterogeneity that was associated with patient outcomes, existed at the scale of individual glands, and was significantly reduced in patient-derived organoid cultures. Tumor cells co-expressing classical and basal markers were present in >90% of tumors, existed on a basal-classical polarization continuum, and were enriched in tumors containing a greater admixture of basal and classical cell populations. Cell-cell neighbor analyses within tumor glands further suggested that co-expressor cells may represent an intermediate state between expression subtype poles. The extensive intra-tumoral heterogeneity identified through this clinically applicable mIF pipeline may inform prognosis and treatment selection for patients with PDAC.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3050
Dis Model Mech. 2022 Nov 01. pii: dmm049673. [Epub ahead of print]15(11):

Reducing the aneuploid cell burden - cell competition and the ribosome connection.

Nicholas E Baker, Cristina Montagna.

  Aneuploidy, the gain or loss of chromosomes, is the cause of birth defects and miscarriage and is almost ubiquitous in cancer cells. Mosaic aneuploidy causes cancer predisposition, as well as age-related disorders. Despite the cell-intrinsic mechanisms that prevent aneuploidy, sporadic aneuploid cells do arise in otherwise normal tissues. These aneuploid cells can differ from normal cells in the copy number of specific dose-sensitive genes, and may also experience proteotoxic stress associated with mismatched expression levels of many proteins. These differences may mark aneuploid cells for recognition and elimination. The ribosomal protein gene dose in aneuploid cells could be important because, in Drosophila, haploinsufficiency for these genes leads to elimination by the process of cell competition. Constitutive haploinsufficiency for human ribosomal protein genes causes Diamond Blackfan anemia, but it is not yet known whether ribosomal protein gene dose contributes to aneuploid cell elimination in mammals. In this Review, we discuss whether cell competition on the basis of ribosomal protein gene dose is a tumor suppressor mechanism, reducing the accumulation of aneuploid cells. We also discuss how this might relate to the tumor suppressor function of p53 and the p53-mediated elimination of aneuploid cells from murine embryos, and how cell competition defects could contribute to the cancer predisposition of Diamond Blackfan anemia.

Keywords:  Aging; Aneuploidy; Cancer; Cell competition; Ribosomal protein gene

DOI:  https://doi.org/10.1242/dmm.049673
Nat Commun. 2022 Nov 28. 13(1): 7338

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.

Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M Bernard, Nourdine Bah, Mariana Silva Dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore, James I MacRae, Maria Greco, Thomas Reinheckel, Matthias Trost, Maximiliano G Gutierrez.

Transient lysosomal damage after infection with cytosolic pathogens or silica crystals uptake results in protease leakage. Whether limited leakage of lysosomal contents into the cytosol affects the function of cytoplasmic organelles is unknown. Here, we show that sterile and non-sterile lysosomal damage triggers a cell death independent proteolytic remodelling of the mitochondrial proteome in macrophages. Mitochondrial metabolic reprogramming required leakage of lysosomal cathepsins and was independent of mitophagy, mitoproteases and proteasome degradation. In an in vivo mouse model of endomembrane damage, live lung macrophages that internalised crystals displayed impaired mitochondrial function. Single-cell RNA-sequencing revealed that lysosomal damage skewed metabolic and immune responses in alveolar macrophages subsets with increased lysosomal content. Functionally, drug modulation of macrophage metabolism impacted host responses to Mycobacterium tuberculosis infection in an endomembrane damage dependent way. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprograming after endomembrane damage.

DOI: https://doi.org/10.1038/s41467-022-34632-8
Cell Rep Methods. 2022 Nov 21. 2(11): 100340

Assessment of spatial transcriptomics for oncology discovery.

Anna Lyubetskaya, Brian Rabe, Andrew Fisher, Anne Lewin, Isaac Neuhaus, Constance Brett, Todd Brett, Ethel Pereira, Ryan Golhar, Sami Kebede, Alba Font-Tello, Kathy Mosure, Nicholas Van Wittenberghe, Konstantinos J Mavrakis, Kenzie MacIsaac, Benjamin J Chen, Eugene Drokhlyansky.

  Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for oncology discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis, which provides a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell-type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.

Keywords:  biomarkers; cancer biology; cancer genomics; digital pathology; genomics; oncology; pancreatic cancer; spatial genomics; spatial transcriptomics; tumors

DOI:  https://doi.org/10.1016/j.crmeth.2022.100340
Nat Metab. 2022 Nov 28.

Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.

McKenzie Patrick, Zhimin Gu, Gen Zhang, R Max Wynn, Pranita Kaphle, Hui Cao, Hieu Vu, Feng Cai, Xiaofei Gao, Yuannyu Zhang, Mingyi Chen, Min Ni, David T Chuang, Ralph J DeBerardinis, Jian Xu.

The branched-chain aminotransferase isozymes BCAT1 and BCAT2, segregated into distinct subcellular compartments and tissues, initiate the catabolism of branched-chain amino acids (BCAAs). However, whether and how BCAT isozymes cooperate with downstream enzymes to control BCAA homeostasis in an intact organism remains largely unknown. Here, we analyse system-wide metabolomic changes in BCAT1- and BCAT2-deficient mouse models. Loss of BCAT2 but not BCAT1 leads to accumulation of BCAAs and branched-chain α-keto acids (BCKAs), causing morbidity and mortality that can be ameliorated by dietary BCAA restriction. Through proximity labelling, isotope tracing and enzymatic assays, we provide evidence for the formation of a mitochondrial BCAA metabolon involving BCAT2 and branched-chain α-keto acid dehydrogenase. Disabling the metabolon contributes to BCAT2 deficiency-induced phenotypes, which can be reversed by BCAT1-mediated BCKA reamination. These findings establish a role for metabolon formation in BCAA metabolism in vivo and suggest a new strategy to modulate this pathway in diseases involving dysfunctional BCAA metabolism.

DOI: https://doi.org/10.1038/s42255-022-00689-4
J Cachexia Sarcopenia Muscle. 2022 Nov 29.

Hand grip strength-based cachexia index as a predictor of cancer cachexia and prognosis in patients with cancer.

Hailun Xie, Guotian Ruan, Lishuang Wei, Heyang Zhang, Yizhong Ge, Qi Zhang, Shiqi Lin, Mengmeng Song, Xi Zhang, Xiaoyue Liu, Xiangrui Li, Kangping Zhang, Ming Yang, Meng Tang, Chun-Hua Song, Jialiang Gan, Han-Ping Shi.

   BACKGROUND: The cachexia index is a useful predictor for cancer cachexia and prognostic assessment. However, its use is limited because of high testing costs and complicated testing procedures. Thus, in this study, we aimed to develop a hand grip strength (HGS)-based cancer cachexia index (H-CXI) as a potential predictor of cancer cachexia and prognosis in patients with cancer.
METHODS: Here, 14 682 patients with cancer were studied, including the discovery (6592), internal validation (2820) and external validation (5270) cohorts. The H-CXI was calculated as [HGS (kg)/height (m)2 × serum albumin (g/L)]/neutrophil-to-lymphocyte ratio. The Kaplan-Meier method was used to create survival curves, and the log-rank test was used to compare time-event relationships between groups. A Cox proportional hazard regression model was used to determine independent risk factors for overall survival (OS). Logistic regression analysis was used to assess the association of the H-CXI with short-term outcomes and cancer cachexia.
RESULTS: There was a significant non-linear relationship between the H-CXI and OS in all cohorts. Patients with a low H-CXI had significantly lower OS than those with a high H-CXI in the discovery cohort (6-year survival percentage: 55.72% vs. 76.70%, log-rank P < 0.001), internal validation cohort (6-year survival percentage: 55.81% vs. 76.70%, log-rank P < 0.001), external validation cohort (6-year survival percentage: 56.05% vs. 75.48%, log-rank P < 0.001) and total cohort (6-year survival percentage: 55.86% vs. 76.27%, log-rank P < 0.001). Notably, the prognostic stratification effect of the H-CXI in patients with advanced-stage disease was more significant than that in patients with early-stage disease. The multivariate Cox proportional risk regression model confirmed that a low H-CXI negatively affected the prognosis of patients with cancer in the discovery cohort [hazard ratio (HR) 0.75, 95% confidence interval (CI) 0.71-0.80, P < 0.001], internal validation cohort (HR 0.79, 95 %CI 0.72-0.86, P < 0.001), external validation cohort (HR 0.84, 95% CI 0.79-0.89, P < 0.001) and total cohort (HR 0.80, 95% CI 0.77-0.83, P < 0.001). Multivariate logistic regression models showed that a low H-CXI was an independent risk factor predicting adverse short-term outcomes and cancer cachexia in patients with cancer.
CONCLUSIONS: The simple and practical H-CXI is a promising predictor for cancer cachexia and prognosis in patients with cancer.

Keywords:  HGS-based cachexia index; cachexia; cancer; prognosis

DOI:  https://doi.org/10.1002/jcsm.13139
Sci Adv. 2022 Dec 02. 8(48): eabo0876

MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells.

Dan Sun, Deepak K Singh, Saul Carcamo, Dan Filipescu, Bassem Khalil, Xin Huang, Brett A Miles, William Westra, Karl Christoph Sproll, Dan Hasson, Emily Bernstein, Julio A Aguirre-Ghiso.

MacroH2A variants have been linked to inhibition of metastasis through incompletely understood mechanisms. Here, we reveal that solitary dormant disseminated cancer cells (DCCs) display increased levels of macroH2A variants in head and neck squamous cell carcinoma PDX in vivo models and patient samples compared to proliferating primary or metastatic lesions. We demonstrate that dormancy-inducing transforming growth factor-β2 and p38α/β pathways up-regulate macroH2A expression and that macroH2A variant overexpression is sufficient to induce DCC dormancy and suppress metastasis in vivo. Notably, inducible expression of the macroH2A2 variant in vivo suppresses metastasis via a reversible growth arrest of DCCs. This state does not require the dormancy-regulating transcription factors DEC2 and NR2F1; instead, transcriptomic analysis reveals that macroH2A2 overexpression inhibits cell cycle and oncogenic signaling programs, while up-regulating dormancy and senescence-associated inflammatory cytokines. We conclude that the macroH2A2-enforced dormant phenotype results from tapping into transcriptional programs of both quiescence and senescence to limit metastatic outgrowth.

DOI: https://doi.org/10.1126/sciadv.abo0876
Nat Aging. 2022 Sep;2 851-866

3-deazaadenosine (3DA) alleviates senescence to promote cellular fitness and cell therapy efficiency in mice.

Ana Guerrero, Andrew J Innes, Pierre-François Roux, Sonja C Buisman, Johannes Jung, Laura Ortet, Victoria Moiseeva, Verena Wagner, Lucas Robinson, Albertina Ausema, Anna Potapova, Eusebio Perdiguero, Ellen Weersing, Marieke Aarts, Nadine Martin, Torsten Wuestefeld, Pura Muñoz-Cánoves, Gerald de Haan, Oliver Bischof, Jesús Gil.

  Cellular senescence is a stable type of cell cycle arrest triggered by different stresses. As such, senescence drives age-related diseases and curbs cellular replicative potential. Here, we show that 3-deazaadenosine (3DA), an S-adenosyl homocysteinase (AHCY) inhibitor, alleviates replicative and oncogene-induced senescence. 3DA-treated senescent cells showed reduced global Histone H3 Lysine 36 trimethylation (H3K36me3), an epigenetic modification that marks the bodies of actively transcribed genes. By integrating transcriptome and epigenome data, we demonstrate that 3DA treatment affects key factors of the senescence transcriptional program. Remarkably, 3DA treatment alleviated senescence and increased the proliferative and regenerative potential of muscle stem cells from very old mice in vitro and in vivo. Moreover, ex vivo 3DA treatment was sufficient to enhance the engraftment of human umbilical cord blood (UCB) cells in immunocompromised mice. Together, our results identify 3DA as a promising drug enhancing the efficiency of cellular therapies by restraining senescence.

Keywords:  3DA; AHCY; cord blood cells; muscle stem cells; senescence

DOI:  https://doi.org/10.1038/s43587-022-00279-9
Cell Biol Int. 2022 Dec 01.

Understanding and targeting anoikis in metastasis for cancer therapies.

Farzad Sattari Fard, Nazila Jalilzadeh, Amir Mehdizadeh, Fakhrosadat Sajjadian, Kobra Velaei.

  The development of effective treatments for cancers requires investigations for a more detailed and comprehensive understanding of the basic cellular mechanisms involved in carcinogenesis, cancer progression, and metastasis. One of those driving mechanisms is anoikis, a special type of apoptosis, which is induced by losing anchorage from the extracellular matrix (ECM). In other words, resisting death in detached cells (cells without ECM) forms an anoikis-resistant phenotype. Since the anoikis-resistance state compensates for the initial steps of cancer metastasis, this review aimed to discuss mechanisms of gaining anoikis/anoikis resistance phenotype in tumor cells. Finally, we highlighted the significance of anoikis in malignancies so as to provide clear insight into cancer diagnosis and therapy development.

Keywords:  anoikis; anoikis resistance; cancer; metastasis

DOI:  https://doi.org/10.1002/cbin.11970
Cell Death Differ. 2022 Nov 29.

Elevated FSP1 protects KRAS-mutated cells from ferroptosis during tumor initiation.

Fabienne Müller, Jonathan K M Lim, Christina M Bebber, Eric Seidel, Sofya Tishina, Alina Dahlhaus, Jenny Stroh, Julia Beck, Fatma Isil Yapici, Keiko Nakayama, Lucia Torres Fernández, Johannes Brägelmann, Gabriel Leprivier, Silvia von Karstedt.

Oncogenic KRAS is the key driver oncogene for several of the most aggressive human cancers. One key feature of oncogenic KRAS expression is an early increase in cellular reactive oxygen species (ROS) which promotes cellular transformation if cells manage to escape cell death, mechanisms of which remain incompletely understood. Here, we identify that expression of oncogenic as compared to WT KRAS in isogenic cellular systems renders cells more resistant to ferroptosis, a recently described type of regulated necrosis. Mechanistically, we find that cells with mutant KRAS show a specific lack of ferroptosis-induced lipid peroxidation. Interestingly, KRAS-mutant cells upregulate expression of ferroptosis suppressor protein 1 (FSP1). Indeed, elevated levels of FSP1 in KRAS-mutant cells are responsible for mediating ferroptosis resistance and FSP1 is upregulated as a consequence of MAPK and NRF2 pathway activation downstream of KRAS. Strikingly, FSP1 activity promotes cellular transformation in soft agar and its overexpression is sufficient to promote spheroid growth in 3D in KRAS WT cells. Moreover, FSP1 expression and its activity in ferroptosis inhibition accelerates tumor onset of KRAS WT cells in the absence of oncogenic KRAS in vivo. Consequently, we find that pharmacological induction of ferroptosis in pancreatic organoids derived from the LsL-KRASG12D expressing mouse model is only effective in combination with FSP1 inhibition. Lastly, FSP1 is upregulated in non-small cell lung cancer (NSCLC), colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) as compared to the respective normal tissue of origin and correlates with NRF2 expression in PDAC patient datasets. Based on these data, we propose that KRAS-mutant cells must navigate a ferroptosis checkpoint by upregulating FSP1 during tumor establishment. Consequently, ferroptosis-inducing therapy should be combined with FSP1 inhibitors for efficient therapy of KRAS-mutant cancers.

DOI: https://doi.org/10.1038/s41418-022-01096-8
Cancer Res. 2022 Dec 02. 82(23): 4322-4324

A Time and Place for Inhibiting Autophagy.

Boyi Gan.

Autophagy is an attractive therapeutic target in cancer. Successful autophagy-focused clinical intervention will require a detailed understanding of when and where autophagy is important during tumorigenesis. In this issue of Cancer Research, Khayati and colleagues use state-of-the-art genetically engineered mouse models to demonstrate that transient systemic inhibition of autophagy can irreversibly impair the growth of established lung tumors with a good tolerability in normal tissues, suggesting a therapeutic strategy for cancer treatment. See related article by Khayati et al., p. 4429.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3024
J Invest Dermatol. 2022 Nov 25. pii: S0022-202X(22)02821-4. [Epub ahead of print]

Therapeutic silencing of p120 in fascia fibroblasts ameliorate tissue repair.

Vijayanand Rajendran, Pushkar Ramesh, Ruoxuan Dai, Shruthi Kalgudde Gopal, Haifeng Ye, Hans-Günther Machens, Heiko Adler, Dongsheng Jiang, Yuval Rinkevich.

  Deep skin wounds rapidly heal by mobilizing extracellular matrix and cells from the fascia, deep beneath the dermal layer of the skin, to form scars. Despite wounds being an extensively studied area and an unmet clinical need, the biochemistry driving this patch-like repair remains obscure. Lacking also are efficacious therapeutic means to modulate scar formation in vivo. Here, we identify a central role for p120 in mediating fascia mobilization and wound repair. Injury triggers p120 expression, largely within engrailed-1 lineage positive fibroblasts (EPFs) of the fascia that exhibit a supra-cellular organization. Using adeno-associated virus (AAV) mediated gene silencing, we show that p120 establishes the supracellular organization of fascia EPFs, without which fascia mobilization is impaired. Gene silencing of p120 in fascia fibroblasts disentangles their supracellular organization, reducing the transfer of fascial cells and extracellular matrix into wounds, and augments wound healing. Our findings place p120 as essential for fascia mobilization, opening a new therapeutic avenue for targeted intervention in the treatment of a variety of skin scar conditions.

Keywords:  AAV; Fascia; Fibroblasts; Scar; Skin; Wound; p120

DOI:  https://doi.org/10.1016/j.jid.2022.10.018
J Mol Cell Biol. 2022 Dec 02. pii: mjac064. [Epub ahead of print]

Decellularized extracellular matrix as scaffold for cancer organoid cultures of colorectal peritoneal metastases.

Luca Varinelli, Marcello Guaglio, Silvia Brich, Susanna Zanutto, Antonino Belfiore, Federica Zanardi, Fabio Iannelli, Amanda Oldani, Elisa Costa, Matteo Chighizola, Ewelina Lorenc, Simone P Minardi, Stefano Fortuzzi, Martina Filugelli, Giovanna Garzone, Federica Pisati, Manuela Vecchi, Giancarlo Pruneri, Shigeki Kusamura, Dario Baratti, Laura Cattaneo, Dario Parazzoli, Alessandro Podestà, Massimo Milione, Marcello Deraco, Marco A Pierotti, Manuela Gariboldi.

  Peritoneal metastases (PM) from colorectal cancer (CRC) are associated with poor survival. The extracellular matrix (ECM) plays a fundamental role in modulating the homing of CRC metastases to the peritoneum. The mechanisms underlying the interactions between metastatic cells and the ECM, however, remain poorly understood, and the number of in vitro models available for the study of the peritoneal metastatic process is limited. Here, we show that decellularized ECM of the peritoneal cavity allows the growth of organoids obtained from PM, favoring the development of three-dimensional (3D) nodules that maintain the characteristics of in vivo PM. Organoids preferentially grow on scaffolds obtained from neoplastic peritoneum, which are characterized by greater stiffness than normal scaffolds. A gene expression analysis of organoids grown on different substrates reflected faithfully the clinical and biological characteristics of the organoids. An impact of the ECM on the response to standard chemotherapy treatment for PM was also observed. The ex vivo 3D model, obtained by combining patient-derived decellularized ECM with organoids to mimic the metastatic niche, could be an innovative tool to develop new therapeutic strategies in a biologically relevant context to personalize treatments.

Keywords:  ECM stiffness; colorectal cancer; decellularized extracellular matrix; engineered disease model; extracellular matrix (ECM); organoids; peritoneal metastasis

DOI:  https://doi.org/10.1093/jmcb/mjac064
Clin Transl Immunology. 2022 ;11(12): e1430

Epigenetic modulation enhances immunotherapy for pancreatic ductal adenocarcinoma.

Yan Li, Young K Hong, Xingtong Wang, Harshul Pandit, Qianqian Zheng, Youxi Yu, Xiaoju Shi, Yujia Chen, Min Tan, Zachary Pulliam, Neal Bhutiani, Andrew Lin, Jeremy Badach, Ping Zhang, Robert Cg Martin.

   Objectives: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a poor prognosis. PDAC has poor response to immunotherapy because of its unique tumour microenvironment (TME). In an attempt to stimulate immunologically silent pancreatic cancer, we investigated the role of epigenetic therapy in modulating the TME to improve immunogenicity.
Methods: In vitro human PDAC cell lines MiaPaca2 and S2-013 were treated with 5μ m 3-Deazaneplanocin A (DZNep, an EZH2 inhibitor) and 5 μ m 5-Azacytidine (5-AZA, a DNMT1 inhibitor). In vivo orthotopic murine tumour models using both murine PAN02 cells and KPC cells inoculated in immunocompetent C56/BL7 mice were treated with anti-PD-L1 combined with DZNep and 5-AZA. Short hairpin knockdown (KD) of EZH2 and DNMT1 in PAN02 cells for the orthotopic murine tumour model was established to validate the drug treatment (DZNep and 5-AZA). qRT-PCR and microarray assays were performed for the evaluation of Th1-attracting chemokines and cancer-associated antigen induction.
Results: Drug treatments induced significant upregulation of gene expressions of Th1-attracting chemokines, CXCL9 and CXCL10, and the cancer-testis antigens, NY-ESO-1, LAGE and SSX-4 (P < 0.05). In orthotopic tumour models, inoculation of PAN02 cells or KPC cells demonstrated significant tumour regression with corresponding increased apoptosis and infiltration of cytotoxic T lymphocytes in the combination treatment group. In the orthotopic Pan02-KD model, the anti-PD-L1 treatment also caused significant tumour regression.
Conclusion: We demonstrate that immunotherapy for PDAC can be potentiated with epigenetic therapy by increasing cancer-associated antigen expression and increased T-cell trafficking across the immunosuppressive tumour microenvironment via upregulation of the repressed chemokines and increased apoptosis with subsequent tumour regression.

Keywords:  checkpoint inhibitors; epigenetic modulation; immunotherapy; pancreatic ductal adenocarcinoma (PDAC)

DOI:  https://doi.org/10.1002/cti2.1430
Nutrition. 2022 Oct 21. pii: S0899-9007(22)00293-3. [Epub ahead of print]106 111880

Cachexia staging score predicts survival in patients with cancer who receive palliative care.

Junko Ueshima, Keisuke Maeda, Akio Shimizu, Ayano Nagano, Yuria Ishida, Tomoko Takeuchi, Tomoyuki Nonogaki, Remi Matsuyama, Yosuke Yamanaka, Kenta Murotani, Naoharu Mori.

   OBJECTIVE: The aim of this study was to validate the cachexia staging score (CSS), a multidimensional, item-based diagnostic method of cachexia severity, for patients with advanced cancer receiving palliative care.
METHODS: Eligible patients were those with cancer who received palliative care during hospitalization between May 2019 and April 2020. All data were collected retrospectively from medical records. Cachexia was graded into four levels according to the CSS. Kaplan-Meier curves were constructed with or without death as the outcome, comparing prognoses among different levels of cachexia with Bonferroni correction. Cox proportional hazards regression analysis was performed to identify factors affecting mortality.
RESULTS: The mean age of the 196 patients was 65.8 ± 14 y. Men made up 42% of the study population. Lower body mass index, increased rate of weight loss, increased strength, assistance walking, rising from a chair, climbing stairs, and falls (SARC-F) points, decline in activities of daily living, appetite loss, and abnormal blood biomarkers were significantly more common with increasing severity of cachexia, and survival was shorter (P < 0.001). The hazard ratio (HR) increased with worsening severity of cachexia according to CSS classification (precachexia: HR, 2.78; 95% confidence interval [CI], 0.62-12.46, P = 0.182; cachexia: HR, 4.77; 95% CI, 1.09-20.80; P = 0.038; and refractory cachexia: HR, 11.00; 95% CI, 2.37-51.07; P = 0.002).
CONCLUSIONS: The CSS predicted life expectancy in a population of patients receiving palliative care and had excellent prognostic discriminative power to classify patients at different stages of cachexia.

Keywords:  Cancer cachexia; Palliative care team; Prognostic indices; SARC-F; Skeletal muscle mass

DOI:  https://doi.org/10.1016/j.nut.2022.111880
Cell Rep Methods. 2022 Nov 21. 2(11): 100348

Spatial statistics is a comprehensive tool for quantifying cell neighbor relationships and biological processes via tissue image analysis.

Huw D Summers, John W Wills, Paul Rees.

  Automated microscopy and computational image analysis has transformed cell biology, providing quantitative, spatially resolved information on cells and their constituent molecules from the sub-micron to the whole-organ scale. Here we explore the application of spatial statistics to the cellular relationships within tissue microscopy data and discuss how spatial statistics offers cytometry a powerful yet underused mathematical tool set for which the required data are readily captured using standard protocols and microscopy equipment. We also highlight the often-overlooked need to carefully consider the structural heterogeneity of tissues in terms of the applicability of different statistical measures and their accuracy and demonstrate how spatial analyses offer a great deal more than just basic quantification of biological variance. Ultimately, we highlight how statistical modeling can help reveal the hierarchical spatial processes that connect the properties of individual cells to the establishment of biological function.

Keywords:  cell imaging; cytometry; spatial statistics; tissue analysis

DOI:  https://doi.org/10.1016/j.crmeth.2022.100348
Front Physiol. 2022 ;13 993995

p62/Sqstm1 rescue in muscle retards the progression of steatohepatitis in p62/Sqstm1-null mice fed a high-fat diet.

Ikuru Miura, Kosuke Okada, Akiko Ishii, Eiji Warabi, Takahisa Watahiki, Keii To, Hitoshi Shimano, Shunichi Ariizumi, Junichi Shoda.

  Introduction: Obesity is a risk factor for many diseases because it leads to a reduction in skeletal muscle mass and promotes insulin resistance. p62/Sqstm1-knockout mice are a model of metabolic syndrome; show obesity, insulin resistance, and non-alcoholic fatty liver (NAFL); and develop non-alcoholic steatohepatitis (NASH) in response to the feeding of a high-fat diet (HFD). These phenotypes suggest that muscle p62 may prevent obesity-induced muscle dysfunction. In the present study, we aimed to determine the effects of muscle p62 on skeletal muscle mass, muscle strength, insulin resistance, and NASH pathology. Methods: We generated muscle-specific p62 gene rescue mice (p62-mRes), which express p62 only in muscle and were derived from p62-knock out mice (p62 KIKI ) using the cre/loxp system. p62 KIKI and p62-mRes mice were fed an HFD for 20 weeks and their phenotypes were compared. Results: HFD-feeding caused severe obesity in both p62 KIKI and p62-mRes mice, but there was no effect of muscle p62 on body mass. Limb skeletal muscle mass, grip strength, and the cross-sectional area of muscle fibers were higher in p62-mRes mice than in p62 KIKI . The glucose tolerance and insulin sensitivity of the p62-mRes mice were also superior. The protein expression of mechanistic target of rapamycin, which promotes muscle protein synthesis, and GLUT4, a glucose transporter in skeletal muscle, were higher in the p62-mRes mice. p62 KIKI mice developed severe NASH when fed an HFD, but the progression of NASH was retarded by p62 gene rescue in muscle, and the expression of Tgf-β1, which encodes a factor that promotes hepatic fibrosis, was reduced. Conclusion: Rescue of muscle-specific p62 in the whole-body p62 knock-out mice ameliorates the insulin resistance and retards the progression of NASH caused by systemic p62 ablation.

Keywords:  insulin resistance; non-alcoholic steatohepatitis; obesity; p62/SQSTM1; skeletal muscle

DOI:  https://doi.org/10.3389/fphys.2022.993995
Mol Cell. 2022 Nov 22. pii: S1097-2765(22)01070-X. [Epub ahead of print]

POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells.

Ondrej Belan, Marie Sebald, Marek Adamowicz, Roopesh Anand, Aleksandra Vancevska, Joana Neves, Vera Grinkevich, Graeme Hewitt, Sandra Segura-Bayona, Roberto Bellelli, Helen M R Robinson, Geoff S Higgins, Graeme C M Smith, Stephen C West, David S Rueda, Simon J Boulton.

  POLQ is a key effector of DSB repair by microhomology-mediated end-joining (MMEJ) and is overexpressed in many cancers. POLQ inhibitors confer synthetic lethality in HR and Shieldin-deficient cancer cells, which has been proposed to reflect a critical dependence on the DSB repair pathway by MMEJ. Whether POLQ also operates independent of MMEJ remains unexplored. Here, we show that POLQ-deficient cells accumulate post-replicative ssDNA gaps upon BRCA1/2 loss or PARP inhibitor treatment. Biochemically, cooperation between POLQ helicase and polymerase activities promotes RPA displacement and ssDNA-gap fill-in, respectively. POLQ is also capable of microhomology-mediated gap skipping (MMGS), which generates deletions during gap repair that resemble the genomic scars prevalent in POLQ overexpressing cancers. Our findings implicate POLQ in mutagenic post-replicative gap sealing, which could drive genome evolution in cancer and whose loss places a critical dependency on HR for gap protection and repair and cellular viability.

Keywords:  BRCA; BRCA genes; PARP; PARP inhibitors; POLQ; homologous recombination; post-replicative gap repair; replication stress

DOI:  https://doi.org/10.1016/j.molcel.2022.11.008
Science. 2022 Dec 02. 378(6623): 996-1000

The human signal peptidase complex acts as a quality control enzyme for membrane proteins.

Andrea Zanotti, João P L Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Dönem Avci, Martin Zacharias, Robert B Russell, Marius K Lemberg, Matthias J Feige.

Cells need to detect and degrade faulty membrane proteins to maintain homeostasis. In this study, we identify a previously unknown function of the human signal peptidase complex (SPC)-the enzyme that removes endoplasmic reticulum (ER) signal peptides-as a membrane protein quality control factor. We show that the SPC cleaves membrane proteins that fail to correctly fold or assemble into their native complexes at otherwise hidden cleavage sites, which our study reveals to be abundant in the human membrane proteome. This posttranslocational cleavage synergizes with ER-associated degradation to sustain membrane protein homeostasis and contributes to cellular fitness. Cryptic SPC cleavage sites thus serve as predetermined breaking points that, when exposed, help to target misfolded or surplus proteins for degradation, thereby maintaining a healthy membrane proteome.

DOI: https://doi.org/10.1126/science.abo5672
Lancet Oncol. 2022 Dec;pii: S1470-2045(22)00699-4. [Epub ahead of print]23(12): e526

Dexamethasone for cancer-related dyspnoea - Authors' reply.

David Hui, Sandra K Hanneman, Donald A Mahler, Eduardo Bruera.

DOI: https://doi.org/10.1016/S1470-2045(22)00699-4
Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2201600119

Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane.

Ana Lisica, Jonathan Fouchard, Manasi Kelkar, Tom P J Wyatt, Julia Duque, Anne-Betty Ndiaye, Alessandra Bonfanti, Buzz Baum, Alexandre J Kabla, Guillaume T Charras.

  The direction in which a cell divides is set by the orientation of its mitotic spindle and is important for determining cell fate, controlling tissue shape, and maintaining tissue architecture. Divisions parallel to the epithelial plane sustain tissue expansion. By contrast, divisions perpendicular to the plane promote tissue stratification and lead to the loss of epithelial cells from the tissue-an event that has been suggested to promote metastasis. Much is known about the molecular machinery involved in orienting the spindle, but less is known about the contribution of mechanical factors, such as tissue tension, in ensuring spindle orientation in the plane of the epithelium. This is important as epithelia are continuously subjected to mechanical stresses. To explore this further, we subjected suspended epithelial monolayers devoid of extracellular matrix to varying levels of tissue tension to study the orientation of cell divisions relative to the tissue plane. This analysis revealed that lowering tissue tension by compressing epithelial monolayers or by inhibiting myosin contractility increased the frequency of out-of-plane divisions. Reciprocally, increasing tissue tension by elevating cell contractility or by tissue stretching restored accurate in-plane cell divisions. Moreover, a characterization of the geometry of cells within these epithelia suggested that spindles can sense tissue tension through its impact on tension at subcellular surfaces, independently of their shape. Overall, these data suggest that accurate spindle orientation in the plane of the epithelium relies on a threshold level of tension at intercellular junctions.

Keywords:  epithelium; out-of-plane division; spindle orientation; tissue tension

DOI:  https://doi.org/10.1073/pnas.2201600119
Elife. 2022 Nov 29. pii: e79903. [Epub ahead of print]11

Fixation can change the appearance of phase separation in living cells.

Shawn Irgen-Gioro, Shawn Ryohei Yoshida, Victoria Walling, Shasha Chong.

  Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.

Keywords:  cell biology; none; physics of living systems

DOI:  https://doi.org/10.7554/eLife.79903
Handb Exp Pharmacol. 2022 Dec 02.

Metabolomics in Cell Biology.

Zuhal Eraslan, Marta Cascante, Ulrich L Günther.

  Metabolomics has long been used in a biomedical context. The most typical samples are body fluids in which small molecules can be detected and quantified using technologies such as Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). Many studies, in particular in the wider field of cancer research, are based on cellular models. Different cancer cells can have vastly different ways of regulating metabolism and responses to drug treatments depend on specific metabolic mechanisms which are often cell type specific. This has led to a series of publications using metabolomics to study metabolic mechanisms. Cell-based metabolomics has specific requirements and allows for interesting approaches where metabolism is followed in real-time. Here applications of metabolomics in cell biology have been reviewed, providing insight into specific technologies used and showing exemplary case studies with an emphasis towards applications which help to understand drug mechanisms.

Keywords:  Cell biology; Metabolomics

DOI:  https://doi.org/10.1007/164_2022_619
Int J Biol Sci. 2022 ;18(16): 6176-6188

Lipid Droplets: A Cellular Organelle Vital for Thermogenesis.

Lupeng Chen, Yi Jin, Jian Wu, Zhuqing Ren.

  Mammals maintain a constant core body temperature through adaptive thermogenesis which includes shivering and non-shivering thermogenesis. Non-shivering thermogenesis relies primarily on mitochondrial uncoupling protein 1 (UCP1) in thermogenic fat (including brown and beige adipose tissue) to burn substrates, such as fatty acids (FAs), and convert chemical energy into heat. Lipid droplets (LDs), which are organelles that store lipids, are present in large numbers in thermogenic fat and are essential for adipose thermogenesis. Upon cold stimulation, LDs rapidly release FAs through autophagy or lipase-mediated lipolysis and rapidly translocate FAs into the mitochondria by interacting with mitochondria to burn and so promote thermogenesis. In addition, LD proteins promote the expression of UCP1 by activating the transcriptional activity of thermogenesis-related proteins. Here, the progress of research on the important role of LDs in thermogenesis is reviewed, mainly in terms of LD proteins, LD-organelle interactions, and LD autophagy (lipophagy). The emerging rationale for the involvement of LDs in each thermogenic pathway is described and the remaining unanswered questions in this field are highlighted.

Keywords:  Brown/beige adipose tissue; Lipid droplets; Lipophagy; Thermogenesis

DOI:  https://doi.org/10.7150/ijbs.77051
Front Physiol. 2022 ;13 999883

Alteration of cholesterol distribution at the plasma membrane of cancer cells: From evidence to pathophysiological implication and promising therapy strategy.

Mauriane Maja, Donatienne Tyteca.

  Cholesterol-enriched domains are nowadays proposed to contribute to cancer cell proliferation, survival, death and invasion, with important implications in tumor progression. They could therefore represent promising targets for new anticancer treatment. However, although diverse strategies have been developed over the years from directly targeting cholesterol membrane content/distribution to adjusting sterol intake, all approaches present more or less substantial limitations. Those data emphasize the need to optimize current strategies, to develop new specific cholesterol-targeting anticancer drugs and/or to combine them with additional strategies targeting other lipids than cholesterol. Those objectives can only be achieved if we first decipher (i) the mechanisms that govern the formation and deformation of the different types of cholesterol-enriched domains and their interplay in healthy cells; (ii) the mechanisms behind domain deregulation in cancer; (iii) the potential generalization of observations in different types of cancer; and (iv) the specificity of some alterations in cancer vs. non-cancer cells as promising strategy for anticancer therapy. In this review, we will discuss the current knowledge on the homeostasis, roles and membrane distribution of cholesterol in non-tumorigenic cells. We will then integrate documented alterations of cholesterol distribution in domains at the surface of cancer cells and the mechanisms behind their contribution in cancer processes. We shall finally provide an overview on the potential strategies developed to target those cholesterol-enriched domains in cancer therapy.

Keywords:  anticancer therapy; apoptosis; cancer; caveolae; cell migration; cell proliferation; lipid rafts; submicrometric domains

DOI:  https://doi.org/10.3389/fphys.2022.999883