bims-cagime 2021-11-07 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2021‒11‒07
thirty-five papers selected by
Kıvanç Görgülü
Technical University of Munich

Cancer-associated fibroblast heterogeneity is associated with organ-specific metastasis in pancreatic ductal adenocarcinoma.
Radiosensitizing pancreatic cancer via effective autophagy inhibition.
The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors.
Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer.
Induction FOLFIRINOX for patients with locally unresectable pancreatic ductal adenocarcinoma.
Activation of Akt-mTORC1 signalling reverts cancer-dependent muscle wasting.
Endothelial cell autophagy keeps neutrophil trafficking under control.
Modeling Metastatic Colonization in a Decellularized Organ scaffold-based Perfusion Bioreactor.
Association of Systemic Inflammation and Overall Survival in Elderly Patients with Cancer Cachexia - Results from a Multicenter Study.
Novel small molecule inhibition of IKK/NF-κB activation reduces markers of senescence and improves healthspan in mouse models of aging.
Diminished efficacy of PD-(L)1 inhibition in STK11- and KEAP1-mutant lung adenocarcinoma is impacted by KRAS mutation status.
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface.
The context-specific role of germline pathogenicity in tumorigenesis.
Extracellular Matrix Signals as Drivers of Mitochondrial Bioenergetics and Metabolic Plasticity of Cancer Cells During Metastasis.
A gene toolbox for monitoring autophagy transcription.
Local and systemic effects of Interleukin-6 (IL-6) in inflammation and cancer.
MC3R links nutritional state to childhood growth and the timing of puberty.
Predicting physiological aging rates from a range of quantitative traits using machine learning.
Mitochondrial respiration contributes to the interferon gamma response in antigen presenting cells.
Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.
Sympathetic nerve-adipocyte interactions in response to acute stress.
Ameliorating cancer cachexia by inhibiting cancer cell release of Hsp70 and Hsp90 with omeprazole.
Nanoliposomal irinotecan plus fluorouracil and folinic acid as a second-line treatment option in patients with metastatic pancreatic ductal adenocarcinoma: a retrospective cohort study.
An improved macromolecular crowding sensor CRONOS for detection of crowding changes in membrane-less organelles under stressed conditions.
Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution.
Molecular programs of fibrotic change in aging human lung.
L-carnitine ameliorates the muscle wasting of cancer cachexia through the AKT/FOXO3a/MaFbx axis.
Stress and Telomere Shortening: Insights from Cellular Mechanisms.
Mitochondrial NDUFA4L2 is a novel regulator of skeletal muscle mass and force.
BAG3 induces fibroblasts to release key cytokines involved in pancreatic cell migration.
Application of Single-Cell Multi-Omics in Dissecting Cancer Cell Plasticity and Tumor Heterogeneity.
Improved prediction of immune checkpoint blockade efficacy across multiple cancer types.
Lipidomic landscape in cancer: Actionable insights for membrane-based therapy and diagnoses.
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography.
Discovery of the pancreatic basal cell: a new candidate for an adult stem cell emerges.

J Hematol Oncol. 2021 Nov 02. 14(1): 184

Cancer-associated fibroblast heterogeneity is associated with organ-specific metastasis in pancreatic ductal adenocarcinoma.

Xingyi Pan, Jiaojiao Zhou, Qian Xiao, Kenji Fujiwara, Mengwen Zhang, Guanglan Mo, Wei Gong, Lei Zheng.

  BACKGROUND: Metastasis occurs in the majority of pancreatic ductal adenocarcinoma (PDAC) patients at diagnosis or following resection. Patients with liver metastasis and those with lung metastasis have significantly different prognosis. Here, we sought to understand how cancer-associated fibroblasts (CAFs) play roles in the development of organ-specific metastasis.METHODS: PDAC tumor cell lines established from the primary tumors with liver and lung metastasis potentials, respectively, in Kras/p53 mutation conditional knock-in (KPC) mice were co-cultured with matched CAFs or mouse mesenchymal stem cells. CAFs were isolated from metastases and subjected to DNA methylation and whole transcriptomic RNA sequencing analysis.
RESULTS: The ability of mouse PDAC tumor cell lines in developing liver or lung-specific metastases was demonstrated in orthotopic models. Tumor cells associated with liver metastasis potential, but not those associated with lung metastasis potential, induced the methylation of metabolism genes including NQO1 and ALDH1a3 and subsequent downregulated mRNA expression of a broader group of metabolism genes in CAFs. DNA methylation and downregulation of metabolism genes in CAFs in liver metastasis, but not those in lung metastasis, appeared to be regulated by DNA methyltransferase. Tumor cells associated with liver metastasis potential, but not those associated with lung metastasis potential, induce inflammatory CAF (iCAF) signatures. CAFs from liver metastasis demonstrated a more homogenous iCAF phenotype, whereas CAFs from lung metastasis maintained the heterogeneity.
CONCLUSIONS: PDAC with organ-specific metastatic potentials has different capacities in inducing methylation of metabolism genes in CAFs, modulating CAF phenotypes, and resulting in different levels of heterogeneity of CAFs in different metastatic niches.

Keywords:  Cancer-associated fibroblast; DNA methylation; Heterogeneity; Organ-specific metastasis; Pancreatic cancer

DOI:  https://doi.org/10.1186/s13045-021-01203-1
Mol Cancer Ther. 2021 Nov 01. pii: molcanther.1103.2021. [Epub ahead of print]

Radiosensitizing pancreatic cancer via effective autophagy inhibition.

Taha Yazal, Justine Bailleul, Yangjingyi Ruan, David Sung, Fang-I Chu, Daisy Palomera, Amy Dao, Anahita Sehgal, Vibha Gurunathan, Laila Aryan, Mansoureh Eghbali, Erina Vlashi.

Despite aggressive treatments, pancreatic ductal adenocarcinoma (PDAC) remains an intractable disease, largely because it is refractory to therapeutic interventions. To overcome its nutrient-poor microenvironment, PDAC heavily relies on autophagy for metabolic needs to promote tumor growth and survival. Here, we explore autophagy inhibition as a method to enhance the effects of radiation therapy (RT) on PDAC tumors. Hydroxychloroquine (HCQ) is an autophagy inhibitor at the focus of many PDAC clinical trials, including in combination with RT. However, its acid-labile properties likely reduce its intratumoral efficacy. Here, we demonstrate that EAD1, a synthesized analogue of HCQ, is a more effective therapeutic for sensitizing PDAC tumors of various KRAS mutations to RT. Specifically, in vitro models show that EAD1 is an effective inhibitor of autophagic flux in PDAC cells, accompanied by a potent inhibition of proliferation. When combined with RT, EAD1 is consistently superior to HCQ not only as a single agent, but also in radiosensitizing PDAC cells, and perhaps most importantly, in decreasing the self-renewal capacity of PDAC cancer stem cells (PCSCs). The more pronounced sensitizing effects of autophagy inhibitors on pancreatic stem over differentiated cells points to a new understanding that PCSCs may be more dependent on autophagy to counter the effects of radiation toxicity, a potential mechanism explaining the resistance of PCSCs to RT. Finally, in vivo sub-cutaneous tumor models demonstrate that combination of RT and EAD1 is the most successful at controlling tumor growth. The models also confirmed a similar toxicity profile between EAD1 and HCQ.

DOI: https://doi.org/10.1158/1535-7163.MCT-20-1103
Nat Commun. 2021 Nov 01. 12(1): 6274

The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors.

Teklab Gebregiworgis, Yoshihito Kano, Jonathan St-Germain, Nikolina Radulovich, Molly L Udaskin, Ahmet Mentes, Richard Huang, Betty P K Poon, Wenguang He, Ivette Valencia-Sama, Claire M Robinson, Melissa Huestis, Jinmin Miao, Jen Jen Yeh, Zhong-Yin Zhang, Meredith S Irwin, Jeffrey E Lee, Ming-Sound Tsao, Brian Raught, Christopher B Marshall, Michael Ohh, Mitsuhiko Ikura.

Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant.

DOI: https://doi.org/10.1038/s41467-021-26526-y
Nat Cancer. 2021 Oct;2(10): 1071-1085

Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer.

Peter M K Westcott, Nathan J Sacks, Jason M Schenkel, Zackery A Ely, Olivia Smith, Haley Hauck, Alex M Jaeger, Daniel Zhang, Coralie M Backlund, Mary C Beytagh, J J Patten, Ryan Elbashir, George Eng, Darrell J Irvine, Omer H Yilmaz, Tyler Jacks.

Immune evasion is a hallmark of cancer, and therapies that restore immune surveillance have proven highly effective in cancers with high tumor mutation burden (TMB) (e.g., those with microsatellite instability (MSI)). Whether low TMB cancers, which are largely refractory to immunotherapy, harbor potentially immunogenic neoantigens remains unclear. Here, we show that tumors from all patients with microsatellite stable (MSS) colorectal cancer (CRC) express clonal predicted neoantigens despite low TMB. Unexpectedly, these neoantigens are broadly expressed at lower levels compared to those in MSI CRC. Using a versatile platform for modulating neoantigen expression in CRC organoids and transplantation into the distal colon of mice, we show that low expression precludes productive cross priming and drives immediate T cell dysfunction. Strikingly, experimental or therapeutic rescue of priming rendered T cells capable of controlling tumors with low neoantigen expression. These findings underscore a critical role of neoantigen expression level in immune evasion and therapy response.

DOI: https://doi.org/10.1038/s43018-021-00247-z
J Surg Oncol. 2021 Oct 31.

Induction FOLFIRINOX for patients with locally unresectable pancreatic ductal adenocarcinoma.

Caitlin A McIntyre, Noah A Cohen, Debra A Goldman, Mithat Gonen, Eran Sadot, Eileen M O'Reilly, Anna M Varghese, Kenneth H Yu, Vinod P Balachandran, Kevin C Soares, Michael I D'Angelica, Jeffrey A Drebin, T P Kingham, Peter J Allen, Alice C Wei, William R Jarnagin.

  OBJECTIVES: Patients with locally advanced pancreatic adenocarcinoma (PDAC) receive induction chemotherapy with or without radiation, with the goal of R0 resection and improving survival. Herein, we evaluate the outcomes of patients who presented with Stage III PDAC and received induction FOLFIRINOX.METHODS: An institutional database was queried for consecutive patients who received induction FOLFIRINOX for locally unresectable PDAC between 2010 and 2016. Clinical and radiographic parameters were assessed pre- and posttreatment, and clinical outcomes were evaluated.
RESULTS: There were 200 patients who met the inclusion criteria. The median number of cycles of FOLFIRINOX was 8, 70% (n = 140) received radiation, and 18% (n = 36) underwent resection. Median overall survival (OS) in resected patients was 36 months (95% confidence interval [CI]: 24-56), and this group had improved OS compared to patients that did not undergo resection (hazard ratio (95% CI): 0.41 (0.26-0.64), p < 0.001). Patients (n = 112) who did not progress on induction therapy but remained unresectable had a median OS of 23.9 months (95% CI: 21.1-25.4).
CONCLUSION: Nearly 20% of patients with locally advanced PDAC responded sufficiently to induction FOLFIRINOX to undergo resection, which was associated with improved OS compared to patients that did not undergo resection. Patients with stable disease who remain unresectable represent a group of patients with locally advanced PDAC who may benefit from optimization of additional nonoperative treatment.

Keywords:  FOLFIRINOX; induction chemotherapy; locally advanced pancreatic cancer

DOI:  https://doi.org/10.1002/jso.26735
J Cachexia Sarcopenia Muscle. 2021 Nov 06.

Activation of Akt-mTORC1 signalling reverts cancer-dependent muscle wasting.

Alessia Geremia, Roberta Sartori, Martina Baraldo, Leonardo Nogara, Valeria Balmaceda, Georgia Ana Dumitras, Stefano Ciciliot, Marco Scalabrin, Hendrik Nolte, Bert Blaauw.

  BACKGROUND: Cancer-related muscle wasting occurs in most cancer patients. An important regulator of adult muscle mass and function is the Akt-mTORC1 pathway. While Akt-mTORC1 signalling is important for adult muscle homeostasis, it is also a major target of numerous cancer treatments. Which role Akt-mTORC1 signalling plays during cancer cachexia in muscle is currently not known. Here, we aimed to determine how activation or inactivation of the pathway affects skeletal muscle during cancer cachexia.METHODS: We used inducible, muscle-specific Raptor ko (mTORC1) mice to determine the effect of reduced mTOR signalling during cancer cachexia. On the contrary, in order to understand if skeletal muscles maintain their anabolic capacity and if activation of Akt-mTORC1 signalling can reverse cancer cachexia, we generated mice in which we can inducibly activate Akt specifically in skeletal muscles.
RESULTS: We found that mTORC1 signalling is impaired during cancer cachexia, using the Lewis lung carcinoma and C26 colon cancer model, and is accompanied by a reduction in protein synthesis rates of 57% (P < 0.01). Further reduction of mTOR signalling, as seen in Raptor ko animals, leads to a 1.5-fold increase in autophagic flux (P > 0.001), but does not further increase muscle wasting. On the other hand, activation of Akt-mTORC1 signalling in already cachectic animals completely reverses the 15-20% loss in muscle mass and force (P < 0.001). Interestingly, Akt activation only in skeletal muscle completely normalizes the transcriptional deregulation observed in cachectic muscle, despite having no effect on tumour size or spleen mass. In addition to stimulating muscle growth, it is also sufficient to prevent the increase in protein degradation normally observed in muscles from tumour-bearing animals.
CONCLUSIONS: Here, we show that activation of Akt-mTORC1 signalling is sufficient to completely revert cancer-dependent muscle wasting. Intriguingly, these results show that skeletal muscle maintains its anabolic capacities also during cancer cachexia, possibly giving a rationale behind some of the beneficial effects observed in exercise in cancer patients.

Keywords:  Akt; Cancer cachexia; Muscle growth; Raptor; Skeletal muscle force; mTOR

DOI:  https://doi.org/10.1002/jcsm.12854
Autophagy. 2021 Oct 31. 1-3

Endothelial cell autophagy keeps neutrophil trafficking under control.

Natalia Reglero-Real, Lorena Pérez-Gutiérrez, Sussan Nourshargh.

  A defining feature of an inflammatory reaction is infiltration of neutrophils into tissues, a response that requires breaching of endothelial cells (ECs) that line the lumenal aspect of blood vessels. Dysregulated neutrophil trafficking is a hallmark of pathology, but details of the molecular mechanisms that terminate neutrophil breaching of venular walls remain unclear. In this work, we have identified EC autophagy as a negative regulator of neutrophil diapedesis in acute physiological inflammation. Specifically, in vivo, inflamed venular ECs upregulate autophagy, a response that is selectively localized to EC contacts and temporally aligned with the peak of neutrophil trafficking. Genetic ablation of EC autophagy leads to excessive neutrophil tissue infiltration in multiple inflammatory models and supports enhanced neutrophil transendothelial migration (TEM), while pharmacological induction of autophagy inhibits neutrophil migration. Mechanistically, autophagy machinery regulates the architecture of EC contacts and controls the reorganization and degradation of adhesion molecules, constituting a physiological brake on leukocyte trafficking.

Keywords:  ATG16L1; ATG5; endothelium; inflammation; junctions; neutrophils

DOI:  https://doi.org/10.1080/15548627.2021.1987675
Adv Healthc Mater. 2021 Nov 03. e2100684

Modeling Metastatic Colonization in a Decellularized Organ scaffold-based Perfusion Bioreactor.

Maria Rafaeva, Edward R Horton, Adina R D Jensen, Chris D Madsen, Raphael Reuten, Oliver Willacy, Christian B Brøchner, Thomas H Jensen, Kamilla Westarp Zornhagen, Marina Crespo, Dina S Grønseth, Sebastian R Nielsen, Manja Idorn, Per Thor Straten, Kristoffer Rohrberg, Iben Spanggaard, Martin Højgaard, Ulrik Lassen, Janine T Erler, Alejandro E Mayorca-Guiliani.

  Metastatic cancer spread is responsible for most cancer-related deaths. To colonize a new organ, invading cells adapt to, and remodel, the local extracellular matrix (ECM), a network of proteins and proteoglycans underpinning all tissues, and a critical regulator of homeostasis and disease. However, there is a major lack in tools to study cancer cell behavior within native three-dimensional ECM. Here, we present an in-house designed bioreactor, where mouse organ ECM scaffolds are perfused and populated with cells that are challenged to colonize it. Using a specialized bioreactor chamber, it is possible to monitor cell behavior microscopically (e.g., proliferation, migration) within the organ scaffold. Cancer cells in this system recapitulate cell signaling observed in vivo and remodel complex native ECM. Moreover, our bioreactors are compatible with co-culturing cell types of different genetic origin comprising the normal and tumor microenvironment. This degree of experimental flexibility in an organ-specific and three-dimensional context, opens new possibilities to study cell-cell and cell-ECM interplay, and to model diseases in a controllable organ-specific system ex vivo. This article is protected by copyright. All rights reserved.

Keywords:  cancer metastasis; experimental methods; extracellular matrix; specialized bioreactor

DOI:  https://doi.org/10.1002/adhm.202100684
J Inflamm Res. 2021 ;14 5527-5540

Association of Systemic Inflammation and Overall Survival in Elderly Patients with Cancer Cachexia - Results from a Multicenter Study.

Guo-Tian Ruan, Ming Yang, Xiao-Wei Zhang, Meng-Meng Song, Chun-Lei Hu, Yi-Zhong Ge, Hai-Lun Xie, Tong Liu, Meng Tang, Qi Zhang, Xi Zhang, Kang-Ping Zhang, Xiang-Rui Li, Qin-Qin Li, Yong-Bing Chen, Kai-Ying Yu, Ming-Hua Cong, Kun-Hua Wang, Han-Ping Shi.

  Background: Systemic inflammation and cachexia are associated with adverse clinical outcomes in elderly patients with cancer. The survival outcomes of elderly patients with cancer cachexia (EPCC) with high inflammation and a high risk of mortality are unknown. This study aimed to investigate the impact of high inflammation on the prognosis of EPCC patients with high mortality.Patients and Methods: This multicenter cohort study included 746 EPCC (age >65 years) with a mean age of 72.00 ± 5.24 years, of whom 489 (65.5%) were male. The cut-off value for the inflammation index was obtained using the optimal survival curve. The different inflammatory indicators were assessed using the concordance index (C-index), decision curve analysis (DCA), and prognostic receiver operating characteristic (ROC). The high mortality risk group of EPCC was defined by the 2011 Fearon Cancer Diagnostic Consensus. EPCC were divided into the high-risk group, which satisfies three diagnostic criteria, and a low-risk group, which satisfies only one or two diagnostic criteria.
Results: The C-index, DCA, and prognostic ROC indicated the superiority of advanced lung cancer inflammation index (ALI) compared with other indicators, including neutrophil-lymphocyte ratio (NLR), prognostic nutritional index (PNI), systemic immune-inflammation index (SII), and platelet-lymphocyte ratio (PLR). Whether ALI was used as a continuous or a categorical variable, ALI had a better prognostic value in EPCC compared with other inflammatory indicators. In particular, patients with low ALI (<25.03) had a worse overall survival (OS) than patients with high ALI (≥25.03) (P < 0.001, HR [95% CI] = 2.092 [1.590-2.751]). The combination effect analysis showed that the risk of mortality of the patients in the low-ALI and high-risk groups was 3.095-fold higher than that of patients in the high-ALI and low-risk groups.
Conclusion: The prognostic and discriminative value of the inflammatory indicator ALI was better than that of NLR, PNI, SII, and PLR in EPCC. The high-risk group of EPCC with a low ALI would increase the death risk of OS.

Keywords:  ALI; cancer cachexia; elderly; overall survival; systemic inflammation

DOI:  https://doi.org/10.2147/JIR.S332408
Aging Cell. 2021 Nov 03. e13486

Novel small molecule inhibition of IKK/NF-κB activation reduces markers of senescence and improves healthspan in mouse models of aging.

Lei Zhang, Jing Zhao, Xiaodong Mu, Sara J McGowan, Luise Angelini, Ryan D O'Kelly, Matthew J Yousefzadeh, Ayumi Sakamoto, Zaira Aversa, Nathan K LeBrasseur, Yousin Suh, Johnny Huard, Theodore M Kamenecka, Laura J Niedernhofer, Paul D Robbins.

  Constitutive NF-κB activation is associated with cellular senescence and stem cell dysfunction and rare variants in NF-κB family members are enriched in centenarians. We recently identified a novel small molecule (SR12343) that inhibits IKK/NF-κB activation by disrupting the association between IKKβ and NEMO. Here we investigated the therapeutic effects of SR12343 on senescence and aging in three different mouse models. SR12343 reduced senescence-associated beta-galactosidase (SA-β-gal) activity in oxidative stress-induced senescent mouse embryonic fibroblasts as well as in etoposide-induced senescent human IMR90 cells. Chronic administration of SR12343 to the Ercc1-/ ∆ and Zmpste24-/- mouse models of accelerated aging reduced markers of cellular senescence and SASP and improved multiple parameters of aging. SR12343 also reduced markers of senescence and increased muscle fiber size in 2-year-old WT mice. Taken together, these results demonstrate that IKK/NF-κB signaling pathway represents a promising target for reducing markers of cellular senescence, extending healthspan and treating age-related diseases.

Keywords:  NEMO; NF-κB; SR12343; aging; senescence

DOI:  https://doi.org/10.1111/acel.13486
J Thorac Oncol. 2021 Nov 02. pii: S1556-0864(21)03284-6. [Epub ahead of print]

Diminished efficacy of PD-(L)1 inhibition in STK11- and KEAP1-mutant lung adenocarcinoma is impacted by KRAS mutation status.

Biagio Ricciuti, Kathryn C Arbour, Jessica J Lin, Amir Vajdi, Natalie Vokes, Lingzhi Hong, Jianjun Zhang, Michael Y Tolstorukov, Yvonne Y Li, Liam F Spurr, Andrew D Cherniack, Gonzalo Recondo, Giuseppe Lamberti, Xinan Wang, Deepti Venkatraman, Joao V Alessi, Victor R Vaz, Hira Rizvi, Jacklynn Egger, Andrew J Plodkowski, Sara Khosrowjerdi, Subba Digumarthy, Hyesun Park, Nuno Vaz, Mizuki Nishino, Lynette M Sholl, David Barbie, Mehmet Altan, John V Heymach, Ferdinandos Skoulidis, Justin F Gainor, Matthew D Hellmann, Mark M Awad.

  INTRODUCTION: STK11 and KEAP1 mutations (STK11MUT and KEAP1MUT) are among the most commonly mutated genes in lung adenocarcinoma (LUAD). While STK11MUT has been associated with resistance to PD-(L)1 inhibition in KRAS mutant (KRASMUT) LUAD, its impact on immunotherapy efficacy in KRAS wild-type (KRASWT) LUAD is currently unknown. Whether KEAP1MUT differentially impacts outcomes to PD-(L)1 inhibition in KRASMUT and KRASWT LUAD is also unknown.METHODS: Clinicopathologic and genomic data were collected from September 2013 to September 2020 from patients with advanced LUAD at the Dana-Farber Cancer Institute/Massachusetts General Hospital (DFCI/MGH cohort), and Memorial Sloan Kettering Cancer Center/MD Anderson Cancer Center (MSKCC/MDACC cohort). Clinical outcomes to PD-(L)1 inhibition were analyzed according to KRAS, STK11, and KEAP1 mutation status in two independent cohorts. TCGA transcriptomic data were interrogated to identify differences in tumor gene expression and tumor immune cell subsets, respectively, according to KRAS/STK11 and KRAS/KEAP1 co-mutation status.
RESULTS: In the combined cohort (DFCI/MGH + MSKCC/MDACC) of 1261 patients (median age 61 years [range:22-92], 708 women [56.1%], 1065 smokers [84.4%]), KRAS mutations were detected in 536 (42.5%) cases, deleterious STK11 and KEAP1 mutations were found in 20.6% (260/1261), and 19.2% (231/1202) of evaluable cases, respectively. In each independent cohort, as well as in the combined cohort, STK11 and KEAP1 mutations were associated with significantly worse progression-free (STK11 HR: 2.04, P<0.0001; KEAP1 HR 2.05, P<0.0001), and overall survival (STK11 HR: 2.09 ,P<0.0001; KEAP1 HR 2.24, P<0.0001) to immunotherapy uniquely among KRASMUT but not KRASWT LUADs. Gene expression ontology and immune cell enrichment analyses revealed that the presence of STK11 and/or KEAP1 mutations result in distinct immunophenotypes in KRASMUT, but not in KRASWT, lung cancers.
CONCLUSION: STK11 and KEAP1 mutations confer worse outcomes to immunotherapy among patients with KRASMUT but not among KRASWT lung adenocarcinoma. Tumors harboring concurrent KRAS/STK11 and KRAS/KEAP1 mutations display distinct immune profiles in terms of gene expression and immune cell infiltration.

Keywords:  KEAP1; KRAS; NSCLC; PD-(L)1 blockade; STK11

DOI:  https://doi.org/10.1016/j.jtho.2021.10.013
Nat Commun. 2021 Nov 01. 12(1): 6278

Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface.

Miranda V Hunter, Reuben Moncada, Joshua M Weiss, Itai Yanai, Richard M White.

During tumor progression, cancer cells come into contact with various non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq to characterize tumor-microenvironment interactions at the tumor boundary. Using a zebrafish model of melanoma, we identify a distinct "interface" cell state where the tumor contacts neighboring tissues. This interface is composed of specialized tumor and microenvironment cells that upregulate a common set of cilia genes, and cilia proteins are enriched only where the tumor contacts the microenvironment. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress cilia genes outside of the interface. A cilia-enriched interface is conserved in human patient samples, suggesting it is a conserved feature of human melanoma. Our results demonstrate the power of spatially resolved transcriptomics in uncovering mechanisms that allow tumors to adapt to new environments.

DOI: https://doi.org/10.1038/s41467-021-26614-z
Nat Genet. 2021 Nov;53(11): 1577-1585

The context-specific role of germline pathogenicity in tumorigenesis.

Preethi Srinivasan, Chaitanya Bandlamudi, Philip Jonsson, Yelena Kemel, Shweta S Chavan, Allison L Richards, Alexander V Penson, Craig M Bielski, Christopher Fong, Aijazuddin Syed, Gowtham Jayakumaran, Meera Prasad, Jason Hwee, Selcuk Onur Sumer, Ino de Bruijn, Xiang Li, JianJiong Gao, Nikolaus Schultz, Roy Cambria, Jesse Galle, Semanti Mukherjee, Joseph Vijai, Karen A Cadoo, Maria I Carlo, Michael F Walsh, Diana Mandelker, Ozge Ceyhan-Birsoy, Jinru Shia, Ahmet Zehir, Marc Ladanyi, David M Hyman, Liying Zhang, Kenneth Offit, Mark E Robson, David B Solit, Zsofia K Stadler, Michael F Berger, Barry S Taylor.

Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.

DOI: https://doi.org/10.1038/s41588-021-00949-1
Front Cell Dev Biol. 2021 ;9 751301

Extracellular Matrix Signals as Drivers of Mitochondrial Bioenergetics and Metabolic Plasticity of Cancer Cells During Metastasis.

Félix A Urra, Sebastián Fuentes-Retamal, Charlotte Palominos, Yarcely A Rodríguez-Lucart, Camila López-Torres, Ramiro Araya-Maturana.

  The role of metabolism in tumor growth and chemoresistance has received considerable attention, however, the contribution of mitochondrial bioenergetics in migration, invasion, and metastasis is recently being understood. Migrating cancer cells adapt their energy needs to fluctuating changes in the microenvironment, exhibiting high metabolic plasticity. This occurs due to dynamic changes in the contributions of metabolic pathways to promote localized ATP production in lamellipodia and control signaling mediated by mitochondrial reactive oxygen species. Recent evidence has shown that metabolic shifts toward a mitochondrial metabolism based on the reductive carboxylation, glutaminolysis, and phosphocreatine-creatine kinase pathways promote resistance to anoikis, migration, and invasion in cancer cells. The PGC1a-driven metabolic adaptations with increased electron transport chain activity and superoxide levels are essential for metastasis in several cancer models. Notably, these metabolic changes can be determined by the composition and density of the extracellular matrix (ECM). ECM stiffness, integrins, and small Rho GTPases promote mitochondrial fragmentation, mitochondrial localization in focal adhesion complexes, and metabolic plasticity, supporting enhanced migration and metastasis. Here, we discuss the role of ECM in regulating mitochondrial metabolism during migration and metastasis, highlighting the therapeutic potential of compounds affecting mitochondrial function and selectively block cancer cell migration.

Keywords:  ECM stiffness; OXPHOS (oxidative phosphorylation); TCA cycle; integrin; metabolic shift; migrastatics; migrating cancer cells

DOI:  https://doi.org/10.3389/fcell.2021.751301
Cell Death Dis. 2021 Nov 02. 12(11): 1044

A gene toolbox for monitoring autophagy transcription.

Matteo Bordi, Rossella De Cegli, Beatrice Testa, Ralph A Nixon, Andrea Ballabio, Francesco Cecconi.

Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field. We identified 604 genes and created main categories: MTOR and upstream pathways, autophagy core, autophagy transcription factors, mitophagy, docking and fusion, lysosome and lysosome-related genes. We then classified such genes in sub-groups, based on their functions or on their sub-cellular localization. Moreover, we have curated two shorter sub-lists to predict the extent of autophagy activation and/or lysosomal biogenesis; we next validated the "induction list" by Real-time PCR in cell lines during fasting or MTOR inhibition, identifying ATG14, ATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets. We also demonstrated that our list of autophagy genes can be particularly useful during an effective RNA-sequencing analysis. Thus, we propose our lists as a useful toolbox for performing an informative and functionally-prognostic gene scan of autophagy steps.

DOI: https://doi.org/10.1038/s41419-021-04121-9
FEBS Lett. 2021 Nov 05.

Local and systemic effects of Interleukin-6 (IL-6) in inflammation and cancer.

Stefan Rose-John.

  Interleukin-6 (IL-6) is an inflammatory cytokine the level of which is highly elevated in most, if not all, inflammatory states. IL-6 triggers cell-type specific responses and acts on target cells via a specific Interleukin-6 receptor (IL-6R), which, together with IL-6, binds to and induces the dimerization of a second receptor subunit, gp130. IL-6 also binds to soluble IL-6R and this complex interacts with gp130, regardless of IL-6R expression. This allows cells that do not express IL-6R and would be otherwise insensitive to IL-6 to respond to it. We have generated a constitutively active version of gp130 by forced leucine-zipper mediated dimerization, named L-gp130. Once inserted into the Rosa26 locus of mice, L-gp130 can be activated in a cell-autonomous manner by crossing these mice with any Cre-recombinase transgenic mouse strain. Activation of gp130 in hepatocytes produced liver-specific effects such as the induction of acute phase proteins but it also had profound systemic effects on the immune system. Such local and systemic effects of Interleukin-6 will be reviewed.

Keywords:  Interleukin-6; cancer; inflammation; pancreatitis; trans-signaling

DOI:  https://doi.org/10.1002/1873-3468.14220
Nature. 2021 Nov 03.

MC3R links nutritional state to childhood growth and the timing of puberty.

Genes & Health Research Team

The state of somatic energy stores in metazoans is communicated to the brain, which regulates key aspects of behaviour, growth, nutrient partitioning and development1. The central melanocortin system acts through melanocortin 4 receptor (MC4R) to control appetite, food intake and energy expenditure2. Here we present evidence that MC3R regulates the timing of sexual maturation, the rate of linear growth and the accrual of lean mass, which are all energy-sensitive processes. We found that humans who carry loss-of-function mutations in MC3R, including a rare homozygote individual, have a later onset of puberty. Consistent with previous findings in mice, they also had reduced linear growth, lean mass and circulating levels of IGF1. Mice lacking Mc3r had delayed sexual maturation and an insensitivity of reproductive cycle length to nutritional perturbation. The expression of Mc3r is enriched in hypothalamic neurons that control reproduction and growth, and expression increases during postnatal development in a manner that is consistent with a role in the regulation of sexual maturation. These findings suggest a bifurcating model of nutrient sensing by the central melanocortin pathway with signalling through MC4R controlling the acquisition and retention of calories, whereas signalling through MC3R primarily regulates the disposition of calories into growth, lean mass and the timing of sexual maturation.

DOI: https://doi.org/10.1038/s41586-021-04088-9
Aging (Albany NY). 2021 Oct 29. 13(20): 23471-23516

Predicting physiological aging rates from a range of quantitative traits using machine learning.

Eric D Sun, Yong Qian, Richard Oppong, Thomas J Butler, Jesse Zhao, Brian H Chen, Toshiko Tanaka, Jian Kang, Carlo Sidore, Francesco Cucca, Stefania Bandinelli, Gonçalo R Abecasis, Myriam Gorospe, Luigi Ferrucci, David Schlessinger, Ilya Goldberg, Jun Ding.

  It is widely thought that individuals age at different rates. A method that measures "physiological age" or physiological aging rate independent of chronological age could therefore help elucidate mechanisms of aging and inform an individual's risk of morbidity and mortality. Here we present machine learning frameworks for inferring individual physiological age from a broad range of biochemical and physiological traits including blood phenotypes (e.g., high-density lipoprotein), cardiovascular functions (e.g., pulse wave velocity) and psychological traits (e.g., neuroticism) as main groups in two population cohorts SardiNIA (~6,100 participants) and InCHIANTI (~1,400 participants). The inferred physiological age was highly correlated with chronological age (R2 > 0.8). We further defined an individual's physiological aging rate (PAR) as the ratio of the predicted physiological age to the chronological age. Notably, PAR was a significant predictor of survival, indicating an effect of aging rate on mortality. Our trait-based PAR was correlated with DNA methylation-based epigenetic aging score (r = 0.6), suggesting that both scores capture a common aging process. PAR was also substantially heritable (h2~0.3), and a subsequent genome-wide association study of PAR identified significant associations with two genetic loci, one of which is implicated in telomerase activity. Our findings support PAR as a proxy for an underlying whole-body aging mechanism. PAR may thus be useful to evaluate the efficacy of treatments that target aging-related deficits and controllable epidemiological factors.

Keywords:  aging clock; machine learning; mortality; personalized medicine; physiological aging rate; quantitative trait

DOI:  https://doi.org/10.18632/aging.203660
Elife. 2021 Nov 02. pii: e65109. [Epub ahead of print]10

Mitochondrial respiration contributes to the interferon gamma response in antigen presenting cells.

Michael C Kiritsy, Katelyn McCann, Daniel Mott, Stephen M Holland, Samuel M Behar, Christopher M Sassetti, Andrew J Olive.

  The immunological synapse allows antigen presenting cells (APC) to convey a wide array of functionally distinct signals to T cells, which ultimately shape the immune response. The relative effect of stimulatory and inhibitory signals is influenced by the activation state of the APC, which is determined by an interplay between signal transduction and metabolic pathways. While pathways downstream of toll-like receptors rely on glycolytic metabolism for the proper expression of inflammatory mediators, little is known about the metabolic dependencies of other critical signals such as interferon gamma (IFNg). Using CRISPR-Cas9, we performed a series of genome-wide knockout screens in murine macrophages to identify the regulators of IFNg-inducible T cell stimulatory or inhibitory proteins MHCII, CD40, and PD-L1. Our multi-screen approach enabled us to identify novel pathways that control these functionally distinct markers. Further integration of these screening data implicated complex I of the mitochondrial respiratory chain in the expression of all three markers, and by extension the IFNg signaling pathway. We report that the IFNg response requires mitochondrial respiration, and APCs are unable to activate T cells upon genetic or chemical inhibition of complex I. These findings suggest a dichotomous metabolic dependency between IFNg and toll-like receptor signaling, implicating mitochondrial function as a fulcrum of innate immunity.

Keywords:  human; immunology; inflammation; mouse

DOI:  https://doi.org/10.7554/eLife.65109
Nat Commun. 2021 Nov 04. 12(1): 6396

Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.

Georgette Tanner, David R Westhead, Alastair Droop, Lucy F Stead.

Intratumour heterogeneity provides tumours with the ability to adapt and acquire treatment resistance. The development of more effective and personalised treatments for cancers, therefore, requires accurate characterisation of the clonal architecture of tumours, enabling evolutionary dynamics to be tracked. Many methods exist for achieving this from bulk tumour sequencing data, involving identifying mutations and performing subclonal deconvolution, but there is a lack of systematic benchmarking to inform researchers on which are most accurate, and how dataset characteristics impact performance. To address this, we use the most comprehensive tumour genome simulation tool available for such purposes to create 80 bulk tumour whole exome sequencing datasets of differing depths, tumour complexities, and purities, and use these to benchmark subclonal deconvolution pipelines. We conclude that i) tumour complexity does not impact accuracy, ii) increasing either purity or purity-corrected sequencing depth improves accuracy, and iii) the optimal pipeline consists of Mutect2, FACETS and PyClone-VI. We have made our benchmarking datasets publicly available for future use.

DOI: https://doi.org/10.1038/s41467-021-26698-7
J Mol Med (Berl). 2021 Nov 04.

Sympathetic nerve-adipocyte interactions in response to acute stress.

Gabryella S P Santos, Alinne C Costa, Caroline C Picoli, Beatriz G S Rocha, Sheu O Sulaiman, Debora C Radicchi, Mauro C X Pinto, Miguel L Batista, Jaime H Amorim, Vasco A C Azevedo, Rodrigo R Resende, Niels O S Câmara, Akiva Mintz, Alexander Birbrair.

  Psychological stress predisposes our body to several disorders. Understanding the cellular and molecular mechanisms involved in the physiological responses to psychological stress is essential for the success of therapeutic applications. New studies show, by using in vivo inducible Cre/loxP-mediated approaches in combination with pharmacological blockage, that sympathetic nerves, activated by psychological stress, induce brown adipocytes to produce IL-6. Strikingly, this cytokine promotes gluconeogenesis in hepatocytes, that results in the decline of tolerance to inflammatory organ damage. The comprehension arising from this research will be crucial for the handling of many inflammatory diseases. Here, we review recent advances in our comprehension of the sympathetic nerve-adipocyte axis in the tissue microenvironment.

Keywords:  Adipocytes; Hepatocytes; IL-6; Microenvironment; Sympathetic nerves

DOI:  https://doi.org/10.1007/s00109-021-02157-0
J Cachexia Sarcopenia Muscle. 2021 Nov 02.

Ameliorating cancer cachexia by inhibiting cancer cell release of Hsp70 and Hsp90 with omeprazole.

Zhelong Liu, Jian Xiong, Song Gao, Michael X Zhu, Kai Sun, Min Li, Guohua Zhang, Yi-Ping Li.

  BACKGROUND: Cancer cachexia, characterized by muscle and fat tissue wasting, is a major determinant of cancer-related mortality without established treatment. Recent animal data revealed that cancer cells induce muscle wasting by releasing Hsp70 and Hsp90 as surface proteins on extracellular vesicles (EVs). Here, we test a therapeutic strategy for ameliorating cancer cachexia by inhibiting the release of Hsp70 and Hsp90 using proton pump inhibitor omeprazole.METHODS: Omeprazole effect on Hsp70/90 release through EVs by Lewis lung carcinoma (LLC) cells in vitro, serum levels of Hsp70/90 and Hsp70/90-carrying EVs in LLC tumour-bearing mice, and LLC-induced muscle protein degradation pathways in C2C12 myotubes and mice were determined. Omeprazole effect on endolysosomal pH and Rab27b expression in LLC cells were analysed.
RESULTS: Omeprazole treatment of LLC cells inhibited Hsp70/90 and Hsp70/90-carrying EV release in a dose-dependent manner (1 to 10 μM) and attenuated the catabolic activity of LLC cell-conditioned medium on C2C12 myotubes. Systemic omeprazole administration to LLC tumour-bearing mice (5 mg/kg/day subcutaneously) for 2 weeks blocked elevation of serum Hsp70, Hsp90, and Hsp70/90-carrying EVs, abrogated skeletal muscle catabolism, and prevented loss of muscle function as well as muscle and epididymal fat mass without altering tumour growth. Consequently, median survival increased by 23.3%. Mechanistically, omeprazole increased cancer cell endolysosomal pH level dose-dependently (0.1 to 1 μM) by inhibiting vacuolar H+ -ATPase. Further, omeprazole suppressed the highly elevated expression of Rab27b, a key regulator of EV release, in LLC cells.
CONCLUSIONS: Omeprazole ameliorates cancer cachexia by inhibiting cancer cell release of Hsp70 and Hsp90.

Keywords:  Fat tissue wasting; Hsp70; Hsp90; Lewis lung carcinoma; Muscle wasting; Rab27b; Vacuolar H+-ATPase

DOI:  https://doi.org/10.1002/jcsm.12851
BMC Cancer. 2021 Nov 03. 21(1): 1176

Nanoliposomal irinotecan plus fluorouracil and folinic acid as a second-line treatment option in patients with metastatic pancreatic ductal adenocarcinoma: a retrospective cohort study.

Se Jun Park, Hyunho Kim, Kabsoo Shin, Tae Ho Hong, Ja Hee Suh, Myung Ah Lee.

  BACKGROUND: According to the NAPOLI-1 trial, nanoliposomal irinotecan (nal-IRI) plus fluorouracil/folinic acid (5-FU/LV) showed improved overall survival compared to fluorouracil alone for patients with metastatic pancreatic cancer who were previously treated with gemcitabine-based therapy. In that trial, Asian patients had frequent dose modification due to haematological toxicity. There has been limited information on the clinical benefits and toxicity of this regimen in real-world settings. In this study, we assessed real-world experience of nal-IRI plus 5-FU/LV in patients with advanced pancreatic cancer after gemcitabine failure.METHODS: We conducted a single institution, retrospective analysis of response, survival and safety in patients who had been treated with nal-IRI with 5-FU/LV. Patients with metastatic pancreatic ductal adenocarcinoma previously treated with gemcitabine-based therapy received nal-IRI (80 mg/m2) with 5-FU/LV every 2 weeks. Kaplan-Meier analysis was performed to obtain median progression free survival and median overall survival. The hazard ratio and 95% confidence interval (CI) were estimated using a stratified Cox regression model. A multivariate Cox proportional hazards regression model was used to identify the effects of clinical factors.
RESULTS: Fifty-one patients received nal-IRI plus 5-FU/LV between January 2015 and December 2020. The median age was 67 years, and males were 58.8%. A total of 40 (78.4%) and 11 (21.6%) patients had received one and two lines of prior chemotherapy before enrollment, respectively. Median progression-free survival was 2.8 months (95% CI 1.8-3.7) and median overall survival was 7.0 months (95% CI 6.0-7.9). Chemotherapy doses were reduced or delayed in 33 (64.7%) patients during the first 6 weeks and median relative dose intensity was 0.87. Thirty-six (70.6%) patients experienced grade 3 or 4 adverse events, most commonly neutropenia (58.8%). Most non-haematologic adverse events were under grade 2. Since the start of first-line chemotherapy, median overall survival was 16.3 months (95% CI 14.1-18.4).
CONCLUSIONS: Nal-IRI plus 5-FU/LV seems to be effective, with manageable toxicities, following gemcitabine-based treatment in patients with metastatic pancreatic ductal adenocarcinoma. Nal-IRI plus 5-FU/LV following gemcitabine with nab-paclitaxel is a feasible sequential treatment option in patients with metastatic pancreatic cancer.
TRIAL REGISTRATION: Retrospectively registered.

Keywords:  Gemcitabine-refractory; Liposomal irinotecan; Pancreatic cancer; Second-line treatment

DOI:  https://doi.org/10.1186/s12885-021-08887-1
Biochem Biophys Res Commun. 2021 Oct 27. pii: S0006-291X(21)01464-9. [Epub ahead of print]583 29-34

An improved macromolecular crowding sensor CRONOS for detection of crowding changes in membrane-less organelles under stressed conditions.

Tamami Miyagi, Yoshiaki Yamanaka, Yuichiro Harada, Satoshi Narumi, Yuhei Hayamizu, Masahiko Kuroda, Kohsuke Kanekura.

  Membrane-less organelles (MLOs) formed by liquid-liquid phase separation (LLPS) play pivotal roles in biological processes. During LLPS, proteins and nucleotides are extremely condensed, resulting in changes in their conformation and biological functions. Disturbed LLPS homeostasis in MLOs is thought to associate with fatal diseases such as amyotrophic lateral sclerosis. Therefore, it is important to detect changes in the degree of crowding in MLOs. However, it has not been investigated well due to the lack of an appropriate method. To address this, we developed a genetically encoded macromolecular crowding sensor CRONOS (crowding sensor with mNeonGreen and mScarlet-I) that senses the degree of macromolecular crowding in MLOs using a fluorescence resonance energy transfer (FRET) system. CRONOS is a bright biosensor with a wide dynamic range and successfully detects changes in the macromolecular volume fraction in solution. By fusing to the scaffold protein of each MLO, we delivered CRONOS to MLO of interest and detected previously undescribed differences in the degree of crowding in each MLO. CRONOS also detected changes in the degree of macromolecular crowding in nucleolus induced by environmental stress or inhibition of transcription. These findings suggest that CRONOS can be a useful tool for the determination of molecular crowding and detection of pathological changes in MLOs in live cells.

Keywords:  FRET; Liquid-liquid phase separation (LLPS); Macromolecular crowding; Membrane-less organelle (MLO); Protein-based biosensor

DOI:  https://doi.org/10.1016/j.bbrc.2021.10.055
Cell Rep Methods. 2021 Sep 27. pii: 100061. [Epub ahead of print]1(5):

Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution.

Kyung Lock Kim, Peter van Galen, Volker Hovestadt, Gilbert J Rahme, Ekaterina N Andreishcheva, Abhijeet Shinde, Elizabeth Gaskell, Daniel R Jones, Efrat Shema, Bradley E Bernstein.

Epigenetic modifications control the stability and translation of mRNA molecules. Here, we present a microscopy-based platform for quantifying modified RNA molecules and for relating the modification patterns to single-cell phenotypes. We directly capture mRNAs from cell lysates on oligo-dT-coated coverslips, then visually detect and sequence individual m6A-immunolabled transcripts without amplification. Integration of a nanoscale device enabled us to isolate single cells on the platform, and thereby relate single-cell m6A modification states to gene expression signatures and cell surface markers. Application of the platform to MUTZ3 leukemia cells revealed a marked reduction in cellular m6A levels as CD34+ leukemic progenitors differentiate to CD14+ myeloid cells. We then coupled single-molecule m6A detection with fluorescence in situ hybridization (FISH) to relate mRNA and m6A levels of individual genes to single-cell phenotypes. This single-cell multi-modal assay suite can empower investigations of RNA modifications in rare populations and single cells.

DOI: https://doi.org/10.1016/j.crmeth.2021.100061
Nat Commun. 2021 Nov 02. 12(1): 6309

Molecular programs of fibrotic change in aging human lung.

Seoyeon Lee, Mohammad Naimul Islam, Kaveh Boostanpour, Dvir Aran, Guangchun Jin, Stephanie Christenson, Michael A Matthay, Walter L Eckalbar, Daryle J DePianto, Joseph R Arron, Liam Magee, Sunita Bhattacharya, Rei Matsumoto, Masaru Kubota, Donna L Farber, Jahar Bhattacharya, Paul J Wolters, Mallar Bhattacharya.

Lung fibrosis is increasingly detected with aging and has been associated with poor outcomes in acute lung injury or infection. However, the molecular programs driving this pro-fibrotic evolution are unclear. Here we profile distal lung samples from healthy human donors across the lifespan. Gene expression profiling by bulk RNAseq reveals both increasing cellular senescence and pro-fibrotic pathway activation with age. Quantitation of telomere length shows progressive shortening with age, which is associated with DNA damage foci and cellular senescence. Cell type deconvolution analysis of the RNAseq data indicates a progressive loss of lung epithelial cells and an increasing proportion of fibroblasts with age. Consistent with this pro-fibrotic profile, second harmonic imaging of aged lungs demonstrates increased density of interstitial collagen as well as decreased alveolar expansion and surfactant secretion. In this work, we reveal the transcriptional and structural features of fibrosis and associated functional impairment in normal lung aging.

DOI: https://doi.org/10.1038/s41467-021-26603-2
Nutr Metab (Lond). 2021 Nov 01. 18(1): 98

L-carnitine ameliorates the muscle wasting of cancer cachexia through the AKT/FOXO3a/MaFbx axis.

Changpeng Wu, Mingxing Zhu, Zongliang Lu, Yaowen Zhang, Long Li, Na Li, Liangyu Yin, He Wang, Wei Song, Hongxia Xu.

  BACKGROUND: Recent studies suggest potential benefits of applying L-carnitine in the treatment of cancer cachexia, but the precise mechanisms underlying these benefits remain unknown. This study was conducted to determine the mechanism by which L-carnitine reduces cancer cachexia.METHODS: C2C12 cells were differentiated into myotubes by growing them in DMEM for 24 h (hrs) and then changing the media to DMEM supplemented with 2% horse serum. Differentiated myotubes were treated for 2 h with TNF-α to establish a muscle atrophy cell model. After treated with L-carnitine, protein expression of MuRF1, MaFbx, FOXO3, p-FOXO3a, Akt, p-Akt, p70S6K and p-p70S6K was determined by Western blotting. Then siRNA-Akt was used to determine that L-carnitine ameliorated cancer cachexia via the Akt/FOXO3/MaFbx. In vivo, the cancer cachexia model was established by subcutaneously transplanting CT26 cells into the left flanks of the BALB/c nude mice. After treated with L-carnitine, serum levels of IL-1, IL-6 and TNF-α, and the skeletal muscle content of MuRF1, MaFbx, FOXO3, p-FOXO3a, Akt, p-Akt, p70S6K and p-p70S6K were measured.
RESULTS: L-carnitine increased the gastrocnemius muscle (GM) weight in the CT26-bearing cachexia mouse model and the cross-sectional fiber area of the GM and myotube diameters of C2C12 cells treated with TNF-α. Additionally, L-carnitine reduced the protein expression of MuRF1, MaFbx and FOXO3a, and increased the p-FOXO3a level in vivo and in vitro. Inhibition of Akt, upstream of FOXO3a, reversed the effects of L-carnitine on the FOXO3a/MaFbx pathway and myotube diameters, without affecting FOXO3a/MuRF-1. In addition to regulating the ubiquitination of muscle proteins, L-carnitine also increased the levels of p-p70S6K and p70S6K, which are involved in protein synthesis. Akt inhibition did not reverse the effects of L-carnitine on p70S6K and p-p70S6K. Hence, L-carnitine ameliorated cancer cachexia via the Akt/FOXO3/MaFbx and p70S6K pathways. Moreover, L-carnitine reduced the serum levels of IL-1 and IL-6, factors known to induce cancer cachexia. However, there were minimal effects on TNF-α, another inducer of cachexia, in the in vivo model.
CONCLUSION: These results revealed a novel mechanism by which L-carnitine protects muscle cells and reduces inflammation related to cancer cachexia.

Keywords:  AKT; C2C12 cells; Cancer cachexia; Colon-26; FOXO3a; L-carnitine; Muscle atrophy; p70S6K

DOI:  https://doi.org/10.1186/s12986-021-00623-7
Ageing Res Rev. 2021 Nov 01. pii: S1568-1637(21)00254-3. [Epub ahead of print] 101507

Stress and Telomere Shortening: Insights from Cellular Mechanisms.

Jue Lin, Elissa Epel.

  Short telomeres confer risk of degenerative diseases. Chronic psychological stress can lead to disease through many pathways, and research from in vitro studies to human longitudinal studies has pointed to stress-induced telomere damage as an important pathway. However, there has not been a comprehensive model to describe how changes in stress physiology and neuroendocrine pathways can lead to changes in telomere biology. Critically short telomeres or the collapse of the telomere structure caused by displacement of telomere binding protein complex shelterin elicit a DNA damage response and lead to senescence or apoptosis. In this narrative review, we summarize the key roles glucocorticoids, reactive oxygen species (ROS) and mitochondria, and inflammation play in mediating the relationship between psychological stress and telomere maintenance. We emphasis that these mediators are inter-connected and reinforce each other in positive feedback loops. Telomere length has not been studied across the lifespan yet, but the initial setting point at birth appears to be the most influential point, as it sets the lifetime trajectory, and is influenced by stress. We describe two types of intergenerational stress effects on telomeres - prenatal stress effects on telomeres during fetal development, and 'telotype transmission" -the directly inherited transmission of short telomeres from parental germline. It is clear that the initial simplistic view of telomere length as a mitotic clock has evolved into a far more complex picture of both transgenerational telomere influences, and of interconnected molecular and cellular pathways and networks, as hallmarks of aging where telomere maintenance is a key player interacting with mitochondria. Further mechanistic investigations, testing this comprehensive model of stress mediators shaping telomere biology and the telomere-mitochondrial nexus will lead to better understanding from cell to human lifespan aging, and could lead to anti-aging interventions.

Keywords:  glucocorticoid; inflammation; reactive oxidative species; shelterin complex; stress; telomerase; telomeres

DOI:  https://doi.org/10.1016/j.arr.2021.101507
FASEB J. 2021 Dec;35(12): e22010

Mitochondrial NDUFA4L2 is a novel regulator of skeletal muscle mass and force.

Zhengye Liu, Thomas Chaillou, Estela Santos Alves, Theresa Mader, Baptiste Jude, Duarte M S Ferreira, Heidi Hynynen, Arthur J Cheng, William O Jonsson, Gianluigi Pironti, Daniel C Andersson, Ellinor Kenne, Jorge L Ruas, Pasi Tavi, Johanna T Lanner.

  The hypoxia-inducible nuclear-encoded mitochondrial protein NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 (NDUFA4L2) has been demonstrated to decrease oxidative phosphorylation and production of reactive oxygen species in neonatal cardiomyocytes, brain tissue and hypoxic domains of cancer cells. Prolonged local hypoxia can negatively affect skeletal muscle size and tissue oxidative capacity. Although skeletal muscle is a mitochondrial rich, oxygen sensitive tissue, the role of NDUFA4L2 in skeletal muscle has not previously been investigated. Here we ectopically expressed NDUFA4L2 in mouse skeletal muscles using adenovirus-mediated expression and in vivo electroporation. Moreover, femoral artery ligation (FAL) was used as a model of peripheral vascular disease to induce hind limb ischemia and muscle damage. Ectopic NDUFA4L2 expression resulted in reduced mitochondrial respiration and reactive oxygen species followed by lowered AMP, ADP, ATP, and NAD+ levels without affecting the overall protein content of the mitochondrial electron transport chain. Furthermore, ectopically expressed NDUFA4L2 caused a ~20% reduction in muscle mass that resulted in weaker muscles. The loss of muscle mass was associated with increased gene expression of atrogenes MurF1 and Mul1, and apoptotic genes caspase 3 and Bax. Finally, we showed that NDUFA4L2 was induced by FAL and that the Ndufa4l2 mRNA expression correlated with the reduced capacity of the muscle to generate force after the ischemic insult. These results show, for the first time, that mitochondrial NDUFA4L2 is a novel regulator of skeletal muscle mass and force. Specifically, induced NDUFA4L2 reduces mitochondrial activity leading to lower levels of important intramuscular metabolites, including adenine nucleotides and NAD+ , which are hallmarks of mitochondrial dysfunction and hence shows that dysfunctional mitochondrial activity may drive muscle wasting.

Keywords:  NDUFA4L2; mitochondria; muscle mass; skeletal muscle

DOI:  https://doi.org/10.1096/fj.202100066R
J Cell Biochem. 2021 Nov 06.

BAG3 induces fibroblasts to release key cytokines involved in pancreatic cell migration.

Beatrice Dufrusine, Verena Damiani, Emily Capone, Damiana Pieragostino, Enrico Dainese, Margot De Marco, Francesca Reppucci, Maria C Turco, Alessandra Rosati, Liberato Marzullo, Gianluca Sala, Michele Sallese, Vincenzo De Laurenzi.

  Pancreatic ductal adenoma carcinoma (PDAC) is considered one of the deadliest solid cancers as it is usually diagnosed in advanced stages and has a poor response to treatment. The enormous effort made in the last 2 decades in the oncology field has not led to significant progress in improving early diagnosis or therapy for PDAC. The stroma of PDAC plays an active role in tumour initiation and progression and includes immune cells and stromal cells. We previously reported that Bcl2-associated athanogene (BAG3) secreted by PDAC cells activates tumour-associated macrophages to promote tumour growth. The disruption of this tumour-stroma axis by the anti-BAG3 H2L4 therapeutic antibody is sufficient to delay tumour growth and limit metastatic spreading in different PDAC preclinical models. In the present study, we examined the role of BAG3 to activate human fibroblasts (HF) in releasing cytokines capable of supporting tumour progression. Treatment of fibroblasts with recombinant BAG3 induced important changes in the organisation of the cytoskeleton of these cells and stimulated the production of interleukin-6, monocyte chemoattractant protein-1/C-C motif chemokine ligand 2, and hepatocyte growth factor. Specifically, we observed that BAG3 triggered a depolymerisation of microtubules at the periphery of the cell while they were conserved in the perinuclear area. Conversely, the vimentin-based intermediate filaments increased and spread to the edges of the cells. Finally, the conditioned medium (CM) collected from BAG3-treated HF promoted the survival, proliferation, and migration of the PDAC cells. Blocking of the PDAC-fibroblast axis by the H2L4 therapeutic anti-BAG3 antibody, resulted in inhibition of cytokine release and, consequently, the inhibition of the migratory phenotype conferred by the CM to PDAC cells.

Keywords:  BAG3; CCL2; HGF; cytokines; fibroblasts; pancreatic ductal adenoma carcinoma

DOI:  https://doi.org/10.1002/jcb.30172
Front Mol Biosci. 2021 ;8 757024

Application of Single-Cell Multi-Omics in Dissecting Cancer Cell Plasticity and Tumor Heterogeneity.

Deshen Pan, Deshui Jia.

  Tumor heterogeneity, a hallmark of cancer, impairs the efficacy of cancer therapy and drives tumor progression. Exploring inter- and intra-tumoral heterogeneity not only provides insights into tumor development and progression, but also guides the design of personalized therapies. Previously, high-throughput sequencing techniques have been used to investigate the heterogeneity of tumor ecosystems. However, they could not provide a high-resolution landscape of cellular components in tumor ecosystem. Recently, advance in single-cell technologies has provided an unprecedented resolution to uncover the intra-tumoral heterogeneity by profiling the transcriptomes, genomes, proteomes and epigenomes of the cellular components and also their spatial distribution, which greatly accelerated the process of basic and translational cancer research. Importantly, it has been demonstrated that some cancer cells are able to transit between different states in order to adapt to the changing tumor microenvironment, which led to increased cellular plasticity and tumor heterogeneity. Understanding the molecular mechanisms driving cancer cell plasticity is critical for developing precision therapies. In this review, we summarize the recent progress in dissecting the cancer cell plasticity and tumor heterogeneity by use of single-cell multi-omics techniques.

Keywords:  cellular plasticity; clone evolution; precision therapy; single-cell techniques; tumor heterogeneity

DOI:  https://doi.org/10.3389/fmolb.2021.757024
Nat Biotechnol. 2021 Nov 01.

Improved prediction of immune checkpoint blockade efficacy across multiple cancer types.

Diego Chowell, Seong-Keun Yoo, Cristina Valero, Alessandro Pastore, Chirag Krishna, Mark Lee, Douglas Hoen, Hongyu Shi, Daniel W Kelly, Neal Patel, Vladimir Makarov, Xiaoxiao Ma, Lynda Vuong, Erich Y Sabio, Kate Weiss, Fengshen Kuo, Tobias L Lenz, Robert M Samstein, Nadeem Riaz, Prasad S Adusumilli, Vinod P Balachandran, George Plitas, A Ari Hakimi, Omar Abdel-Wahab, Alexander N Shoushtari, Michael A Postow, Robert J Motzer, Marc Ladanyi, Ahmet Zehir, Michael F Berger, Mithat Gönen, Luc G T Morris, Nils Weinhold, Timothy A Chan.

Only a fraction of patients with cancer respond to immune checkpoint blockade (ICB) treatment, but current decision-making procedures have limited accuracy. In this study, we developed a machine learning model to predict ICB response by integrating genomic, molecular, demographic and clinical data from a comprehensively curated cohort (MSK-IMPACT) with 1,479 patients treated with ICB across 16 different cancer types. In a retrospective analysis, the model achieved high sensitivity and specificity in predicting clinical response to immunotherapy and predicted both overall survival and progression-free survival in the test data across different cancer types. Our model significantly outperformed predictions based on tumor mutational burden, which was recently approved by the U.S. Food and Drug Administration for this purpose1. Additionally, the model provides quantitative assessments of the model features that are most salient for the predictions. We anticipate that this approach will substantially improve clinical decision-making in immunotherapy and inform future interventions.

DOI: https://doi.org/10.1038/s41587-021-01070-8
Med Res Rev. 2021 Oct 31.

Lipidomic landscape in cancer: Actionable insights for membrane-based therapy and diagnoses.

Prema K Agarwala, Ritu Aneja, Shobhna Kapoor.

  Cancer cells display altered cellular lipid metabolism, including disruption in endogenous lipid synthesis, storage, and exogenous uptake for membrane biogenesis and functions. Altered lipid metabolism and, consequently, lipid composition impacts cellular function by affecting membrane structure and properties, such as fluidity, rigidity, membrane dynamics, and lateral organization. Herein, we provide an overview of lipid membranes and how their properties affect cellular functions. We also detail how the rewiring of lipid metabolism impacts the lipidomic landscape of cancer cell membranes and influences the characteristics of cancer cells. Furthermore, we discuss how the altered cancer lipidome provides cues for developing lipid-inspired innovative therapeutic and diagnostic strategies while improving our limited understanding of the role of lipids in cancer initiation and progression. We also present the arcade of membrane characterization techniques to cement their relevance in cancer diagnosis and monitoring of treatment response.

Keywords:  cancer; fluidity; lipid biomarkers; lipid membranes; lipid therapy; lipidomics

DOI:  https://doi.org/10.1002/med.21868
Nat Methods. 2021 Nov 04.

Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography.

C L Walsh, P Tafforeau, W L Wagner, D J Jafree, A Bellier, C Werlein, M P Kühnel, E Boller, S Walker-Samuel, J L Robertus, D A Long, J Jacob, S Marussi, E Brown, N Holroyd, D D Jonigk, M Ackermann, P D Lee.

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)'s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).

DOI: https://doi.org/10.1038/s41592-021-01317-x
Gut. 2021 Nov 03. pii: gutjnl-2021-325694. [Epub ahead of print]

Discovery of the pancreatic basal cell: a new candidate for an adult stem cell emerges.

Simone Benitz, Howard Crawford.



Keywords:  pancreatic cancer; pancreatitis

DOI:  https://doi.org/10.1136/gutjnl-2021-325694