bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023‒06‒18
43 papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.
  2. Autophagy fuels mitochondrial function through regulation of iron metabolism in pancreatic cancer.
  3. Autophagy in a Nutshell.
  4. KRAS-Dependency in Pancreatic Ductal Adenocarcinoma: Mechanisms of Escaping in Resistance to KRAS Inhibitors and Perspectives of Therapy.
  5. Hand grip strength in patients with advanced cancer: A prospective study.
  6. Pancreatic cancer epigenetics: adaptive metabolism reprograms starving primary tumors for widespread metastatic outgrowth.
  7. DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs.
  8. Cell protrusions and contractions generate long-range membrane tension propagation.
  9. Molecular Oncology and the EACR: new partners in communicating and supporting cancer research.
  10. The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity.
  11. Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response.
  12. Syk inhibition reprograms tumor-associated macrophages and overcomes gemcitabine-induced immunosuppression in pancreatic ductal adenocarcinoma.
  13. Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria.
  14. Species-Deconvolved Proteomics for In Situ Investigation of Tumor-Stroma Interactions after Treatment of Pancreatic Cancer Patient-Derived Xenografts with Combined Gemcitabine and Paclitaxel.
  15. RAS and Other Molecular Targets in Pancreatic Cancer: The Next Wave Is Coming.
  16. LC3B is lipidated to large lipid droplets during prolonged starvation for noncanonical autophagy.
  17. PHAF1/MYTHO is a novel autophagy regulator that controls muscle integrity.
  18. Nanosensor-based monitoring of autophagy-associated lysosomal acidification in vivo.
  19. Identification of a humanized mouse model for functional testing of immune-mediated biomaterial foreign body response.
  20. Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma.
  21. Clinical and genetic characteristics in pancreatic cancer from Chinese patients revealed by whole exome sequencing.
  22. Single-cell RNA sequencing revealed subclonal heterogeneity and gene signatures of gemcitabine sensitivity in pancreatic cancer.
  23. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector.
  24. Combining the antianginal drug perhexiline with chemotherapy induces complete pancreatic cancer regression in vivo.
  25. Forced and spontaneous symmetry breaking in cell polarization.
  26. Pancreatic Tissue Dissection to Isolate Viable Single Cells.
  27. MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma.
  28. Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution.
  29. Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity.
  30. Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells.
  31. Migration speed of captured breast cancer subpopulations correlates with metastatic fitness.
  32. The neuroscience of cancer.
  33. A locally activatable sensor for robust quantification of organellar glutathione.
  34. Targeted alveolar regeneration with Frizzled-specific agonists.
  35. The (social) lives, deaths, and biophysical phases of lipid droplets.
  36. Cells in the polyaneuploid cancer cell (PACC) state have increased metastatic potential.
  37. Live Biotherapeutic Products as Cancer Treatments.
  38. Ex vivo immunocapture and functional characterization of cell-type-specific mitochondria using MitoTag mice.
  39. Nascent Proteomics: Chemical Tools for Monitoring Newly Synthesized Proteins.
  40. PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
  41. Subcellular distribution of membrane lipids revealed by freeze-fracture electron microscopy.
  42. Identifying mechanisms of resistance by circulating tumour DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at time of PARP Inhibitor Progression.
  43. Cell shape characterization, alignment and comparison using FlowShape.
  1. Cell Metab. 2023 Jun 07. pii: S1550-4131(23)00185-7. [Epub ahead of print]
    Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia.
    Miriam Ferrer, Nicholas Mourikis, Emma E Davidson, Sam O Kleeman, Marta Zaccaria, Jill Habel, Rachel Rubino, Qing Gao, Thomas R Flint, Lisa Young, Claire M Connell, Michael J Lukey, Marcus D Goncalves, Eileen P White, Ashok R Venkitaraman, Tobias Janowitz.
      Glucose dependency of cancer cells can be targeted with a high-fat, low-carbohydrate ketogenic diet (KD). However, in IL-6-producing cancers, suppression of the hepatic ketogenic potential hinders the utilization of KD as energy for the organism. In IL-6-associated murine models of cancer cachexia, we describe delayed tumor growth but accelerated cachexia onset and shortened survival in mice fed KD. Mechanistically, this uncoupling is a consequence of the biochemical interaction of two NADPH-dependent pathways. Within the tumor, increased lipid peroxidation and, consequently, saturation of the glutathione (GSH) system lead to the ferroptotic death of cancer cells. Systemically, redox imbalance and NADPH depletion impair corticosterone biosynthesis. Administration of dexamethasone, a potent glucocorticoid, increases food intake, normalizes glucose levels and utilization of nutritional substrates, delays cachexia onset, and extends the survival of tumor-bearing mice fed KD while preserving reduced tumor growth. Our study emphasizes the need to investigate the effects of systemic interventions on both the tumor and the host to accurately assess therapeutic potential. These findings may be relevant to clinical research efforts that investigate nutritional interventions such as KD in patients with cancer.
    Keywords:  GDF-15; IL-6; NADPH; cachexia; cancer; corticosterone; ferroptosis; ketogenic diet; lipid peroxidation; steroid
    DOI:  https://doi.org/10.1016/j.cmet.2023.05.008
  2. Autophagy. 2023 Jun 13. 1-2
    Autophagy fuels mitochondrial function through regulation of iron metabolism in pancreatic cancer.
    Subhadip Mukhopadhyay, Joel Encarnacion-Rosado, Alec C Kimmelman.
      Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest 5-year survival rates of any cancer in the United States. Our previous work has shown that autophagy can promote PDAC progression. We recently established the importance of autophagy in regulating bioavailable iron to control mitochondrial metabolism in PDAC. We found that inhibition of autophagy in PDAC leads to mitochondrial dysfunction due to abrogation of succinate dehydrogenase complex iron sulfur subunit B (SDHB) expression. Additionally, we observed that cancer-associated fibroblasts (CAFs) can provide iron to autophagy-inhibited PDAC tumor cells, thereby increasing their resistance to autophagy inhibition. To impede such metabolic compensation, we used a low iron diet together with autophagy inhibition and demonstrated a significant improvement of tumor response in syngeneic PDAC models.Abbreviations: PDAC: Pancreatic ductal adenocarcinoma; CAFs: cancer-associated fibroblasts; SDHB: succinate dehydrogenase complex iron sulfur subunit B; ISCA1: iron sulfur cluster assembly protein 1; FPN: ferroportin; LIP: labile iron pool; FAC: ferric ammonium chloride; OCR: oxygen consumption rate; OXPHOS: oxidative phosphorylation, IL6: interleukin 6; Fe-S: iron sulfur; ATP: adenosine triphosphate.
    Keywords:  Autophagy; cancer associated fibroblasts; iron metabolism; lysosome; mitochondria; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.1080/15548627.2023.2223473
  3. FEBS Lett. 2023 Jun 16.
    Autophagy in a Nutshell.
    Oren Shatz, Zvulun Elazar.
      Autophagy is an intracellular catabolic process that eliminates cytoplasmic constituents selectively by tight engulfment in an isolation membrane or recycles bulk cytoplasm by nonselective sequestration. Completion of the isolation membrane forms a double membrane vesicle, termed autophagosome, that proceeds to fusion with the lysosome, where the inner membrane and its cytoplasmic content are degraded. Autophagosome biogenesis is unique in that the newly-formed membrane, termed phagophore, is elongated by direct lipid flow from a proximal ER-associated donor membrane. Recent years mark a tremendous advancement in delineating the direct regulation of this process by different lipid species and associated protein complexes. Here we schematically summarize the current view of autophagy and autophagosome biogenesis.
    Keywords:  PAS; autophagosome biogenesis; autophagy; lysosome; phagophore; vacuole
    DOI:  https://doi.org/10.1002/1873-3468.14679
  4. Int J Mol Sci. 2023 May 26. pii: 9313. [Epub ahead of print]24(11):
    KRAS-Dependency in Pancreatic Ductal Adenocarcinoma: Mechanisms of Escaping in Resistance to KRAS Inhibitors and Perspectives of Therapy.
    Enrico Gurreri, Giannicola Genovese, Luigi Perelli, Antonio Agostini, Geny Piro, Carmine Carbone, Giampaolo Tortora.
      Pancreatic ductal adenocarcinoma (PDAC) is still one of the deadliest cancers in oncology because of its increasing incidence and poor survival rate. More than 90% of PDAC patients are KRAS mutated (KRASmu), with KRASG12D and KRASG12V being the most common mutations. Despite this critical role, its characteristics have made direct targeting of the RAS protein extremely difficult. KRAS regulates development, cell growth, epigenetically dysregulated differentiation, and survival in PDAC through activation of key downstream pathways, such as MAPK-ERK and PI3K-AKT-mammalian target of rapamycin (mTOR) signaling, in a KRAS-dependent manner. KRASmu induces the occurrence of acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN) and leads to an immunosuppressive tumor microenvironment (TME). In this context, the oncogenic mutation of KRAS induces an epigenetic program that leads to the initiation of PDAC. Several studies have identified multiple direct and indirect inhibitors of KRAS signaling. Therefore, KRAS dependency is so essential in KRASmu PDAC that cancer cells have secured several compensatory escape mechanisms to counteract the efficacy of KRAS inhibitors, such as activation of MEK/ERK signaling or YAP1 upregulation. This review will provide insights into KRAS dependency in PDAC and analyze recent data on inhibitors of KRAS signaling, focusing on how cancer cells establish compensatory escape mechanisms.
    Keywords:  KRAS; KRAS inhibitors; KRAS-dependency; escaping; pancreatic cancer; resistance
    DOI:  https://doi.org/10.3390/ijms24119313
  5. J Cachexia Sarcopenia Muscle. 2023 Jun 15.
    Hand grip strength in patients with advanced cancer: A prospective study.
    Sara Hadzibegovic, Jan Porthun, Alessia Lena, Pia Weinländer, Laura C Lück, Sophia K Potthoff, Lukas Rösnick, Ann-Kathrin Fröhlich, Luisa Valentina Ramer, Frederike Sonntag, Ursula Wilkenshoff, Johann Ahn, Ulrich Keller, Lars Bullinger, Amir A Mahabadi, Matthias Totzeck, Tienush Rassaf, Stephan von Haehling, Andrew J S Coats, Stefan D Anker, Eric J Roeland, Ulf Landmesser, Markus S Anker.
      BACKGROUND: Hand grip strength (HGS) is a widely used functional test for the assessment of strength and functional status in patients with cancer, in particular with cancer cachexia. The aim was to prospectively evaluate the prognostic value of HGS in patients with mostly advanced cancer with and without cachexia and to establish reference values for a European-based population.METHODS: In this prospective study, 333 patients with cancer (85% stage III/IV) and 65 healthy controls of similar age and sex were enrolled. None of the study participants had significant cardiovascular disease or active infection at baseline. Repetitive HGS assessment was performed using a hand dynamometer to measure the maximal HGS (kilograms). Presence of cancer cachexia was defined when patients had ≥5% weight loss within 6 months or when body mass index was <20.0 kg/m2 with ≥2% weight loss (Fearon's criteria). Cox proportional hazard analyses were performed to assess the relationship of maximal HGS to all-cause mortality and to determine cut-offs for HGS with the best predictive power. We also assessed associations with additional relevant clinical and functional outcome measures at baseline, including anthropometric measures, physical function (Karnofsky Performance Status and Eastern Cooperative of Oncology Group), physical activity (4-m gait speed test and 6-min walk test), patient-reported outcomes (EQ-5D-5L and Visual Analogue Scale appetite/pain) and nutrition status (Mini Nutritional Assessment).
    RESULTS: The mean age was 60 ± 14 years; 163 (51%) were female, and 148 (44%) had cachexia at baseline. Patients with cancer showed 18% lower HGS than healthy controls (31.2 ± 11.9 vs. 37.9 ± 11.6 kg, P < 0.001). Patients with cancer cachexia had 16% lower HGS than those without cachexia (28.3 ± 10.1 vs. 33.6 ± 12.3 kg, P < 0.001). Patients with cancer were followed for a mean of 17 months (range 6-50), and 182 (55%) patients died during follow-up (2-year mortality rate 53%) (95% confidence interval 48-59%). Reduced maximal HGS was associated with increased mortality (per -5 kg; hazard ratio [HR] 1.19; 1.10-1.28; P < 0.0001; independently of age, sex, cancer stage, cancer entity and presence of cachexia). HGS was also a predictor of mortality in patients with cachexia (per -5 kg; HR 1.20; 1.08-1.33; P = 0.001) and without cachexia (per -5 kg; HR 1.18; 1.04-1.34; P = 0.010). The cut-off for maximal HGS with the best predictive power for poor survival was <25.1 kg for females (sensitivity 54%, specificity 63%) and <40.2 kg for males (sensitivity 69%, specificity 68%).
    CONCLUSIONS: Reduced maximal HGS was associated with higher all-cause mortality, reduced overall functional status and decreased physical performance in patients with mostly advanced cancer. Similar results were found for patients with and without cancer cachexia.
    Keywords:  cachexia; cancer; functional assessment; hand grip strength; methodology; prognostication
    DOI:  https://doi.org/10.1002/jcsm.13248
  6. Cancer Metastasis Rev. 2023 Jun 15.
    Pancreatic cancer epigenetics: adaptive metabolism reprograms starving primary tumors for widespread metastatic outgrowth.
    Arnaldo J Franco Torres, Jeffrey Duryea, Oliver G McDonald.
      Pancreatic cancer is a paradigm for adaptation to extreme stress. That is because genetic drivers are selected during tissue injury with epigenetic imprints encoding wound healing responses. Ironically, epigenetic memories of trauma that facilitate neoplasia can also recreate past stresses to restrain malignant progression through symbiotic tumor:stroma crosstalk. This is best exemplified by positive feedback between neoplastic chromatin outputs and fibroinflammatory stromal cues that encase malignant glands within a nutrient-deprived desmoplastic stroma. Because epigenetic imprints are chemically encoded by nutrient-derived metabolites bonded to chromatin, primary tumor metabolism adapts to preserve malignant epigenetic fidelity during starvation. Despite these adaptations, stromal stresses inevitably awaken primordial drives to seek more hospitable climates. The invasive migrations that ensue facilitate entry into the metastatic cascade. Metastatic routes present nutrient-replete reservoirs that accelerate malignant progression through adaptive metaboloepigenetics. This is best exemplified by positive feedback between biosynthetic enzymes and nutrient transporters that saturate malignant chromatin with pro-metastatic metabolite byproducts. Here we present a contemporary view of pancreatic cancer epigenetics: selection of neoplastic chromatin under fibroinflammatory pressures, preservation of malignant chromatin during starvation stresses, and saturation of metastatic chromatin by nutritional excesses that fuel lethal metastasis.
    Keywords:  Cancer; Epigenetics; Metabolism; Metastasis; Pancreatic
    DOI:  https://doi.org/10.1007/s10555-023-10116-z
  7. Cell. 2023 Jun 09. pii: S0092-8674(23)00580-9. [Epub ahead of print]
    DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs.
    Hongshan Guo, Joanna A Vuille, Ben S Wittner, Emily M Lachtara, Yu Hou, Maoxuan Lin, Ting Zhao, Ayush T Raman, Hunter C Russell, Brittany A Reeves, Haley M Pleskow, Chin-Lee Wu, Andreas Gnirke, Alexander Meissner, Jason A Efstathiou, Richard J Lee, Mehmet Toner, Martin J Aryee, Michael S Lawrence, David T Miyamoto, Shyamala Maheswaran, Daniel A Haber.
      Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells and four IFI16-related interferon-inducible genes implicated in innate immunity. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs.
    Keywords:  CD1A; DNA hypomethylation; IFI16; NKT cells; circulating tumor cells; immune surveillance; lipid antigens; prostate cancer; single-cell sequencing; tumorigenesis
    DOI:  https://doi.org/10.1016/j.cell.2023.05.028
  8. Cell. 2023 Jun 05. pii: S0092-8674(23)00533-0. [Epub ahead of print]
    Cell protrusions and contractions generate long-range membrane tension propagation.
    Henry De Belly, Shannon Yan, Hudson Borja da Rocha, Sacha Ichbiah, Jason P Town, Patrick J Zager, Dorothy C Estrada, Kirstin Meyer, Hervé Turlier, Carlos Bustamante, Orion D Weiner.
      Membrane tension is thought to be a long-range integrator of cell physiology. Membrane tension has been proposed to enable cell polarity during migration through front-back coordination and long-range protrusion competition. These roles necessitate effective tension transmission across the cell. However, conflicting observations have left the field divided as to whether cell membranes support or resist tension propagation. This discrepancy likely originates from the use of exogenous forces that may not accurately mimic endogenous forces. We overcome this complication by leveraging optogenetics to directly control localized actin-based protrusions or actomyosin contractions while simultaneously monitoring the propagation of membrane tension using dual-trap optical tweezers. Surprisingly, actin-driven protrusions and actomyosin contractions both elicit rapid global membrane tension propagation, whereas forces applied to cell membranes alone do not. We present a simple unifying mechanical model in which mechanical forces that engage the actin cortex drive rapid, robust membrane tension propagation through long-range membrane flows.
    Keywords:  actin cytoskeleton; actomyosin contractility; cell cortex; cell mechanics; cell migration; cell polarity; cell protrusion; membrane tension; optical tweezers; optogenetics
    DOI:  https://doi.org/10.1016/j.cell.2023.05.014
  9. Mol Oncol. 2023 Jun;17(6): 919-920
    Molecular Oncology and the EACR: new partners in communicating and supporting cancer research.
    Kevin M Ryan, Jane Smith, René Bernards.
      The formation of organisations and societies within all areas of scientific research facilitates the bringing together of researchers in a given field and serves to aid communication, collaboration, progress of science and career development. Even greater gain can be attained when individual organisations form partnerships to complement each other's activities and to increase the scope of their endeavours. Within this editorial, we highlight the key points of a new partnership formed between two non-profit bodies within cancer research, the European Association for Cancer Research (EACR) and Molecular Oncology, a journal wholly owned by the Federation of European Biochemical Societies (FEBS).
    DOI:  https://doi.org/10.1002/1878-0261.13445
  10. Cancer Cell. 2023 Jun 05. pii: S1535-6108(23)00181-2. [Epub ahead of print]
    The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity.
    Patricia Ho, Johannes C Melms, Meri Rogava, Chris J Frangieh, Joanna Poźniak, Shivem B Shah, Zachary Walsh, Oleksandr Kyrysyuk, Amit Dipak Amin, Lindsay Caprio, Benjamin T Fullerton, Rajesh Kumar Soni, Casey R Ager, Jana Biermann, Yiping Wang, Mohsen Khosravi-Maharlooei, Giorgia Zanetti, Michael Mu, Hijab Fatima, Emily K Moore, Neil Vasan, Samuel F Bakhoum, Steven L Reiner, Chantale Bernatchez, Megan Sykes, Emily M Mace, Kai W Wucherpfennig, Dirk Schadendorf, Oliver Bechter, Parin Shah, Gary K Schwartz, Jean-Christophe Marine, Benjamin Izar.
      The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.
    Keywords:  CD2; CD58; CRISPR-Cas9 screen; PDL1; balance of co-inhibitory/co-stimulator; cancer immune evasion; cancer immunology; cancer immunotherapy; immune checkpoint blockade; mass spec screen; resistance to immune checkpoint blockade; single-cell RNA-sequencing
    DOI:  https://doi.org/10.1016/j.ccell.2023.05.014
  11. EMBO J. 2023 Jun 12. e113349
    Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response.
    Ryo Ikeda, Daisuke Noshiro, Hideaki Morishita, Shuhei Takada, Shun Kageyama, Yuko Fujioka, Tomoko Funakoshi, Satoko Komatsu-Hirota, Ritsuko Arai, Elena Ryzhii, Manabu Abe, Tomoaki Koga, Hozumi Motohashi, Mitsuyoshi Nakao, Kenji Sakimura, Arata Horii, Satoshi Waguri, Yoshinobu Ichimura, Nobuo N Noda, Masaaki Komatsu.
      NRF2 is a transcription factor responsible for antioxidant stress responses that is usually regulated in a redox-dependent manner. p62 bodies formed by liquid-liquid phase separation contain Ser349-phosphorylated p62, which participates in the redox-independent activation of NRF2. However, the regulatory mechanism and physiological significance of p62 phosphorylation remain unclear. Here, we identify ULK1 as a kinase responsible for the phosphorylation of p62. ULK1 colocalizes with p62 bodies, directly interacting with p62. ULK1-dependent phosphorylation of p62 allows KEAP1 to be retained within p62 bodies, thus activating NRF2. p62S351E/+ mice are phosphomimetic knock-in mice in which Ser351, corresponding to human Ser349, is replaced by Glu. These mice, but not their phosphodefective p62S351A/S351A counterparts, exhibit NRF2 hyperactivation and growth retardation. This retardation is caused by malnutrition and dehydration due to obstruction of the esophagus and forestomach secondary to hyperkeratosis, a phenotype also observed in systemic Keap1-knockout mice. Our results expand our understanding of the physiological importance of the redox-independent NRF2 activation pathway and provide new insights into the role of phase separation in this process.
    Keywords:  KEAP1; NRF2/NFE2L2; ULK1; liquid-liquid phase separation; p62/SQSTM1
    DOI:  https://doi.org/10.15252/embj.2022113349
  12. Cancer Res. 2023 Jun 12. pii: CAN-22-3645. [Epub ahead of print]
    Syk inhibition reprograms tumor-associated macrophages and overcomes gemcitabine-induced immunosuppression in pancreatic ductal adenocarcinoma.
    Deepak Rohila, In Hwan Park, Timothy V Pham, Jonathan Weitz, Tatiana Hurtado de Mendoza, Suresh Madheswaran, Mehreen Ishfaq, Cooper Beaman, Elisabette Tapia, Siming Sun, Jay Patel, Pablo Tamayo, Andrew M Lowy, Shweta Joshi.
      Pancreatic ductal adenocarcinoma (PDAC) is an insidious disease with a low five-year survival rate. PDAC is characterized by infiltration of abundant tumor-associated macrophages (TAMs) that promote immune tolerance and immunotherapeutic resistance. Here we report that macrophage spleen tyrosine kinase (Syk) promotes PDAC growth and metastasis. In orthotopic PDAC mouse models, genetic deletion of myeloid Syk reprogrammed macrophages into immunostimulatory phenotype, increased the infiltration, proliferation, and cytotoxicity of CD8+ T cells, and repressed PDAC growth and metastasis. Furthermore, gemcitabine (Gem) treatment induced an immunosuppressive microenvironment in PDAC by promoting pro-tumorigenic polarization of macrophages. In contrast, treatment with the FDA-approved Syk inhibitor R788 (fostamatinib) remodeled the tumor immune microenvironment, "re-educated" pro-tumorigenic macrophages towards an immunostimulatory phenotype and boosted CD8+ T cell responses in Gem-treated PDAC in orthotopic mouse models and an ex vivo human pancreatic slice culture model. These findings illustrate the potential of Syk inhibition for enhancing the anti-tumor immune responses in PDAC and support the clinical evaluation of R788 either alone or together with Gem as a potential treatment strategy for PDAC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-3645
  13. Life Sci Alliance. 2023 Sep;pii: e202302127. [Epub ahead of print]6(9):
    Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria.
    Jun Yong Kim, Ilian Atanassov, Frederik Dethloff, Lara Kroczek, Thomas Langer.
      Mitochondrial dysfunction and cellular senescence are hallmarks of aging. However, the relationship between these two phenomena remains incompletely understood. In this study, we investigated the rewiring of mitochondria upon development of the senescent state in human IMR90 fibroblasts. Determining the bioenergetic activities and abundance of mitochondria, we demonstrate that senescent cells accumulate mitochondria with reduced OXPHOS activity, resulting in an overall increase of mitochondrial activities in senescent cells. Time-resolved proteomic analyses revealed extensive reprogramming of the mitochondrial proteome upon senescence development and allowed the identification of metabolic pathways that are rewired with different kinetics upon establishment of the senescent state. Among the early responding pathways, the degradation of branched-chain amino acid was increased, whereas the one carbon folate metabolism was decreased. Late-responding pathways include lipid metabolism and mitochondrial translation. These signatures were confirmed by metabolic flux analyses, highlighting metabolic rewiring as a central feature of mitochondria in cellular senescence. Together, our data provide a comprehensive view on the changes in mitochondrial proteome in senescent cells and reveal how the mitochondrial metabolism is rewired in senescent cells.
    DOI:  https://doi.org/10.26508/lsa.202302127
  14. J Proteome Res. 2023 Jun 13.
    Species-Deconvolved Proteomics for In Situ Investigation of Tumor-Stroma Interactions after Treatment of Pancreatic Cancer Patient-Derived Xenografts with Combined Gemcitabine and Paclitaxel.
    Xue Wang, Jin Niu, Shuo Qian, Shichen Shen, Robert M Straubinger, Jun Qu.
      Tumor-stroma interactions are critical in pancreatic ductal adenocarcinoma (PDAC) progression and therapeutics. Patient-derived xenograft (PDX) models recapitulate tumor-stroma interactions, but the conventional antibody-based immunoassay is inadequate to discriminate tumor and stromal proteins. Here, we describe a species-deconvolved proteomics approach embedded in IonStar that can unambiguously quantify the tumor (human-derived) and stromal (mouse-derived) proteins in PDX samples, enabling unbiased investigation of tumor and stromal proteomes with excellent quantitative reproducibility. With this strategy, we studied tumor-stroma interactions in PDAC PDXs that responded differently to Gemcitabine combined with nab-Paclitaxel (GEM+PTX) treatment. By analyzing 48 PDX animals 24 h/192 h after treatment with/without GEM+PTX, we quantified 7262 species-specific proteins under stringent cutoff criteria, with high reproducibility. For the PDX sensitive to GEM+PTX, the drug-dysregulated proteins in tumor cells were involved in suppressed oxidative phosphorylation and the TCA cycle, and in the stroma, inhibition of glycolytic activity was predominant, suggesting a relieved reverse Warburg effect by the treatment. In GEM+PTX-resistant PDXs, protein changes suggested extracellular matrix deposition and activation of tumor cell proliferation. Key findings were validated by immunohistochemistry (IHC). Overall, this approach provides a species-deconvolved proteomic platform that could advance cancer therapeutic studies by enabling unbiased exploration of tumor-stroma interactions in the large number of PDX samples required for such investigations.
    Keywords:  UHR-IonStar; pancreatic ductal adenocarcinoma; patient-derived xenografts; proteomics; reverse Warburg effect; species deconvolution; species-specific proteins
    DOI:  https://doi.org/10.1021/acs.jproteome.3c00164
  15. Curr Treat Options Oncol. 2023 Jun 10.
    RAS and Other Molecular Targets in Pancreatic Cancer: The Next Wave Is Coming.
    Lisa Miller-Phillips, Eric A Collisson.
      OPINION STATEMENT: Since the discovery of oncogenes in the 1970s, cancer doctors and researchers alike have understood the promise of discovering drugs to block the dominantly acting function of mutated signaling proteins in cancer. This promise was delivered, first slowly, with early signals inhibiting HER2 and BCR-Abl in the 1990s and 2000s, and then quickly, with kinase inhibitors being approved hand over fist in non-small cell lung cancer, melanoma, and many other malignancies. The RAS proteins, however, remained recalcitrant to chemical inhibition for decades, despite being, by far, the most frequently mutated oncogenes in cancers of all types. Nowhere was this deficit more palpable than in pancreatic ductal adenocarcinoma (PDA), where > 90% of cases are driven by single nucleotide substitutions at a single codon of the KRAS gene. The ice began to crack in 2012 when Ostrem and colleagues (Nature 503(7477): 548-551, 2013) synthesized the first KRAS G12C inhibitors, which covalently bind to GDP-bound G12C-mutated KRAS and lock the oncoprotein in its inactive state. In the last decade, the scientific community has established a new foundation on this and other druggable pockets in mutant KRAS. Here we provide an up-to-date overview of drugs targeting KRAS and other molecular targets in pancreatic cancer.
    Keywords:  KRAS; MAPK pathway; Pancreatic ductal adenocarcinoma; RAS; Target therapy
    DOI:  https://doi.org/10.1007/s11864-023-01096-x
  16. Dev Cell. 2023 Jun 08. pii: S1534-5807(23)00242-3. [Epub ahead of print]
    LC3B is lipidated to large lipid droplets during prolonged starvation for noncanonical autophagy.
    Mohyeddine Omrane, Kalthoum Ben M'Barek, Alexandre Santinho, Nathan Nguyen, Shanta Nag, Thomas J Melia, Abdou Rachid Thiam.
      Lipid droplets (LDs) store lipids that can be utilized during times of scarcity via autophagic and lysosomal pathways, but how LDs and autophagosomes interact remained unclear. Here, we discovered that the E2 autophagic enzyme, ATG3, localizes to the surface of certain ultra-large LDs in differentiated murine 3T3-L1 adipocytes or Huh7 human liver cells undergoing prolonged starvation. Subsequently, ATG3 lipidates microtubule-associated protein 1 light-chain 3B (LC3B) to these LDs. In vitro, ATG3 could bind alone to purified and artificial LDs to mediate this lipidation reaction. We observed that LC3B-lipidated LDs were consistently in close proximity to collections of LC3B-membranes and were lacking Plin1. This phenotype is distinct from macrolipophagy, but it required autophagy because it disappeared following ATG5 or Beclin1 knockout. Our data suggest that extended starvation triggers a noncanonical autophagy mechanism, similar to LC3B-associated phagocytosis, in which the surface of large LDs serves as an LC3B lipidation platform for autophagic processes.
    Keywords:  Atg3; LC3B; lipid droplets; noncanonical autophagy; organelle biogenesis; prolonged starvation
    DOI:  https://doi.org/10.1016/j.devcel.2023.05.009
  17. Autophagy. 2023 Jun 12. 1-3
    PHAF1/MYTHO is a novel autophagy regulator that controls muscle integrity.
    Anais Franco-Romero, Jean Philippe Leduc-Gaudet, Sabah Na Hussain, Gilles Gouspillou, Marco Sandri.
      Skeletal muscles play key roles in movement, posture, thermogenesis, and whole-body metabolism. Autophagy plays essential roles in the regulation of muscle mass, function and integrity. However, the molecular machinery that regulates autophagy is still incompletely understood. In our recent study, we identified and characterized a novel Forkhead Box O (FoxO)-dependent gene, PHAF1/MYTHO (phagophore assembly factor 1/macro-autophagy and youth optimizer), as a novel autophagy regulator that controls muscle integrity. MYTHO/PHAF1 is upregulated in multiple conditions leading to muscle atrophy, and downregulation of its expression spares muscle atrophy triggered by fasting, denervation, cachexia and sepsis. Overexpression of PHAF1/MYTHO is sufficient to induce muscle atrophy. Prolonged downregulation of PHAF1/MYTHO causes a severe myopathic phenotype, which is characterized by impaired autophagy, muscle weakness, myofiber degeneration, mammalian target of rapamycin complex 1 (mTORC1) hyperactivation and extensive ultrastructural defects, such as accumulation of proteinaceous and membranous structures and tubular aggregates. This myopathic phenotype is attenuated upon administration of the mTORC1 inhibitor rapamycin. These findings position PHAF1/MYTHO as a novel regulator of skeletal muscle autophagy and tissue integrity.
    Keywords:  FoxO; Myopathy; autophagy; mTOR; muscle atrophy; myotonic dystrophy type 1
    DOI:  https://doi.org/10.1080/15548627.2023.2224206
  18. Nat Chem Biol. 2023 Jun 15.
    Nanosensor-based monitoring of autophagy-associated lysosomal acidification in vivo.
    Mijin Kim, Chen Chen, Zvi Yaari, Rune Frederiksen, Ewelina Randall, Jaina Wollowitz, Christian Cupo, Xiaojian Wu, Janki Shah, Daniel Worroll, Rachel E Lagenbacher, Dana Goerzen, Yue-Ming Li, Heeseon An, YuHuang Wang, Daniel A Heller.
      Autophagy is a cellular process with important functions that drive neurodegenerative diseases and cancers. Lysosomal hyperacidification is a hallmark of autophagy. Lysosomal pH is currently measured by fluorescent probes in cell culture, but existing methods do not allow for quantitative, transient or in vivo measurements. In the present study, we developed near-infrared optical nanosensors using organic color centers (covalent sp3 defects on carbon nanotubes) to measure autophagy-mediated endolysosomal hyperacidification in live cells and in vivo. The nanosensors localize to the lysosomes, where the emission band shifts in response to local pH, enabling spatial, dynamic and quantitative mapping of subtle changes in lysosomal pH. Using the sensor, we observed cellular and intratumoral hyperacidification on administration of mTORC1 and V-ATPase modulators, revealing that lysosomal acidification mirrors the dynamics of S6K dephosphorylation and LC3B lipidation while diverging from p62 degradation. This sensor enables the transient and in vivo monitoring of the autophagy-lysosomal pathway.
    DOI:  https://doi.org/10.1038/s41589-023-01364-9
  19. Sci Adv. 2023 Jun 16. 9(24): eade9488
    Identification of a humanized mouse model for functional testing of immune-mediated biomaterial foreign body response.
    Joshua C Doloff, Minglin Ma, Atieh Sadraei, Hok Hei Tam, Shady Farah, Jennifer Hollister-Lock, Arturo J Vegas, Omid Veiseh, Victor M Quiroz, Amanda Rakoski, Stephanie Aresta-DaSilva, Andrew R Bader, Marissa Griffin, Gordon C Weir, Michael A Brehm, Leonard D Shultz, Robert Langer, Dale L Greiner, Daniel G Anderson.
      Biomedical devices comprise a major component of modern medicine, however immune-mediated fibrosis and rejection can limit their function over time. Here, we describe a humanized mouse model that recapitulates fibrosis following biomaterial implantation. Cellular and cytokine responses to multiple biomaterials were evaluated across different implant sites. Human innate immune macrophages were verified as essential to biomaterial rejection in this model and were capable of cross-talk with mouse fibroblasts for collagen matrix deposition. Cytokine and cytokine receptor array analysis confirmed core signaling in the fibrotic cascade. Foreign body giant cell formation, often unobserved in mice, was also prominent. Last, high-resolution microscopy coupled with multiplexed antibody capture digital profiling analysis supplied spatial resolution of rejection responses. This model enables the study of human immune cell-mediated fibrosis and interactions with implanted biomaterials and devices.
    DOI:  https://doi.org/10.1126/sciadv.ade9488
  20. Nat Commun. 2023 Jun 13. 14(1): 3459
    Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma.
    Charlie Saillard, Flore Delecourt, Benoit Schmauch, Olivier Moindrot, Magali Svrcek, Armelle Bardier-Dupas, Jean Francois Emile, Mira Ayadi, Vinciane Rebours, Louis de Mestier, Pascal Hammel, Cindy Neuzillet, Jean Baptiste Bachet, Juan Iovanna, Nelson Dusetti, Yuna Blum, Magali Richard, Yasmina Kermezli, Valerie Paradis, Mikhail Zaslavskiy, Pierre Courtiol, Aurelie Kamoun, Remy Nicolle, Jerome Cros.
      Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic and theragnostic implications have been described. These molecular subtypes were defined by RNAseq, a costly technique sensitive to sample quality and cellularity, not used in routine practice. To allow rapid PDAC molecular subtyping and study PDAC heterogeneity, we develop PACpAInt, a multi-step deep learning model. PACpAInt is trained on a multicentric cohort (n = 202) and validated on 4 independent cohorts including biopsies (surgical cohorts n = 148; 97; 126 / biopsy cohort n = 25), all with transcriptomic data (n = 598) to predict tumor tissue, tumor cells from stroma, and their transcriptomic molecular subtypes, either at the whole slide or tile level (112 µm squares). PACpAInt correctly predicts tumor subtypes at the whole slide level on surgical and biopsies specimens and independently predicts survival. PACpAInt highlights the presence of a minor aggressive Basal contingent that negatively impacts survival in 39% of RNA-defined classical cases. Tile-level analysis ( > 6 millions) redefines PDAC microheterogeneity showing codependencies in the distribution of tumor and stroma subtypes, and demonstrates that, in addition to the Classical and Basal tumors, there are Hybrid tumors that combine the latter subtypes, and Intermediate tumors that may represent a transition state during PDAC evolution.
    DOI:  https://doi.org/10.1038/s41467-023-39026-y
  21. Front Oncol. 2023 ;13 1167144
    Clinical and genetic characteristics in pancreatic cancer from Chinese patients revealed by whole exome sequencing.
    Yonggang He, Wen Huang, Yichen Tang, Yuming Li, Xuehui Peng, Jing Li, Jing Wu, Nan You, Ling Li, Chuang Liu, Lu Zheng, Xiaobing Huang.
      Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide, mostly as a result of the absence of early detection and specific treatment solutions. Consequently, identifying mutational profiles and molecular biomarkers is essential for increasing the viability of precision therapy for pancreatic cancer.Methods: We collected blood and tumor tissue samples from 47 Chinese pancreatic cancer patients and used whole-exome sequencing (WES) to evaluate the genetic landscape.
    Results: Our results showed the most frequently somatic alteration genes were KRAS (74.5%), TP53(51.1%), SMAD4 (17%), ARID1A (12.8%), CDKN2A (12.8%), TENM4 (10.6%), TTN (8.5%), RNF43(8.5%), FLG (8.5%) and GAS6 (6.4%) in Chinese PDAC patients. We also found that three deleterious germline mutations (ATM c.4852C>T/p. R1618*, WRN c.1105C>T/p. R369*, PALB2 c.2760dupA/p. Q921Tfs*7) and two novel fusions (BRCA1-RPRML, MIR943 (intergenic)-FGFR3). When compared to the Cancer Genome Atlas (TCGA) database, there is a greater mutation frequency of TENM4 (10.6% vs. 1.6%, p = 0.01), GAS6(6.4% vs. 0.5%, p = 0.035), MMP17(6.4% vs. 0.5%, p = 0.035), ITM2B (6.4% vs. 0.5%, p = 0.035) and USP7 (6.4% vs. 0.5%, p= 0.035) as well as a reduced mutation frequency of SMAD4 (17.0% vs. 31.5%, p = 0.075) and CDKN2A (12.8% vs. 47.3%, p < 0.001) were observed in the Chinese cohort. Among the 41 individuals examined for programmed cell death ligand 1(PD-L1) expression, 15 (36.6%) had positive PD-L1 expression. The median tumor mutational burden (TMB) was found to be 12muts (range, 0124). The TMB index was higher in patients with mutant-type KRAS MUT/TP53 MUT (p < 0.001), CDKN2A (p = 0.547), or SMAD4 (p = 0.064) compared to patients with wild-type KRAS/TP53, CDKN2A, or SMAD4.
    Conclusions: We exhibited real-world genetic traits and new alterations in Chinese individuals with cancer of the pancreas, which might have interesting implications for future individualized therapy and medication development.
    Keywords:  KRAS; PD-L1; TMB; gene mutation; pancreatic ductal adenocarcinoma (PDAC); whole-exome sequencing
    DOI:  https://doi.org/10.3389/fonc.2023.1167144
  22. Front Pharmacol. 2023 ;14 1193791
    Single-cell RNA sequencing revealed subclonal heterogeneity and gene signatures of gemcitabine sensitivity in pancreatic cancer.
    Zelin Hou, Jiajing Lin, Yuan Ma, Haizhong Fang, Yuwei Wu, Zhijiang Chen, Xianchao Lin, Fengchun Lu, Shi Wen, Xunbin Yu, Heguang Huang, Yu Pan.
      Introduction: Resistance to gemcitabine is common and critically limits its therapeutic efficacy in pancreatic ductal adenocarcinoma (PDAC). Methods: We constructed 17 patient-derived xenograft (PDX) models from PDAC patient samples and identified the most notable responder to gemcitabine by screening the PDX sets in vivo. To analyze tumor evolution and microenvironmental changes pre- and post-chemotherapy, single-cell RNA sequencing (scRNA-seq) was performed. Results: ScRNA-seq revealed that gemcitabine promoted the expansion of subclones associated with drug resistance and recruited macrophages related to tumor progression and metastasis. We further investigated the particular drug-resistant subclone and established a gemcitabine sensitivity gene panel (GSGP) (SLC46A1, PCSK1N, KRT7, CAV2, and LDHA), dividing PDAC patients into two groups to predict the overall survival (OS) in The Cancer Genome Atlas (TCGA) training dataset. The signature was successfully validated in three independent datasets. We also found that 5-GSGP predicted the sensitivity to gemcitabine in PDAC patients in the TCGA training dataset who were treated with gemcitabine. Discussion and conclusion: Our study provides new insight into the natural selection of tumor cell subclones and remodeling of tumor microenvironment (TME) cells induced by gemcitabine. We revealed a specific drug resistance subclone, and based on the characteristics of this subclone, we constructed a GSGP that can robustly predict gemcitabine sensitivity and prognosis in pancreatic cancer, which provides a theoretical basis for individualized clinical treatment.
    Keywords:  PDAC; gemcitabine; pancreatic cancer; pancreatic ductal adenocarcinoma; single-cell RNA sequencing; therapy resistance
    DOI:  https://doi.org/10.3389/fphar.2023.1193791
  23. Cell Rep Methods. 2023 May 22. 3(5): 100467
    Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector.
    Brian J Haas, Alexander Dobin, Mahmoud Ghandi, Anne Van Arsdale, Timothy Tickle, James T Robinson, Riaz Gillani, Simon Kasif, Aviv Regev.
      Here, we present FusionInspector for in silico characterization and interpretation of candidate fusion transcripts from RNA sequencing (RNA-seq) and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of tumor and normal transcriptomes and identified statistical and experimental features enriched among biologically impactful fusions. Through clustering and machine learning, we identified large collections of fusions potentially relevant to tumor and normal biological processes. We show that biologically relevant fusions are enriched for relatively high expression of the fusion transcript, imbalanced fusion allelic ratios, and canonical splicing patterns, and are deficient in sequence microhomologies between partner genes. We demonstrate that FusionInspector accurately validates fusion transcripts in silico and helps characterize numerous understudied fusions in tumor and normal tissue samples. FusionInspector is freely available as open source for screening, characterization, and visualization of candidate fusions via RNA-seq, and facilitates transparent explanation and interpretation of machine-learning predictions and their experimental sources.
    Keywords:  FusionInspector; RNA-seq; STAR-Fusion; Trinity; cancer; fusion
    DOI:  https://doi.org/10.1016/j.crmeth.2023.100467
  24. iScience. 2023 Jun 16. 26(6): 106899
    Combining the antianginal drug perhexiline with chemotherapy induces complete pancreatic cancer regression in vivo.
    Gabriela Reyes-Castellanos, Nadine Abdel Hadi, Scarlett Gallardo-Arriaga, Rawand Masoud, Julie Garcia, Sophie Lac, Abdessamad El Kaoutari, Tristan Gicquel, Mélanie Planque, Sarah-Maria Fendt, Laetitia Karine Linares, Odile Gayet, Fabienne Guillaumond, Nelson Dusetti, Juan Iovanna, Alice Carrier.
      Pancreatic ductal adenocarcinoma (PDAC) remains one of the human cancers with the poorest prognosis. Interestingly, we found that mitochondrial respiration in primary human PDAC cells depends mainly on the fatty acid oxidation (FAO) to meet basic energy requirements. Therefore, we treated PDAC cells with perhexiline, a well-recognized FAO inhibitor used in cardiac diseases. Some PDAC cells respond efficiently to perhexiline, which acts synergistically with chemotherapy (gemcitabine) in vitro and in two xenografts in vivo. Importantly, perhexiline in combination with gemcitabine induces complete tumor regression in one PDAC xenograft. Mechanistically, this co-treatment causes energy and oxidative stress promoting apoptosis but does not exert inhibition of FAO. Yet, our molecular analysis indicates that the carnitine palmitoyltransferase 1C (CPT1C) isoform is a key player in the response to perhexiline and that patients with high CPT1C expression have better prognosis. Our study reveals that repurposing perhexiline in combination with chemotherapy is a promising approach to treat PDAC.
    Keywords:  Biological sciences; Cancer; Cancer systems biology
    DOI:  https://doi.org/10.1016/j.isci.2023.106899
  25. Nat Comput Sci. 2022 Aug;2(8): 504-511
    Forced and spontaneous symmetry breaking in cell polarization.
    Pearson W Miller, Daniel Fortunato, Cyrill Muratov, Leslie Greengard, Stanislav Shvartsman.
      How does breaking the symmetry of an equation alter the symmetry of its solutions? Here, we systematically examine how reducing underlying symmetries from spherical to axisymmetric influences the dynamics of an archetypal model of cell polarization, a key process of biological spatial self-organization. Cell polarization is characterized by nonlinear and non-local dynamics, but we overcome the theory challenges these traits pose by introducing a broadly applicable numerical scheme allowing us to efficiently study continuum models in a wide range of geometries. Guided by numerical results, we discover a dynamical hierarchy of timescales that allows us to reduce relaxation to a purely geometric problem of area-preserving geodesic curvature flow. Through application of variational results, we analytically construct steady states on a number of biologically relevant shapes. In doing so, we reveal non-trivial solutions for symmetry breaking.
    DOI:  https://doi.org/10.1038/s43588-022-00295-0
  26. J Vis Exp. 2023 05 26.
    Pancreatic Tissue Dissection to Isolate Viable Single Cells.
    Oshri Yosefov-Levi, Sharona Tornovsky, Oren Parnas.
      The pancreas includes two major systems: the endocrine system, which produces and secretes hormones, and the exocrine system, which accounts for approximately 90% of the pancreas and includes cells that produce and secrete digestive enzymes. The digestive enzymes are produced in the pancreatic acinar cells, stored in vesicles called zymogens, and are then released into the duodenum via the pancreatic duct to initiate metabolic processes. The enzymes produced by the acinar cells can kill cells or degrade cell-free RNA. In addition, acinar cells are fragile, and common dissociation protocols result in a large number of dead cells and cell-free proteases and RNases. Therefore, one of the biggest challenges in pancreatic tissue digestion is recovering intact and viable cells, especially acinar cells. The protocol presented in this article shows a two-step method that we developed to meet this need. The protocol can be used to digest normal pancreata, pancreata that include pre-malignant lesions, or pancreatic tumors that include a large number of stromal and immune cells.
    DOI:  https://doi.org/10.3791/64871
  27. Cancer Cell. 2023 Jun 12. pii: S1535-6108(23)00182-4. [Epub ahead of print]
    MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma.
    Yu Qian, Ana Galan-Cobo, Irene Guijarro, Minghao Dang, David Molkentine, Alissa Poteete, Fahao Zhang, Qi Wang, Jing Wang, Edwin Parra, Apekshya Panda, Jacy Fang, Ferdinandos Skoulidis, Ignacio I Wistuba, Svena Verma, Taha Merghoub, Jedd D Wolchok, Kwok-Kin Wong, Ralph J DeBerardinis, John D Minna, Natalie I Vokes, Catherine B Meador, Justin F Gainor, Linghua Wang, Alexandre Reuben, John V Heymach.
      Inactivating STK11/LKB1 mutations are genomic drivers of primary resistance to immunotherapy in KRAS-mutated lung adenocarcinoma (LUAD), although the underlying mechanisms remain unelucidated. We find that LKB1 loss results in enhanced lactate production and secretion via the MCT4 transporter. Single-cell RNA profiling of murine models indicates that LKB1-deficient tumors have increased M2 macrophage polarization and hypofunctional T cells, effects that could be recapitulated by the addition of exogenous lactate and abrogated by MCT4 knockdown or therapeutic blockade of the lactate receptor GPR81 expressed on immune cells. Furthermore, MCT4 knockout reverses the resistance to PD-1 blockade induced by LKB1 loss in syngeneic murine models. Finally, tumors from STK11/LKB1 mutant LUAD patients demonstrate a similar phenotype of enhanced M2-macrophages polarization and hypofunctional T cells. These data provide evidence that lactate suppresses antitumor immunity and therapeutic targeting of this pathway is a promising strategy to reversing immunotherapy resistance in STK11/LKB1 mutant LUAD.
    Keywords:  LKB1; MCT4; PD-1; T cell activation; immunotherapy resistance; lactate; lung adenocarcinoma; macrophage polarization; metabolism
    DOI:  https://doi.org/10.1016/j.ccell.2023.05.015
  28. Science. 2023 Jun 16. 380(6650): eadg0934
    Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution.
    Tzu-Chiao Lu, Maria Brbić, Ye-Jin Park, Tyler Jackson, Jiaye Chen, Sai Saroja Kolluru, Yanyan Qi, Nadja Sandra Katheder, Xiaoyu Tracy Cai, Seungjae Lee, Yen-Chung Chen, Niccole Auld, Chung-Yi Liang, Sophia H Ding, Doug Welsch, Samuel D'Souza, Angela Oliveira Pisco, Robert C Jones, Jure Leskovec, Eric C Lai, Hugo J Bellen, Liqun Luo, Heinrich Jasper, Stephen R Quake, Hongjie Li.
      Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We characterized 163 distinct cell types and performed an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further developed aging clock models to predict fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find distinctive cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.
    DOI:  https://doi.org/10.1126/science.adg0934
  29. Cancer Cell. 2023 Jun 12. pii: S1535-6108(23)00176-9. [Epub ahead of print]41(6): 1170-1185.e12
    Taxanes trigger cancer cell killing in vivo by inducing non-canonical T cell cytotoxicity.
    Claire Vennin, Chiara M Cattaneo, Leontien Bosch, Serena Vegna, Xuhui Ma, Hugo G J Damstra, Moreno Martinovic, Efi Tsouri, Mila Ilic, Leyla Azarang, Jan R T van Weering, Emilia Pulver, Amber L Zeeman, Tim Schelfhorst, Jeroen O Lohuis, Anne C Rios, Johanna F Dekkers, Leila Akkari, Renee Menezes, Rene Medema, Serena R Baglio, Anna Akhmanova, Sabine C Linn, Simone Lemeer, Dirk M Pegtel, Emile E Voest, Jacco van Rheenen.
      Although treatment with taxanes does not always lead to clinical benefit, all patients are at risk of their detrimental side effects such as peripheral neuropathy. Understanding the in vivo mode of action of taxanes can help design improved treatment regimens. Here, we demonstrate that in vivo, taxanes directly trigger T cells to selectively kill cancer cells in a non-canonical, T cell receptor-independent manner. Mechanistically, taxanes induce T cells to release cytotoxic extracellular vesicles, which lead to apoptosis specifically in tumor cells while leaving healthy epithelial cells intact. We exploit these findings to develop an effective therapeutic approach, based on transfer of T cells pre-treated with taxanes ex vivo, thereby avoiding toxicity of systemic treatment. Our study reveals a different in vivo mode of action of one of the most commonly used chemotherapies, and opens avenues to harness T cell-dependent anti-tumor effects of taxanes while avoiding systemic toxicity.
    Keywords:  T cell therapy; T cells; extracellular vesicles; in vivo mode of action; taxanes
    DOI:  https://doi.org/10.1016/j.ccell.2023.05.009
  30. Proteomics. 2023 Jun 13. e2100314
    Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells.
    Sai V Chitti, Taeyoung Kang, Pamali Fonseka, Akbar L Marzan, Sarah Stewart, Sanjay Shahi, Kyle Bramich, Ching-Seng Ang, Mohashin Pathan, Sriram Gummadi, Suresh Mathivanan.
      Cancer cachexia is a wasting syndrome characterised by the loss of fat and/or muscle mass in advanced cancer patients. It has been well-established that cancer cells themselves can induce cachexia via the release of several pro-cachectic and pro-inflammatory factors. However, it is unclear how this process is regulated and the key cachexins that are involved. In this study, we validated C26 and EL4 as cachexic and non-cachexic cell models, respectively. Treatment of adipocytes and myotubes with C26 conditioned medium induced lipolysis and atrophy, respectively. We profiled soluble secreted proteins (secretome) as well as small extracellular vesicles (sEVs) released from cachexia-inducing (C26) and non-inducing (EL4) cancer cells by label-free quantitative proteomics. A total of 1268 and 1022 proteins were identified in the secretome of C26 and EL4, respectively. Furthermore, proteomic analysis of sEVs derived from C26 and EL4 cancer cells revealed a distinct difference in the protein cargo. Functional enrichment analysis using FunRich highlighted the enrichment of proteins that are implicated in biological processes such as muscle atrophy, lipolysis, and inflammation in both the secretome and sEVs derived from C26 cancer cells. Overall, our characterisation of the proteomic profiles of the secretory factors and sEVs from cachexia-inducing and non-inducing cancer cells provides insights into tumour factors that promote weight loss by mediating protein and lipid loss in various organs and tissues. Further investigation of these proteins may assist in highlighting potential therapeutic targets and biomarkers of cancer cachexia.
    Keywords:  cancer cachexia; lipolysis; muscle atrophy; secretory proteins; small extracellular vesicles
    DOI:  https://doi.org/10.1002/pmic.202100314
  31. J Cell Sci. 2023 Jun 14. pii: jcs.260835. [Epub ahead of print]
    Migration speed of captured breast cancer subpopulations correlates with metastatic fitness.
    Nicolas Desjardins-Lecavalier, Matthew G Annis, Alexander Nowakowski, Alexander Kiepas, Loïc Binan, Joannie Roy, Graziana Modica, Steven Hébert, Claudia L Kleinman, Peter M Siegel, Santiago Costantino.
      The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous breast cancer cell populations, based on their migratory ability alone. We show that captured fast cell subpopulations retain higher migration speed and focal adhesion dynamics over many generations due to a motility-related transcriptomic profile. Upregulated genes in fast selected cells encoded integrin subunits, proto-cadherins and numerous other genes associated with cell migration. Dysregulation of several of these genes correlated with poor survival outcomes in patients, while primary tumors established from fast cells generated a higher number of circulating tumor cells and soft tissue metastases in vivo. Subpopulations of cells selected for a highly migratory phenotype demonstrated an increased fitness for metastasis.
    Keywords:  Applied optics; Biophysics; Breast cancer; Cell migration; Metastasis; Microscopy; Photobleaching; Single-cell isolation
    DOI:  https://doi.org/10.1242/jcs.260835
  32. Nature. 2023 Jun;618(7965): 467-479
    The neuroscience of cancer.
    Rebecca Mancusi, Michelle Monje.
      The nervous system regulates tissue stem and precursor populations throughout life. Parallel to roles in development, the nervous system is emerging as a critical regulator of cancer, from oncogenesis to malignant growth and metastatic spread. Various preclinical models in a range of malignancies have demonstrated that nervous system activity can control cancer initiation and powerfully influence cancer progression and metastasis. Just as the nervous system can regulate cancer progression, cancer also remodels and hijacks nervous system structure and function. Interactions between the nervous system and cancer occur both in the local tumour microenvironment and systemically. Neurons and glial cells communicate directly with malignant cells in the tumour microenvironment through paracrine factors and, in some cases, through neuron-to-cancer cell synapses. Additionally, indirect interactions occur at a distance through circulating signals and through influences on immune cell trafficking and function. Such cross-talk among the nervous system, immune system and cancer-both systemically and in the local tumour microenvironment-regulates pro-tumour inflammation and anti-cancer immunity. Elucidating the neuroscience of cancer, which calls for interdisciplinary collaboration among the fields of neuroscience, developmental biology, immunology and cancer biology, may advance effective therapies for many of the most difficult to treat malignancies.
    DOI:  https://doi.org/10.1038/s41586-023-05968-y
  33. Nat Chem. 2023 Jun 15.
    A locally activatable sensor for robust quantification of organellar glutathione.
    Sarah Emmert, Gianluca Quargnali, Sebastian Thallmair, Pablo Rivera-Fuentes.
      Glutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signalling pathways. Achieving a detailed understanding of intracellular GSH homeostasis depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Here we present a GSH-sensing platform for live-cell imaging, termed targetable ratiometric quantitative GSH (TRaQ-G). This chemogenetic sensor possesses a unique reactivity turn-on mechanism, ensuring that the small molecule is only sensitive to GSH in a desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein to give a ratiometric response. Using TRaQ-G fused to a redox-insensitive fluorescent protein, we demonstrate that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. This sensor was used in combination with a redox-sensitive fluorescent protein to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor.
    DOI:  https://doi.org/10.1038/s41557-023-01249-3
  34. Cell. 2023 Jun 08. pii: S0092-8674(23)00541-X. [Epub ahead of print]
    Targeted alveolar regeneration with Frizzled-specific agonists.
    Ahmad N Nabhan, Joshua D Webster, Jarret J Adams, Levi Blazer, Christine Everrett, Celine Eidenschenk, Alexander Arlantico, Isabel Fleming, Hans D Brightbill, Paul J Wolters, Zora Modrusan, Somesekar Seshagiri, Stephane Angers, Sachdev S Sidhu, Kim Newton, Joseph R Arron, Vishva M Dixit.
      Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt signaling is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Fzd5 is uniquely required for alveolar epithelial stem cell activity, whereas fibroblasts utilize distinct Fzd receptors. Using an expanded repertoire of Fzd-Lrp agonists, we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. A Fzd5 agonist (Fzd5ag) or Fzd6ag stimulated alveolar epithelial stem cell activity and promoted survival in mice after lung injury, but only Fzd6ag promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.
    Keywords:  Frizzled; WNT; alveolus; lung; regeneration
    DOI:  https://doi.org/10.1016/j.cell.2023.05.022
  35. Curr Opin Cell Biol. 2023 Jun;pii: S0955-0674(23)00027-3. [Epub ahead of print]82 102178
    The (social) lives, deaths, and biophysical phases of lipid droplets.
    W Mike Henne.
      Lipid droplets (LDs) are major lipid storage organelles, sequestering energy-rich triglycerides and serving as nutrient sinks for cellular homeostasis. Observed for over a century but generally ignored, LDs are now appreciated to play key roles in organismal physiology and disease. They also form numerous functional contacts with other organelles. Here, we highlight recent studies examining LDs from distinct perspectives of their life cycle: their biogenesis, "social" life as they interact with other organelles, and deaths via lipolysis or lipophagy. We also discuss recent work showing how changes in LD lipid content alter the biophysical phases of LD lipids, and how this may fine-tune the LD protein landscape and ultimately LD function.
    DOI:  https://doi.org/10.1016/j.ceb.2023.102178
  36. Clin Exp Metastasis. 2023 Jun 16.
    Cells in the polyaneuploid cancer cell (PACC) state have increased metastatic potential.
    Mikaela M Mallin, Nicholas Kim, Mohammad Ikbal Choudhury, Se Jong Lee, Steven S An, Sean X Sun, Konstantinos Konstantopoulos, Kenneth J Pienta, Sarah R Amend.
      Although metastasis is the leading cause of cancer deaths, it is quite rare at the cellular level. Only a rare subset of cancer cells (~ 1 in 1.5 billion) can complete the entire metastatic cascade: invasion, intravasation, survival in the circulation, extravasation, and colonization (i.e. are metastasis competent). We propose that cells engaging a Polyaneuploid Cancer Cell (PACC) phenotype are metastasis competent. Cells in the PACC state are enlarged, endocycling (i.e. non-dividing) cells with increased genomic content that form in response to stress. Single-cell tracking using time lapse microscopy reveals that PACC state cells have increased motility. Additionally, cells in the PACC state exhibit increased capacity for environment-sensing and directional migration in chemotactic environments, predicting successful invasion. Magnetic Twisting Cytometry and Atomic Force Microscopy reveal that cells in the PACC state display hyper-elastic properties like increased peripheral deformability and maintained peri-nuclear cortical integrity that predict successful intravasation and extravasation. Furthermore, four orthogonal methods reveal that cells in the PACC state have increased expression of vimentin, a hyper-elastic biomolecule known to modulate biomechanical properties and induce mesenchymal-like motility. Taken together, these data indicate that cells in the PACC state have increased metastatic potential and are worthy of further in vivo analysis.
    Keywords:  Chemotaxis; Deformability; Motility; Polyaneuploid cancer cells (PACCs); Polyploid giant cancer cells (PGCCs); Vimentin
    DOI:  https://doi.org/10.1007/s10585-023-10216-8
  37. Cancer Res. 2023 Jun 15. 83(12): 1929-1932
    Live Biotherapeutic Products as Cancer Treatments.
    Arianna Brevi, Amir Zarrinpar.
      Almost every aspect of cancer can be influenced by microbiota including tumor onset, progression, and response to therapy. The increasing evidence of the role of microbiota in human health and disease has reinvigorated the interest in designing microbial products that can affect cancer outcomes. Researchers have made numerous attempts to develop safe, engineered biotherapeutic products for cancer treatment using synthetic biology tools. Despite the progress, only Bacillus Calmette-Guérin is approved for human use. Here, we highlight the recent advances and current challenges in using live bacteria as cancer therapeutics.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-2626
  38. Nat Protoc. 2023 Jun 16.
    Ex vivo immunocapture and functional characterization of cell-type-specific mitochondria using MitoTag mice.
    Natalia Prudente de Mello, Caroline Fecher, Adrian Marti Pastor, Fabiana Perocchi, Thomas Misgeld.
      Mitochondria are key bioenergetic organelles involved in many biosynthetic and signaling pathways. However, their differential contribution to specific functions of cells within complex tissues is difficult to dissect with current methods. The present protocol addresses this need by enabling the ex vivo immunocapture of cell-type-specific mitochondria directly from their tissue context through a MitoTag reporter mouse. While other available methods were developed for bulk mitochondria isolation or more abundant cell-type-specific mitochondria, this protocol was optimized for the selective isolation of functional mitochondria from medium-to-low-abundant cell types in a heterogeneous tissue, such as the central nervous system. The protocol has three major parts: First, mitochondria of a cell type of interest are tagged via an outer mitochondrial membrane eGFP by crossing MitoTag mice to a cell-type-specific Cre-driver line or by delivery of viral vectors for Cre expression. Second, homogenates are prepared from relevant tissues by nitrogen cavitation, from which tagged organelles are immunocaptured using magnetic microbeads. Third, immunocaptured mitochondria are used for downstream assays, e.g., to probe respiratory capacity or calcium handling, revealing cell-type-specific mitochondrial diversity in molecular composition and function. The MitoTag approach enables the identification of marker proteins to label cell-type-specific organelle populations in situ, elucidates cell-type-enriched mitochondrial metabolic and signaling pathways, and reveals functional mitochondrial diversity between adjacent cell types in complex tissues, such as the brain. Apart from establishing the mouse colony (6-8 weeks without import), the immunocapture protocol takes 2 h and functional assays require 1-2 h.
    DOI:  https://doi.org/10.1038/s41596-023-00831-w
  39. Angew Chem Int Ed Engl. 2023 Jun 12. e202305866
    Nascent Proteomics: Chemical Tools for Monitoring Newly Synthesized Proteins.
    Qi Tang, Xing Chen.
      Cellular proteins are dynamically regulated in response to environmental stimuli. Conventional proteomics compares the entire proteome in different cellular states to identify differentially expressed proteins, which suffers from limited sensitivity for analyzing acute and subtle changes. To address this challenge, nascent proteomics has been developed, which selectively analyze the newly synthesized proteins, thus offering a more sensitive and timely insight into the dynamic changes of the proteome. In this Minireview, we discuss recent advancements in nascent proteomics, with an emphasis on methodological developments. Also, we delve into the current challenges and provide an outlook on the future prospects of this exciting field.
    Keywords:  chemoproteomics; metabolic protein labeling; nascent proteomics; newly synthesized proteins; noncanonical amino acids
    DOI:  https://doi.org/10.1002/anie.202305866
  40. EMBO J. 2023 Jun 12. e113908
    PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
    Valerie Perea, Christian Cole, Justine Lebeau, Vivian Dolina, Kelsey R Baron, Aparajita Madhavan, Jeffery W Kelly, Danielle A Grotjahn, R Luke Wiseman.
      Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during acute ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. These two processes lead to the accumulation of PA on the outer mitochondrial membrane where it can induce mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation adapts organellar shape in response to ER stress.
    Keywords:  endoplasmic reticulum (ER) stress; mitochondrial morphology; phosphatidic acid; unfolded protein response (UPR)
    DOI:  https://doi.org/10.15252/embj.2023113908
  41. Anat Sci Int. 2023 Jun 14.
    Subcellular distribution of membrane lipids revealed by freeze-fracture electron microscopy.
    Takuma Tsuji.
      Cell membranes are composed of a large variety of lipids and proteins. While the localization and function of membrane proteins have been extensively investigated, the distribution of membrane lipids, especially in the non-cytoplasmic leaflet of organelle membranes, remains largely unknown. Fluorescent biosensors have been widely used to study membrane lipid distribution; however, they have some limitations. By utilizing the quick-freezing and freeze-fracture replica labeling electron microscopy technique, we can uncover the precise distribution of membrane lipids within cells and assess the function of lipid-transporting proteins. In this review, I summarize recent progress in analyzing intracellular lipid distribution by utilizing this method.
    Keywords:  Electron microscopy; Lipid bilayer; Membrane lipid; Organelle membrane; Scramblase
    DOI:  https://doi.org/10.1007/s12565-023-00731-9
  42. Clin Cancer Res. 2023 Jun 16. pii: CCR-23-0797. [Epub ahead of print]
    Identifying mechanisms of resistance by circulating tumour DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at time of PARP Inhibitor Progression.
    Stephanie Lheureux, Stephenie D Prokopec, Leslie E Oldfield, Eduardo Gonzalez-Ochoa, Jeff P Bruce, Derek Wong, Arnavaz Danesh, Dax Torti, Jonathan Torchia, Alexander Fortuna, Sharanjit Singh, Matthew Irving, Kayla Marsh, Bernard Lam, Vanessa Speers, Aleksandra Yosifova, Ana Oaknin, Ainhoa Madariaga, Neesha C Dhani, Valerie Bowering, Amit M Oza, Trevor J Pugh.
      Purpose To evaluate the use of blood cell-free DNA (cfDNA) to identify emerging mechanisms of resistance to PARP inhibitors (PARPi) in high grade serous ovarian cancer (HGSOC). Patients and Methods We used targeted sequencing (TS) to analyse 78 longitudinal cfDNA samples collected from 30 patients with HGSOC enrolled in a phase II clinical trial evaluating cediranib (VEGF inhibitor) plus olaparib (PARPi) after progression on PARPi alone. cfDNA was collected at baseline, before treatment cycle 2, and at end of treatment. These were compared to whole exome sequencing (WES) of baseline tumour tissues. Results At baseline (time of initial PARPi progression), cfDNA tumour fractions were 0.2-67% (median 3.25%) and patients with high ctDNA levels (>15%) had a higher tumour burden (sum of target lesions; p = 0.043). Across all timepoints, cfDNA detected known from tumour WES with 74.4% sensitivity, and detected 3 of 5 expected BRCA1/2 reversion mutations. In addition, cfDNA identified 10 novel mutations not detected by WES, including 7 TP53 mutations annotated as pathogenic by ClinVar. cfDNA fragmentation analysis attributed 5 of these novel TP53 mutations to clonal hematopoiesis of indeterminate potential (CHIP). At baseline, samples with significant differences in mutant fragment size distribution had shorter time to progression (p = 0.001). Conclusions Longitudinal testing of cfDNA by TS provides a non-invasive tool for detection of tumour-derived mutations and mechanisms of PARPi resistance that may aid in directing patients to appropriate therapeutic strategies. With cfDNA fragmentation analyses, CHIP was identified in several patients and warrants further investigation.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-23-0797
  43. Bioinformatics. 2023 Jun 16. pii: btad383. [Epub ahead of print]
    Cell shape characterization, alignment and comparison using FlowShape.
    Casper van Bavel, Wim Thiels, Rob Jelier.
      MOTIVATION: The shape of a cell is tightly controlled, and reflects important processes including actomyosin activity, adhesion properties, cell differentiation and polarization. Hence, it is informative to link cell shape to genetic and other perturbations. However, most currently used cell shape descriptors capture only simple geometric features such as volume and sphericity. We propose FlowShape, a new framework to study cell shapes in a complete and generic way.RESULTS: In our framework a cell shape is represented by measuring the curvature of the shape and mapping it onto a sphere in a conformal manner. This single function on the sphere is next approximated by a series expansion: the spherical harmonics decomposition. The decomposition facilitates many analyses, including shape alignment and statistical cell shape comparison. The new tool is applied to perform a complete, generic analysis of cell shapes, using the early Caenorhabditis elegans embryo as a model case. We distinguish and characterize the cells at the seven-cell stage. Next, a filter is designed to identify protrusions on the cell shape to highlight lamellipodia in cells. Further, the framework is used to identify any shape changes following a gene knockdown of the Wnt pathway. Cells are first optimally aligned using the fast Fourier transform, followed by calculating an average shape. Shape differences between conditions are next quantified and compared to an empirical distribution. Finally, we put forward a highly performant implementation of the core algorithm, as well as routines to characterize, align and compare cell shapes, through the open-source software package FlowShape.
    AVAILABILITY: The data and code needed to recreate the results are freely available at https://doi.org/10.5281/zenodo.7778752. The most recent version of the software is maintained at https://bitbucket.org/pgmsembryogenesis/flowshape/.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btad383
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